SMTL ID : 2cj9.1

Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with an analog of seryladenylate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: A.324, C.326, E.375, W.416, C.481 Ligands: SSA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.326, A:E.375, A:C.481 ZN.4: 6 residues within 4Å: Chain B: A.324, C.326, E.375, W.416, C.481 Ligands: SSA.6 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.2: 6 residues within 4Å: Chain A: V.260, W.265, Y.323, A.324, Q.325, P.327 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain B: V.260, W.265, Y.323, A.324, Q.325, P.327 Ligand excluded by PLIP

2 x SSA: 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE(Non-covalent)

SSA.3: 19 residues within 4Å: Chain A: A.324, C.326, R.356, E.358, V.368, F.371, R.373, E.375, W.416, Q.420, E.452, F.453, Q.454, N.455, C.481, G.483, G.485, R.488 Ligands: ZN.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:A.324, A:R.356, A:V.368, A:V.368, A:R.373, A:Q.420, A:E.452, A:F.453, A:Q.454, A:N.455, A:G.485, A:R.488 Salt bridges: A:R.356 pi-Stacking: A:F.371, A:F.371 pi-Cation interactions: A:R.488, A:R.488 SSA.6: 19 residues within 4Å: Chain B: A.324, C.326, R.356, E.358, V.368, F.371, R.373, E.375, W.416, Q.420, E.452, F.453, Q.454, N.455, C.481, G.483, G.485, R.488 Ligands: ZN.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:A.324, B:R.356, B:V.368, B:V.368, B:R.373, B:Q.420, B:F.453, B:N.455, B:G.485, B:R.488 Water bridges: B:R.356 Salt bridges: B:R.356 pi-Stacking: B:F.371, B:F.371 pi-Cation interactions: B:R.488, B:R.488

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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