SMTL ID : 6oiw.1

Structure of Escherichia coli dGTPase bound to dGTP-1-thiol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

homo-hexamer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.211, D.268, D.269 Ligands: T8T.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.269 MG.10: 4 residues within 4Å: Chain E: D.268, D.269, Y.272 Ligands: T8T.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.269 MG.13: 3 residues within 4Å: Chain F: D.268, D.269 Ligands: T8T.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.268

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: H.69, H.117, D.118, D.268 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:H.117, A:D.268, A:D.268 MN.4: 5 residues within 4Å: Chain B: H.69, H.117, D.118, D.268 Ligands: T8T.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.117, B:D.268, B:D.268 MN.6: 4 residues within 4Å: Chain C: H.69, H.117, D.118, D.268 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.69, C:H.117, C:D.268 MN.8: 5 residues within 4Å: Chain D: H.69, H.117, D.118, D.268 Ligands: T8T.9 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.69, D:H.117, D:D.118, D:D.268 MN.11: 5 residues within 4Å: Chain E: H.69, H.117, D.118, D.268 Ligands: T8T.12 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.117, E:D.268 MN.14: 5 residues within 4Å: Chain F: H.69, H.117, D.118, D.268 Ligands: T8T.15 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.69, F:H.117, F:D.268

6 x T8T: 2'-deoxyguanosine-5'-O-(1-thiotriphosphate)(Covalent)(Non-covalent)

T8T.3: 15 residues within 4Å: Chain A: Q.53, V.54, H.126, N.186, K.211, Y.212, K.232, D.268, D.269, Y.272, D.276, F.391, V.396, E.400 Ligands: MG.1 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.391 Hydrogen bonds: A:V.54, A:N.186, A:Y.272, B:R.442 Salt bridges: A:K.211, A:K.211, A:K.232, A:K.232, A:E.400 pi-Stacking: A:F.391, A:F.391 pi-Cation interactions: A:F.391 T8T.5: 17 residues within 4Å: Chain B: Q.53, V.54, H.117, D.118, H.126, K.211, Y.212, K.232, D.268, Y.272, D.276, F.391, V.396, E.400 Chain C: R.433, R.442 Ligands: MN.4 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:V.54, B:D.118, B:N.121, B:Y.212, B:D.276, C:R.433, C:R.442 Salt bridges: B:K.211, B:K.231, B:K.232, B:E.400 pi-Stacking: B:F.391 pi-Cation interactions: B:F.391 T8T.7: 15 residues within 4Å: Chain A: R.433, R.442 Chain C: Q.53, V.54, H.126, K.211, Y.212, K.232, D.268, D.269, Y.272, D.276, F.391, V.396, E.400 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.391 Hydrogen bonds: C:V.54, C:D.268, A:R.433, A:R.442 Salt bridges: C:K.211, C:K.211, C:K.232, C:E.400 pi-Stacking: C:H.126, C:F.391, C:F.391 pi-Cation interactions: C:F.391 T8T.9: 16 residues within 4Å: Chain D: Q.53, V.54, D.118, H.126, N.186, K.211, Y.212, K.232, D.268, Y.272, D.276, F.391, V.396, E.400 Chain F: R.442 Ligands: MN.8 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:F.391 Hydrogen bonds: D:V.54, D:V.54, D:D.118, D:N.186, D:Y.212, D:D.276, F:R.442 Water bridges: D:R.66, D:E.184, D:N.186, D:K.232 Salt bridges: D:K.211, D:K.211, D:K.232, D:E.400 pi-Stacking: D:F.391, D:F.391 T8T.12: 21 residues within 4Å: Chain D: R.433, R.442 Chain E: Q.53, V.54, H.117, D.118, H.126, E.184, N.186, K.211, Y.212, K.231, K.232, D.268, Y.272, D.276, F.391, V.396, E.400 Ligands: MG.10, MN.11 19 PLIP interactions: 2 interactions with chain D, 17 interactions with chain E Hydrogen bonds: D:R.433, D:R.442, E:V.54, E:E.184, E:N.186, E:Y.212, E:Y.212, E:Y.212, E:D.276 Hydrophobic interactions: E:F.391 Salt bridges: E:K.211, E:K.211, E:K.231, E:K.232, E:K.232, E:E.400 pi-Stacking: E:F.391, E:F.391 pi-Cation interactions: E:F.391 T8T.15: 18 residues within 4Å: Chain E: R.442 Chain F: Q.53, V.54, D.118, N.121, H.126, E.184, N.186, K.211, Y.212, K.232, Y.272, D.276, F.391, V.396, E.400 Ligands: MG.13, MN.14 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:V.54, F:F.391 Hydrogen bonds: F:V.54, F:N.121, F:N.121, F:N.186, F:N.186, F:Y.272, E:R.442 Salt bridges: F:H.126, F:K.211, F:K.232, F:E.400 pi-Stacking: F:F.391, F:F.391

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barnes, C.O. et al., The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-05-15

Peptides

Deoxyguanosinetriphosphate triphosphohydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Deoxyguanosinetriphosphate triphosphohydrolase

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