SMTL ID : 4qm7.1

Structure of bacterial polynucleotide kinase bound to GTP and pDNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

1 x DC- DC- DT- DG: DNA(Non-covalent)

DC-DC-DT-DG.1: 16 residues within 4Å: Chain A: S.38, R.42, Q.52, T.55, F.59, H.63, A.80, T.81, Q.84, A.87, R.124, V.126, Y.129, V.130, H.134 Ligands: GTP.2 Protein-ligand interaction information (PLIP) not available

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

GTP.2: 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 Ligands: DC-DC-DT-DG.1, MG.3 31 PLIP interactions: 31 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 Water bridges: A:K.22, A:K.22, A:S.23, A:S.23, A:T.24, A:F.25, A:R.117, A:R.117, A:R.121, A:R.121, A:R.121, A:D.123, A:R.124, A:R.124, A:R.124 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.4: 12 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, R.124 Ligands: MG.5 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:G.19, B:S.20, B:G.21, B:K.22, B:S.23, B:T.24, B:T.24, B:R.117 Water bridges: B:F.25, B:T.81, B:R.117, B:R.121, B:R.121, B:R.121, B:R.124, B:R.124, B:E.163, B:E.163, B:E.163 Salt bridges: B:K.22, B:K.22, B:R.121, B:R.121, B:R.121, B:R.124 pi-Cation interactions: B:R.117, B:R.117

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: S.23 Ligands: GTP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.23, H2O.1, H2O.1, H2O.1 MG.5: 3 residues within 4Å: Chain B: S.23, R.124 Ligands: GTP.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.23, H2O.7, H2O.8, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Das, U. et al., Structures of bacterial polynucleotide kinase in a michaelis complex with nucleoside triphosphate (NTP)-Mg2+ and 5'-OH RNA and a mixed substrate-product complex with NTP-Mg2+ and a 5'-phosphorylated oligonucleotide. J.Bacteriol. (2014)

Release Date

2014-10-08

Peptides

Metallophosphoesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Metallophosphoesterase

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