SMTL ID : 2cjb.1

Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with serine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x SER: SERINE(Non-covalent)

SER.1: 10 residues within 4Å: Chain A: A.324, C.326, R.356, R.373, E.375, W.416, Q.420, N.455, G.483 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.373, A:E.375, A:Q.420, A:N.455 Salt bridges: A:R.356, A:R.373 SER.4: 11 residues within 4Å: Chain B: A.324, C.326, R.356, R.373, E.375, W.416, Q.420, N.455, C.481, G.483 Ligands: ZN.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.324, B:R.373, B:Q.420, B:N.455 Salt bridges: B:R.356, B:R.373

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.326, E.375, W.416, C.481 Ligands: SER.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.326, A:E.375, A:C.481 ZN.5: 6 residues within 4Å: Chain B: A.324, C.326, E.375, W.416, C.481 Ligands: SER.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.326, B:E.375, B:C.481

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: V.260, W.265, Y.323, A.324, Q.325, P.327 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain B: V.260, W.265, Y.323, A.324, Q.325, P.327 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bilokapic, S. et al., Structure of the Unusual Seryl-tRNA Synthetase Reveals a Distinct Zinc-Dependent Mode of Substrate Recognition. Embo J. (2006)

Release Date

2006-06-26

Peptides

SERYL-TRNA SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SERYL-TRNA SYNTHETASE

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