SMTL ID : 2cja.1

CRYSTAL STRUCTURE OF METHANOSARCINA BARKERI SERYL-TRNA SYNTHETASE COMPLEXED WITH ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: A.324, C.326, E.375, C.481 Ligands: ATP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.326, A:E.375, A:C.481 ZN.4: 4 residues within 4Å: Chain B: A.324, C.326, E.375, C.481 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: 7 residues within 4Å: Chain A: V.260, W.265, Y.323, A.324, Q.325, P.327, P.328 Ligand excluded by PLIP CL.5: 7 residues within 4Å: Chain B: V.260, W.265, Y.323, A.324, Q.325, P.327, P.328 Ligand excluded by PLIP

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 14 residues within 4Å: Chain A: H.270, Y.323, A.324, R.356, E.358, R.367, V.368, F.371, R.373, E.452, N.455, G.485, R.488 Ligands: ZN.1 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:E.358, A:V.368, A:R.373, A:E.452, A:F.453, A:G.485, A:R.488 Water bridges: A:R.356, A:R.356, A:R.356 Salt bridges: A:H.270, A:R.356, A:R.356, A:R.373 pi-Stacking: A:F.371, A:F.371 pi-Cation interactions: A:R.488, A:R.488 ATP.8: 14 residues within 4Å: Chain B: R.356, E.358, R.367, V.368, F.371, R.373, E.452, F.453, Q.454, N.455, G.485, R.488 Ligands: MG.6, MG.7 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:R.356, B:E.358, B:V.368, B:R.373, B:E.452, B:F.453, B:G.485, B:R.488 Water bridges: B:R.356, B:R.356, B:R.356, B:R.367, B:R.367, B:E.452, B:E.452 Salt bridges: B:R.356, B:R.356, B:R.367, B:R.488 pi-Stacking: B:F.371, B:F.371 pi-Cation interactions: B:R.488, B:R.488

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain B: R.356, E.358 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.358 MG.7: 5 residues within 4Å: Chain B: T.434, D.436, E.452, N.455 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.436, B:E.452

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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