SMTL ID : 3r9w.1 (1 other biounit)

Crystal structure of Era in complex with MgGDPNP and nucleotides 1506-1542 of 16S ribosomal RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.23, T.44 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.23, A:T.44, H2O.1, H2O.2

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.2: 23 residues within 4Å: Chain A: P.18, N.19, V.20, G.21, K.22, S.23, T.24, I.37, S.38, P.39, A.41, G.42, T.43, T.44, G.67, N.129, K.130, D.132, K.133, S.161, A.162, L.163 Ligands: MG.1 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:N.19, A:V.20, A:G.21, A:K.22, A:K.22, A:S.23, A:T.24, A:T.24, A:S.38, A:S.38, A:G.42, A:T.43, A:T.44, A:G.67, A:N.129, A:K.130, A:K.130, A:S.161, A:A.162, A:L.163 Water bridges: A:S.23, A:S.23, A:T.24, A:G.42, A:K.133 Salt bridges: A:D.132

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 1 residues within 4Å: Chain A: W.286 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.286 ACT.4: 3 residues within 4Å: Chain A: E.214 Chain B: G.25, A.26 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.213 ACT.5: 1 residues within 4Å: Chain A: A.101 No protein-ligand interaction detected (PLIP) ACT.6: 4 residues within 4Å: Chain A: E.70, E.111, N.115, F.116 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.116 Hydrogen bonds: A:E.70 Salt bridges: A:R.108 ACT.10: 3 residues within 4Å: Chain B: G.25, A.26, U.27 No protein-ligand interaction detected (PLIP)

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.7: 4 residues within 4Å: Chain A: V.76, H.79, S.80, R.301 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.301 Hydrogen bonds: A:R.301 MRD.8: 2 residues within 4Å: Chain A: H.148, T.155 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:H.148

1 x CA: CALCIUM ION(Non-functional Binders)

CA.9: 2 residues within 4Å: Chain B: U.17, G.18 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tu, C. et al., The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3' end of 16S rRNA. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-06-22

Peptides

GTPase Era: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase Era

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