SMTL ID : 2e7y.1

High resolution structure of T. maritima tRNase Z

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.52, H.53, D.190, H.244 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.52, A:H.53, A:D.190, A:H.244, H2O.5 ZN.2: 5 residues within 4Å: Chain A: H.48, H.50, H.134, D.190 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.48, A:H.50, A:H.134, A:D.190, H2O.5 ZN.7: 5 residues within 4Å: Chain B: D.52, H.53, D.190, H.244 Ligands: ZN.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.52, B:H.53, B:D.190, B:H.244, H2O.11 ZN.8: 4 residues within 4Å: Chain B: H.48, H.50, D.190 Ligands: ZN.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.48, B:H.50, B:D.190, H2O.11

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: A.120, G.121, G.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.121 Water bridges: A:G.122 SO4.4: 4 residues within 4Å: Chain A: K.254, K.258, R.261, Y.271 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.271 Water bridges: A:K.254, A:K.254, A:R.261, A:R.261 Salt bridges: A:K.254, A:K.258, A:R.261

4 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.5: 8 residues within 4Å: Chain A: F.6, W.14, E.28, G.29, V.30, T.33 Chain B: T.32 Ligands: PGO.9 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.32 Hydrogen bonds: A:G.29, A:T.33, A:T.33 Water bridges: A:T.33 PGO.6: 3 residues within 4Å: Chain A: R.150, E.178, E.179 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.178, A:E.179 Hydrogen bonds: A:R.150, A:R.150 PGO.9: 8 residues within 4Å: Chain A: T.32 Chain B: F.6, W.14, E.28, G.29, V.30, T.33 Ligands: PGO.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.14, B:E.28 PGO.10: 4 residues within 4Å: Chain B: K.254, K.258, R.261, Y.271 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.254, B:K.258, B:R.261, B:R.261, B:Y.271, B:Y.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ishii, R. et al., The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes. Acta Crystallogr.,Sect.F (2007)

Release Date

2007-09-11

Peptides

tRNase Z: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNase Z

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