SMTL ID : 4gp7.1

Polynucleotide kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 12 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: MG.2 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:G.19, A:S.20, A:G.21, A:K.22, A:S.23, A:S.23, A:T.24, A:T.24 Water bridges: A:S.18, A:K.22, A:K.22, A:K.22, A:K.22, A:F.25, A:R.117, A:R.121, A:R.121, A:R.121, A:R.121, 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 ATP.4: 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.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:S.23, B:T.24, B:T.24 Water bridges: B:K.22, B:K.22, B:K.22, B:K.22, B:R.117, B:R.121, B:R.121, B:R.121, B:R.121, B:R.121, B:R.121, B:R.121 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: ATP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.23, H2O.2, H2O.2, H2O.2 MG.5: 2 residues within 4Å: Chain B: S.23 Ligands: ATP.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.23, H2O.5, H2O.5, H2O.5

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 4 residues within 4Å: Chain A: N.108, I.142, I.155, N.157 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.155 Hydrogen bonds: A:N.108, A:N.157

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain B: P.7, F.101, R.151, Y.152 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L.K. et al., Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system. Rna (2012)

Release Date

2012-11-14

Peptides

Metallophosphoesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Metallophosphoesterase