SMTL ID : 4jsy.1

Structure of Clostridium thermocellum polynucleotide kinase bound to GTP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 13 residues within 4Å: Chain A: S.17, S.18, G.19, S.20, G.21, K.22, S.23, T.24, R.117, R.121, R.124, E.163 Ligands: MG.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.19, A:S.20, A:G.21, A:K.22, A:S.23, A:T.24, A:T.24, A:R.117, A:E.163 Water bridges: A:K.22, A:K.22, A:F.25, A:R.121, A:R.121, A:R.124, A:E.163 Salt bridges: A:K.22, A:K.22, A:R.121, A:R.121, A:R.121, A:R.124 pi-Cation interactions: A:R.117, A:R.117 GTP.3: 11 residues within 4Å: Chain B: S.17, S.18, G.19, S.20, G.21, K.22, S.23, T.24, R.117, R.121 Ligands: MG.4 29 PLIP interactions: 29 interactions with chain B Hydrogen bonds: B:G.19, B:S.20, B:G.21, B:K.22, B:S.23, B:S.23, B:T.24, B:T.24, B:R.117 Water bridges: B:K.22, B:K.22, B:F.25, B:R.117, B:R.117, B:R.121, B:R.121, B:R.121, B:R.121, B:R.121, B:R.121, B:R.121, B:D.123 Salt bridges: B:K.22, B:K.22, B:R.121, B:R.121, B:R.121 pi-Cation interactions: B:R.117, B:R.117

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.23, D.79, R.124 Ligands: GTP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.23, H2O.1, H2O.1, H2O.3 MG.4: 2 residues within 4Å: Chain B: S.23 Ligands: GTP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.23, H2O.4, H2O.4, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Das, U. et al., Structural and biochemical analysis of the phosphate donor specificity of the polynucleotide kinase component of the bacterial pnkphen1 RNA repair system. Biochemistry (2013)

Release Date

2013-08-28

Peptides

Metallophosphoesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Metallophosphoesterase

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