9Q87 | pdb_00009q87

Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+


Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
30S---
Small ribosomal subunit protein uS2
Small ribosomal subunit protein uS3
Small ribosomal subunit protein uS4
Small ribosomal subunit protein uS5
Small ribosomal subunit protein bS6, fully modified isoform
Small ribosomal subunit protein uS7
Small ribosomal subunit protein uS8
Small ribosomal subunit protein uS9
Small ribosomal subunit protein uS10
Small ribosomal subunit protein uS12
Small ribosomal subunit protein uS13
Small ribosomal subunit protein uS15
Small ribosomal subunit protein uS17
Small ribosomal subunit protein bS18
Small ribosomal subunit protein bS20
Small ribosomal subunit protein bS21
V [auth X]mRNA---
W [auth Z]P-site tRNA---
X [auth 0]Large ribosomal subunit protein bL33
Z [auth 2]Large ribosomal subunit protein bL35
BA [auth 5]Large ribosomal subunit protein uL11
FA [auth c]Large ribosomal subunit protein uL2
GA [auth d]Large ribosomal subunit protein uL3
HA [auth e]Large ribosomal subunit protein uL4
JA [auth g]Large ribosomal subunit protein uL6
KA [auth h]Large ribosomal subunit protein bL9
LA [auth i]Large ribosomal subunit protein uL13
MA [auth j]Large ribosomal subunit protein uL14
NA [auth k]Large ribosomal subunit protein uL15
OA [auth l]Large ribosomal subunit protein uL16
PA [auth m]Large ribosomal subunit protein bL17
RA [auth o]Large ribosomal subunit protein bL19
TA [auth q]Large ribosomal subunit protein bL21
UA [auth r]Large ribosomal subunit protein uL22
VA [auth s]Large ribosomal subunit protein uL23
WA [auth t]Large ribosomal subunit protein uL24
YA [auth v]Large ribosomal subunit protein bL27
ZA [auth w]Large ribosomal subunit protein bL28
AB [auth x]Large ribosomal subunit protein uL29
CB [auth z]Large ribosomal subunit protein bL32
BB [auth y]Large ribosomal subunit protein uL30
XA [auth u]Large ribosomal subunit protein bL25
SA [auth p]Large ribosomal subunit protein bL20
QA [auth n]Large ribosomal subunit protein uL18
IA [auth f]Large ribosomal subunit protein uL5
EA [auth b]5S rRNA---
DA [auth a]23S rRNA---
CA [auth 6]A-site tRNA---
AA [auth 3]Large ribosomal subunit protein bL36
Y [auth 1]Large ribosomal subunit protein bL34
Small ribosomal subunit protein uS19
Small ribosomal subunit protein bS16
Small ribosomal subunit protein uS14
Small ribosomal subunit protein uS11

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR005706Small ribosomal subunit protein uS2, bacteria/mitochondria/plastidFamily
IPR023591Small ribosomal subunit protein uS2, flavodoxin-like domain superfamilyHomologous Superfamily
IPR018130Small ribosomal subunit protein uS2, conserved siteConserved Site
IPR001865Small ribosomal subunit protein uS2Family
IPR005704Small ribosomal subunit protein uS3, bacteriaFamily
IPR001351Small ribosomal subunit protein uS3, C-terminalDomain
IPR009019K homology domain superfamily, prokaryotic typeHomologous Superfamily
IPR004087K Homology domainDomain
IPR004044K Homology domain, type 2Domain
IPR015946K homology domain-like, alpha/betaHomologous Superfamily
IPR036419Ribosomal protein S3, C-terminal domain superfamilyHomologous Superfamily
IPR018280Small ribosomal subunit protein uS3, conserved siteConserved Site
IPR002942RNA-binding S4 domainDomain
IPR022801Small ribosomal subunit protein uS4Family
IPR018079Small ribosomal subunit protein uS4, conserved siteConserved Site
IPR001912Small ribosomal subunit protein uS4, N-terminalDomain
IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
IPR005709Small ribosomal subunit protein uS4, bacteriaFamily
IPR000851Small ribosomal subunit protein uS5Family
IPR005324Small ribosomal subunit protein uS5, C-terminalDomain
IPR005712Small ribosomal subunit protein uS5, bacteriaFamily
IPR013810Small ribosomal subunit protein uS5, N-terminalDomain
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
IPR018192Small ribosomal subunit protein uS5, N-terminal, conserved siteConserved Site
IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
IPR020815Small ribosomal subunit protein bS6, conserved siteConserved Site
IPR000529Small ribosomal subunit protein bS6Family
IPR020814Small ribosomal subunit protein bS6, plastid/chloroplastFamily
IPR035980Small ribosomal subunit protein bS6 superfamilyHomologous Superfamily
IPR014717Translation elongation factor EF1B/small ribosomal subunit protein bS6Homologous Superfamily
IPR020606Small ribosomal subunit protein uS7, conserved siteConserved Site
IPR005717Small ribosomal subunit protein uS7, bacteria/organellaFamily
IPR036823Small ribosomal subunit protein uS7 domain superfamilyHomologous Superfamily
IPR000235Small ribosomal subunit protein uS7Family
IPR023798Small ribosomal subunit protein uS7 domainDomain
IPR000630Small ribosomal subunit protein uS8Family
IPR047863Small ribosomal subunit protein uS8, conserved siteConserved Site
IPR035987Small ribosomal subunit protein uS8 superfamilyHomologous Superfamily
IPR020574Small ribosomal subunit protein uS9, conserved siteConserved Site
IPR023035Small ribosomal subunit protein uS9, bacteria/plastidFamily
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
IPR000754Small ribosomal subunit protein uS9Family
IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
IPR027486Small ribosomal subunit protein uS10 domainDomain
IPR036838Small ribosomal subunit protein uS10 domain superfamilyHomologous Superfamily
IPR018268Small ribosomal subunit protein uS10, conserved siteConserved Site
IPR001848Small ribosomal subunit protein uS10Family
IPR005679Ribosomal protein uS12, bacteriaFamily
IPR006032Small ribosomal subunit protein uS12Family
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR018269Small ribosomal subunit protein uS13, conserved siteConserved Site
IPR027437Small ribosomal subunit protein uS13, C-terminalHomologous Superfamily
IPR001892Small ribosomal subunit protein uS13Family
IPR010979Small ribosomal subunit protein uS13-like, H2THHomologous Superfamily
IPR019980Small ribosomal subunit protein uS13, bacteriaFamily
IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
IPR000589Small ribosomal subunit protein uS15Family
IPR005290Small ribosomal subunit protein uS15, bacteriaFamily
IPR019979Small ribosomal subunit protein uS17, conserved siteConserved Site
IPR019984Small ribosomal subunit protein uS17, bacteria/chloroplastFamily
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR000266Small ribosomal subunit protein uS17Family
IPR001648Small ribosomal subunit protein bS18Family
IPR018275Small ribosomal subunit protein bS18, conserved siteConserved Site
IPR036870Small ribosomal subunit protein bS18 superfamilyHomologous Superfamily
IPR036510Small ribosomal subunit protein bS20 superfamilyHomologous Superfamily
IPR002583Small ribosomal subunit protein bS20Family
IPR038380Small ribosomal subunit protein bS21 superfamilyHomologous Superfamily
IPR018278Small ribosomal subunit protein bS21, conserved siteConserved Site
IPR001911Small ribosomal subunit protein bS21Family
X [auth 0]IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
X [auth 0]IPR038584Large ribosomal subunit protein bL33 superfamilyHomologous Superfamily
X [auth 0]IPR001705Large ribosomal subunit protein bL33Family
X [auth 0]IPR018264Large ribosomal subunit protein bL33, conserved siteConserved Site
Z [auth 2]IPR021137Large ribosomal subunit protein bL35-likeFamily
Z [auth 2]IPR018265Large ribosomal subunit protein bL35, conserved siteConserved Site
Z [auth 2]IPR001706Large ribosomal subunit protein bL35Family
Z [auth 2]IPR037229Large ribosomal subunit protein bL35 superfamilyHomologous Superfamily
BA [auth 5]IPR020785Large ribosomal subunit protein uL11, conserved siteConserved Site
BA [auth 5]IPR020783Large ribosomal subunit protein uL11, C-terminalDomain
BA [auth 5]IPR000911Ribosomal protein uL11Family
BA [auth 5]IPR036769Large ribosomal subunit protein uL11, C-terminal domain superfamilyHomologous Superfamily
BA [auth 5]IPR020784Large ribosomal subunit protein uL11, N-terminalDomain
BA [auth 5]IPR036796Large ribosomal subunit protein uL11, N-terminal domain superfamilyHomologous Superfamily
BA [auth 5]IPR006519Large ribosomal subunit protein uL11, bacteriaFamily
FA [auth c]IPR005880Large ribosomal subunit protein uL2, bacteria/organellaFamily
FA [auth c]IPR022669Large ribosomal subunit protein uL2, C-terminalDomain
FA [auth c]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
FA [auth c]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
FA [auth c]IPR022671Large ribosomal subunit protein uL2, conserved siteConserved Site
FA [auth c]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
FA [auth c]IPR022666Large ribosomal subunit protein uL2, RNA-binding domainDomain
FA [auth c]IPR014726Large ribosomal subunit protein uL2, domain 3Homologous Superfamily
FA [auth c]IPR002171Large ribosomal subunit protein uL2Family
GA [auth d]IPR019926Large ribosomal subunit protein uL3, conserved siteConserved Site
GA [auth d]IPR019927Large ribosomal subunit protein uL3, bacteria/organellaFamily
GA [auth d]IPR009000Translation protein, beta-barrel domain superfamilyHomologous Superfamily
GA [auth d]IPR000597Large ribosomal subunit protein uL3Family
HA [auth e]IPR013005Large ribosomal subunit protein uL4-likeFamily
HA [auth e]IPR002136Large ribosomal subunit protein uL4Family
HA [auth e]IPR023574Large ribosomal subunit protein uL4 domain superfamilyHomologous Superfamily
JA [auth g]IPR020040Large ribosomal subunit protein uL6, alpha-beta domainDomain
JA [auth g]IPR036789Large ribosomal subunit protein uL6-like, alpha-beta domain superfamilyHomologous Superfamily
JA [auth g]IPR000702Large ribosomal subunit protein uL6-likeFamily
JA [auth g]IPR019906Large ribosomal subunit protein uL6, bacteriaFamily
JA [auth g]IPR002358Large ribosomal subunit protein uL6, conserved siteConserved Site
KA [auth h]IPR009027Large ribosomal subunit protein bL9/RNase H1, N-terminalHomologous Superfamily
KA [auth h]IPR020594Large ribosomal subunit protein bL9, bacteria/chloroplastFamily
KA [auth h]IPR036935Large ribosomal subunit protein bL9, N-terminal domain superfamilyHomologous Superfamily
KA [auth h]IPR036791Large ribosomal subunit protein bL9, C-terminal domain superfamilyHomologous Superfamily
KA [auth h]IPR020069Large ribosomal subunit protein bL9, C-terminalDomain
KA [auth h]IPR020070Large ribosomal subunit protein bL9, N-terminalDomain
KA [auth h]IPR000244Large ribosomal subunit protein bL9Family
LA [auth i]IPR023563Large ribosomal subunit protein uL13, conserved siteConserved Site
LA [auth i]IPR005822Large ribosomal subunit protein uL13Family
LA [auth i]IPR005823Large ribosomal subunit protein uL13, bacteriaFamily
LA [auth i]IPR036899Large ribosomal subunit protein uL13 superfamilyHomologous Superfamily
MA [auth j]IPR036853Large ribosomal subunit protein uL14 superfamilyHomologous Superfamily
MA [auth j]IPR000218Large ribosomal subunit protein uL14Family
MA [auth j]IPR019972Large ribosomal subunit protein uL14, conserved siteConserved Site
MA [auth j]IPR005745Large ribosomal subunit protein uL14, bacteriaFamily
NA [auth k]IPR021131Large ribosomal subunit protein uL15/eL18Domain
NA [auth k]IPR030878Large ribosomal subunit protein uL15Family
NA [auth k]IPR001196Large ribosomal subunit protein uL15, conserved siteConserved Site
NA [auth k]IPR036227Large ribosomal subunit protein uL15/eL18 superfamilyHomologous Superfamily
NA [auth k]IPR005749Large ribosomal subunit protein uL15, bacteriaFamily
OA [auth l]IPR000114Large ribosomal subunit protein uL16, bacteriaFamily
OA [auth l]IPR036920Large ribosomal subunit protein uL16 superfamilyHomologous Superfamily
OA [auth l]IPR020798Large ribosomal subunit protein uL16, conserved siteConserved Site
OA [auth l]IPR016180Large ribosomal subunit protein uL16 domainDomain
OA [auth l]IPR047873Large ribosomal subunit protein uL16Family
PA [auth m]IPR036373Large ribosomal subunit protein bL17 superfamilyHomologous Superfamily
PA [auth m]IPR047859Large ribosomal subunit protein bL17, conserved siteConserved Site
PA [auth m]IPR000456Large ribosomal subunit protein bL17Family
RA [auth o]IPR001857Large ribosomal subunit protein bL19Family
RA [auth o]IPR038657Large ribosomal subunit protein bL19 superfamilyHomologous Superfamily
RA [auth o]IPR018257Large ribosomal subunit protein bL19, conserved siteConserved Site
RA [auth o]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
TA [auth q]IPR028909Large ribosomal subunit protein bL21-likeFamily
TA [auth q]IPR001787Large ribosomal subunit protein bL21Family
TA [auth q]IPR036164Large ribosomal subunit protein bL21-like superfamilyHomologous Superfamily
TA [auth q]IPR018258Large ribosomal subunit protein bL21, conserved siteConserved Site
UA [auth r]IPR018260Large ribosomal subunit protein uL22, conserved siteConserved Site
UA [auth r]IPR036394Ribosomal protein uL22 superfamilyHomologous Superfamily
UA [auth r]IPR001063Large ribosomal subunit protein uL22Family
UA [auth r]IPR005727Large ribosomal subunit protein uL22, bacterial/chloroplast-typeFamily
UA [auth r]IPR047867Large ribosomal subunit protein uL22, bacteria/organellaFamily
VA [auth s]IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
VA [auth s]IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
VA [auth s]IPR001014Large ribosomal subunit protein uL23, conserved siteConserved Site
VA [auth s]IPR013025Large ribosomal subunit protein uL23-likeFamily
WA [auth t]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
WA [auth t]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
WA [auth t]IPR003256Large ribosomal subunit protein uL24Family
WA [auth t]IPR041988Large ribosomal subunit protein uL24, KOW domainDomain
WA [auth t]IPR005824KOWDomain
WA [auth t]IPR005825Large ribosomal subunit protein uL24, conserved siteConserved Site
YA [auth v]IPR001684Large ribosomal subunit protein bL27Family
YA [auth v]IPR018261Large ribosomal subunit protein bL27, conserved siteConserved Site
ZA [auth w]IPR037147Large ribosomal subunit protein bL28 superfamilyHomologous Superfamily
ZA [auth w]IPR001383Large ribosomal subunit protein bL28, bacteriaFamily
ZA [auth w]IPR026569Large ribosomal subunit protein bL28Family
ZA [auth w]IPR034704Large ribosomal subunit protein bL28/bL31-like superfamilyHomologous Superfamily
AB [auth x]IPR050063Universal ribosomal protein uL29Family
AB [auth x]IPR001854Large ribosomal subunit protein uL29Family
AB [auth x]IPR036049Large ribosomal subunit protein uL29 superfamilyHomologous Superfamily
AB [auth x]IPR018254Large ribosomal subunit protein uL29, conserved siteConserved Site
CB [auth z]IPR002677Large ribosomal subunit protein bL32Family
CB [auth z]IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
CB [auth z]IPR044957Large ribosomal subunit protein bL32, bacteriaFamily
BB [auth y]IPR036919Large ribosomal subunit protein uL30, ferredoxin-like fold domain superfamilyHomologous Superfamily
BB [auth y]IPR005996Large ribosomal subunit protein uL30, bacteriaFamily
BB [auth y]IPR016082Large ribosomal subunit protein uL30-like, ferredoxin-like fold domainDomain
BB [auth y]IPR018038Large ribosomal subunit protein uL30, conserved siteConserved Site
XA [auth u]IPR020055Ribosomal protein bL25, short-formFamily
XA [auth u]IPR029751Large ribosomal subunit protein bL25, L25 domainDomain
XA [auth u]IPR020056Large ribosomal subunit protein bL25/Gln-tRNA synthetase, N-terminalHomologous Superfamily
XA [auth u]IPR011035Large ribosomal subunit protein bL25/Gln-tRNA synthetase, anti-codon-binding domain superfamilyHomologous Superfamily
XA [auth u]IPR020930Large ribosomal subunit protein uL5, bacteriaFamily
SA [auth p]IPR049946Large ribosomal subunit protein bL20, conserved siteConserved Site
SA [auth p]IPR035566Ribosomal protein bL20, C-terminalHomologous Superfamily
SA [auth p]IPR005813Large ribosomal subunit protein bL20Family
QA [auth n]IPR005484Large ribosomal subunit protein uL18, bacterial/plantae/animaliaFamily
QA [auth n]IPR057268Large ribosomal subunit protein uL18Family
QA [auth n]IPR004389Large ribosomal subunit protein uL18, bacteriaFamily
IA [auth f]IPR020929Large ribosomal subunit protein uL5, conserved siteConserved Site
IA [auth f]IPR022803Large ribosomal subunit protein uL5 domain superfamilyHomologous Superfamily
IA [auth f]IPR031309Large ribosomal subunit protein uL5, C-terminalDomain
IA [auth f]IPR031310Large ribosomal subunit protein uL5, N-terminalDomain
IA [auth f]IPR002132Large ribosomal subunit protein uL5Family
IA [auth f]IPR020930Large ribosomal subunit protein uL5, bacteriaFamily
AA [auth 3]IPR000473Large ribosomal subunit protein bL36Family
AA [auth 3]IPR035977Large ribosomal subunit protein bL36 superfamilyHomologous Superfamily
Y [auth 1]IPR020939Large ribosomal subunit protein bL34, conserved siteConserved Site
Y [auth 1]IPR000271Large ribosomal subunit protein bL34Family
IPR005732Small ribosomal subunit protein uS19, bacteriaFamily
IPR002222Small ribosomal subunit protein uS19Family
IPR023575Small ribosomal subunit protein uS19, superfamilyHomologous Superfamily
IPR020934Small ribosomal subunit protein uS19, conserved siteConserved Site
IPR023803Small ribosomal subunit protein bS16 domain superfamilyHomologous Superfamily
IPR000307Small ribosomal subunit protein bS16Family
IPR020592Small ribosomal subunit protein bS16, conserved siteConserved Site
IPR001209Small ribosomal subunit protein uS14Family
IPR018271Small ribosomal subunit protein uS14, conserved siteConserved Site
IPR023036Small ribosomal subunit protein uS14, bacteria/plastidFamily
IPR001971Small ribosomal subunit protein uS11Family
IPR036967Small ribosomal subunit protein uS11 superfamilyHomologous Superfamily
IPR019981Small ribosomal subunit protein uS11, bacteriaFamily
IPR018102Small ribosomal subunit protein uS11, conserved siteConserved Site

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
2MG Parent Component: G

4OC Parent Component: C

5MC Parent Component: C

G7M Parent Component: G

MA6 Parent Component: A

PSU Parent Component: U

UR3 Parent Component: U

D2T Parent Component: ASP

W [auth Z]4SU Parent Component: U

W [auth Z]5MU Parent Component: U

W [auth Z]H2U Parent Component: U

W [auth Z]OMC Parent Component: C

W [auth Z]PSU Parent Component: U

GA [auth d]MEQ Parent Component: GLN

RESIDAA0071

PSI-MOD :  N5-methyl-L-glutamine MOD:00080
OA [auth l]4D4 Parent Component: ARG

RESIDAA0071

DA [auth a]1MG Parent Component: G

RESIDAA0071

DA [auth a]2MA Parent Component: A

RESIDAA0071

DA [auth a]2MG Parent Component: G

RESIDAA0071

DA [auth a]3TD Parent Component: U

RESIDAA0071

DA [auth a]5MC Parent Component: C

RESIDAA0071

DA [auth a]5MU Parent Component: U

RESIDAA0071

DA [auth a]6MZ Parent Component: A

RESIDAA0071

DA [auth a]AP7 Parent Component: A

DA [auth a]G7M Parent Component: G

RESIDAA0071

DA [auth a]H2U Parent Component: U

RESIDAA0071

DA [auth a]OMC Parent Component: C

RESIDAA0071

DA [auth a]OMG Parent Component: G

RESIDAA0071

DA [auth a]OMU Parent Component: U

RESIDAA0071

DA [auth a]PSU Parent Component: U

RESIDAA0071

IAS RESIDAA0071