SMTL ID : 4mde.1 (1 other biounit)

Structure of bacterial polynucleotide kinase product complex bound to GDP and DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x DC- DC- DT- DG- DT: DNA (5'-D(P*CP*CP*TP*GP*T)-3')(Non-covalent)

DC-DC-DT-DG-DT.1: 22 residues within 4Å: Chain A: S.18, G.19, K.22, S.38, N.39, R.42, Q.52, T.53, T.55, F.59, H.63, A.80, T.81, Q.84, A.87, R.121, R.124, Y.129, V.130, H.134 Ligands: GDP.3, MG.4 Protein-ligand interaction information (PLIP) not available DC-DC-DT-DG-DT.2: 25 residues within 4Å: Chain B: S.18, G.19, K.22, S.38, N.39, R.42, Q.52, T.53, T.55, F.59, H.63, A.80, T.81, Q.84, A.87, R.121, R.124, V.126, Y.129, V.130, R.132, K.133, H.134 Ligands: GDP.5, MG.6 Protein-ligand interaction information (PLIP) not available

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 12 residues within 4Å: Chain A: S.17, G.19, S.20, G.21, K.22, S.23, T.24, R.117, R.121, R.124 Ligands: DC-DC-DT-DG-DT.1, MG.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.17, 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:R.124 Water bridges: A:K.22, A:F.25, A:R.117, A:R.117, A:R.121, A:R.121, A:D.123, A:D.123 Salt bridges: A:K.22, A:R.121, A:R.121 pi-Cation interactions: A:R.117 GDP.5: 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 Ligands: DC-DC-DT-DG-DT.2, MG.6 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:S.17, B:S.18, 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:K.22, B:F.25, B:R.117, B:R.121, B:R.124 Salt bridges: B:K.22, B:R.121, B:R.121 pi-Cation interactions: B:R.117, B:R.117

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: S.23, R.124 Ligands: DC-DC-DT-DG-DT.1, GDP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.23, H2O.1, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain B: S.23, R.124 Ligands: DC-DC-DT-DG-DT.2, GDP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.23, H2O.8, 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 GTP*Mg2+ and 5'-OH oligonucleotide and a product complex with GDP*Mg2+ and 5'-PO4 oligonucleotide reveal a mechanism of general acid-base catalysis and the determinants of phosphoacceptor recognition. Nucleic Acids Res. (2014)

Release Date

2013-11-06

Peptides

Metallophosphoesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Metallophosphoesterase

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