SMTL ID : 4qm6.1

Structure of bacterial polynucleotide kinase bound to GTP and RNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x C- C- U- G- U: RNA(Non-covalent)

C-C-U-G-U.1: 19 residues within 4Å: Chain A: S.38, N.39, R.42, Q.52, T.53, T.55, G.56, F.59, H.63, A.80, T.81, Q.84, A.87, R.124, Y.129, V.130, H.134 Ligands: GTP.3, PO4.5 Protein-ligand interaction information (PLIP) not available C-C-U-G-U.2: 18 residues within 4Å: Chain B: 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.124, V.126, Y.129, V.130, H.134 Ligands: GTP.7 Protein-ligand interaction information (PLIP) not available

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

GTP.3: 14 residues within 4Å: Chain A: S.17, S.18, G.19, S.20, G.21, K.22, S.23, T.24, N.39, R.117, R.121, R.124 Ligands: C-C-U-G-U.1, MG.4 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:T.24, A:T.24, A:N.39 Water bridges: A:S.23, A:S.23, A:S.23, A:F.25, A:N.39, A:T.81, A:R.117, A:R.117, A:R.117, A:R.117, A:R.121, A:R.121, A:R.121 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.7: 14 residues within 4Å: Chain B: S.17, S.18, G.19, S.20, G.21, K.22, S.23, T.24, N.39, R.117, R.121, R.124 Ligands: C-C-U-G-U.2, MG.8 30 PLIP interactions: 30 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:N.39 Water bridges: B:S.23, B:S.23, B:F.25, B:N.39, B:T.81, B:R.117, B:R.117, B:R.117, B:R.117, B:R.121, B:R.121, B:R.121, B:R.121, 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.4: 4 residues within 4Å: Chain A: S.23, D.79, R.124 Ligands: GTP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.23, H2O.1, H2O.1, H2O.2 MG.8: 3 residues within 4Å: Chain B: S.23, R.124 Ligands: GTP.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.23, H2O.10, H2O.11, H2O.11

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 3 residues within 4Å: Chain A: Y.129, R.132 Ligands: C-C-U-G-U.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.136 Salt bridges: A:R.132

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

NA.6: 4 residues within 4Å: Chain A: E.85, R.88, S.141, E.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.88, A:E.148 Water bridges: A:E.85, A:K.140 NA.9: 4 residues within 4Å: Chain B: E.111, R.132, T.135, Q.136 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.111, B:R.132, B:Q.136 Water bridges: B:R.132 NA.10: 3 residues within 4Å: Chain B: N.50, Q.125, V.126 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.50, B:N.50 Water bridges: B:Q.52, B:R.124 NA.11: 2 residues within 4Å: Chain A: R.147 Chain B: E.161 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.161, B:E.161 NA.12: 3 residues within 4Å: Chain B: G.56, A.57, D.60 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.56

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

Related Entries With Identical Sequence