SMTL ID : 2ia5.1 (2 other biounits)

T4 polynucleotide kinase/phosphatase with bound sulfate and magnesium.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: D.165, D.167, G.168, T.169, D.277, D.278 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.167 MG.6: 6 residues within 4Å: Chain B: D.165, D.167, T.169, D.277, D.278, R.279 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.165, B:D.167 MG.11: 3 residues within 4Å: Chain C: D.165, D.167, G.168 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.165, C:D.167 MG.16: 6 residues within 4Å: Chain D: D.165, D.167, G.168, T.169, D.277, D.278 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.165, D:D.167

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 8 residues within 4Å: Chain A: C.10, P.11, G.12, S.13, G.14, K.15, S.16, R.126 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.12, A:S.13, A:G.14, A:K.15, A:S.16 Water bridges: A:R.126, A:R.126, A:R.126 Salt bridges: A:K.15, A:R.126 SO4.3: 5 residues within 4Å: Chain A: D.35, R.38, D.85, T.86, M.139 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.86, A:N.87 Water bridges: A:D.35, A:R.38, A:D.85, A:T.86 Salt bridges: A:R.38 SO4.4: 6 residues within 4Å: Chain A: R.246, R.252, K.253, D.254, R.279, Q.281 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.246, A:D.254, A:Q.281 Salt bridges: A:R.279 SO4.7: 8 residues within 4Å: Chain B: C.10, P.11, G.12, S.13, G.14, K.15, S.16, R.126 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.12, B:S.13, B:G.14, B:K.15, B:S.16 Water bridges: B:R.126 Salt bridges: B:K.15, B:R.126 SO4.8: 3 residues within 4Å: Chain B: R.34, R.38, T.86 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.86, B:T.86 Water bridges: B:D.35, B:R.38, B:D.85, B:N.87, B:L.88, B:N.89 Salt bridges: B:R.38 SO4.9: 6 residues within 4Å: Chain B: R.246, R.252, K.253, D.254, R.279, Q.281 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.254, B:Q.281 Water bridges: B:R.246 Salt bridges: B:R.246, B:R.279 SO4.12: 7 residues within 4Å: Chain C: C.10, G.12, S.13, G.14, K.15, S.16, R.126 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.12, C:S.13, C:G.14, C:K.15, C:S.16, C:T.17 Water bridges: C:R.126 Salt bridges: C:K.15, C:R.126 SO4.13: 7 residues within 4Å: Chain C: R.34, D.35, R.38, D.85, T.86, N.87, M.139 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:T.86, C:N.87 Water bridges: C:D.35, C:R.38, C:R.38, C:D.85, C:R.92 Salt bridges: C:R.38 SO4.14: 5 residues within 4Å: Chain C: R.252, K.253, D.254, R.279, Q.281 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.246, C:D.254, C:Q.281 Water bridges: C:R.279, C:R.279 Salt bridges: C:K.253, C:R.279 SO4.17: 8 residues within 4Å: Chain D: C.10, P.11, G.12, S.13, G.14, K.15, S.16, R.126 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.12, D:S.13, D:G.14, D:K.15, D:S.16 Salt bridges: D:K.15, D:R.126 SO4.18: 6 residues within 4Å: Chain D: R.34, D.35, R.38, D.85, T.86, N.87 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.35, D:T.86, D:N.87 Salt bridges: D:R.38 SO4.19: 5 residues within 4Å: Chain D: R.252, K.253, D.254, R.279, Q.281 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.254, D:Q.281 Salt bridges: D:R.279

4 x ARS: ARSENIC(Non-covalent)

ARS.5: 2 residues within 4Å: Chain A: C.184, W.231 No protein-ligand interaction detected (PLIP) ARS.10: 2 residues within 4Å: Chain B: C.184, W.231 No protein-ligand interaction detected (PLIP) ARS.15: 2 residues within 4Å: Chain C: C.184, W.231 No protein-ligand interaction detected (PLIP) ARS.20: 1 residues within 4Å: Chain D: C.184 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, H. et al., Structure-function analysis of the 3' phosphatase component of T4 polynucleotide kinase/phosphatase. Virology (2007)

Release Date

2007-06-05

Peptides

Polynucleotide kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Polynucleotide kinase

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