SMTL ID : 4xds.1

Deoxyguanosinetriphosphate Triphosphohydrolase from Escherichia coli with Nickel

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

homo-hexamer

Ligands

6 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 3 residues within 4Å: Chain A: H.69, H.117, D.268 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.69, A:H.117, A:D.268, H2O.1, H2O.1, H2O.1 NI.12: 3 residues within 4Å: Chain B: H.69, H.117, D.268 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.69, B:H.117, B:D.268, H2O.1, H2O.1, H2O.1 NI.21: 3 residues within 4Å: Chain C: H.69, H.117, D.268 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.69, C:H.117, C:D.268, H2O.1, H2O.1, H2O.1 NI.37: 3 residues within 4Å: Chain D: H.69, H.117, D.268 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.69, D:H.117, D:D.268, H2O.1, H2O.1, H2O.1 NI.50: 3 residues within 4Å: Chain E: H.69, H.117, D.268 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:H.69, E:H.117, E:D.268, H2O.1, H2O.1, H2O.1 NI.67: 3 residues within 4Å: Chain F: H.69, H.117, D.268 6 PLIP interactions: 3 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:H.69, F:H.117, F:D.268, H2O.1, H2O.1, H2O.1

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

SO4.2: 4 residues within 4Å: Chain A: N.186, K.211, Y.212, K.232 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: R.139, S.156, R.415, S.419 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.433, V.434, K.435 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: R.17, R.38, N.200 Chain B: R.326 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: R.15, H.194, Y.242, R.245 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: V.434, K.435, R.442 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: L.88, K.89, K.92, L.93, L.94, E.95 Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Chain A: R.326, Y.335 Chain B: R.17, R.38, N.200 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: Q.290, H.293 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain A: S.448, T.449 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: N.186, K.211, Y.212, K.232 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: R.139, S.156, R.415, S.419 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: K.431, R.433, V.434, K.435 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: R.15, Y.16, H.194, Y.242 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: V.434, K.435, R.442 Ligand excluded by PLIP SO4.18: 6 residues within 4Å: Chain B: L.88, K.89, K.92, L.93, L.94, E.95 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain B: S.448, T.449 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain B: S.156, R.161 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: N.186, K.211, Y.212, K.232 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain C: R.139, S.156, R.415, S.419 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain C: R.433, V.434, K.435 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain C: R.15, Y.16, H.194, Y.242, R.245 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain C: V.434, K.435, R.442 Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Chain C: R.326, Y.335 Chain D: R.17, R.38, N.200 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain C: H.13, Q.20, G.21 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain C: R.161 Ligand excluded by PLIP SO4.30: 9 residues within 4Å: Chain C: L.210, T.213, Y.235, I.243, R.247, A.253, L.254, Y.255, S.256 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain C: N.365, H.366 Ligand excluded by PLIP SO4.32: 2 residues within 4Å: Chain C: S.448, T.449 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain C: H.182, R.214, K.231 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain C: R.47, M.197, S.448, R.450, H.451 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain C: R.15, Y.16 Ligand excluded by PLIP SO4.36: 6 residues within 4Å: Chain C: R.17, R.38, N.200 Chain D: R.326, M.334, Y.335 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain D: N.186, K.211, Y.212, K.232 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain D: R.139, S.156, R.415, S.419 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain D: R.433, V.434, K.435 Ligand excluded by PLIP SO4.41: 5 residues within 4Å: Chain D: R.15, Y.16, H.194, Y.242, R.245 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain D: V.434, K.435, R.442 Ligand excluded by PLIP SO4.43: 5 residues within 4Å: Chain D: K.89, K.92, L.93, L.94, E.95 Ligand excluded by PLIP SO4.44: 4 residues within 4Å: Chain D: R.137, Q.178, H.182 Ligands: SO4.47 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain D: H.13, P.19, Q.20, G.21 Ligand excluded by PLIP SO4.46: 1 residues within 4Å: Chain D: R.15 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain D: H.182, R.214, K.231 Ligands: SO4.44 Ligand excluded by PLIP SO4.48: 1 residues within 4Å: Chain D: H.366 Ligand excluded by PLIP SO4.49: 9 residues within 4Å: Chain D: L.210, T.213, Y.235, I.243, R.247, A.253, L.254, Y.255, S.256 Ligand excluded by PLIP SO4.51: 4 residues within 4Å: Chain E: N.186, K.211, Y.212, K.232 Ligand excluded by PLIP SO4.52: 4 residues within 4Å: Chain E: R.139, S.156, R.415, S.419 Ligand excluded by PLIP SO4.53: 3 residues within 4Å: Chain E: R.433, V.434, K.435 Ligand excluded by PLIP SO4.54: 5 residues within 4Å: Chain E: R.15, Y.16, H.194, Y.242, R.245 Ligand excluded by PLIP SO4.55: 3 residues within 4Å: Chain E: V.434, K.435, R.442 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain E: K.89, K.92, L.93, L.94, E.95 Ligand excluded by PLIP SO4.57: 5 residues within 4Å: Chain E: R.326, Y.335 Chain F: R.17, R.38, N.200 Ligand excluded by PLIP SO4.58: 4 residues within 4Å: Chain E: P.346, Y.347, Q.350 Ligands: SO4.59 Ligand excluded by PLIP SO4.59: 2 residues within 4Å: Chain E: R.87 Ligands: SO4.58 Ligand excluded by PLIP SO4.60: 3 residues within 4Å: Chain E: H.13, Q.20, G.21 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain E: R.59, N.60 Chain F: Y.492 Ligand excluded by PLIP SO4.62: 1 residues within 4Å: Chain E: R.499 Ligand excluded by PLIP SO4.63: 5 residues within 4Å: Chain E: H.182, R.214, K.231, P.233 Ligands: SO4.64 Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain E: R.137, Q.178, H.182 Ligands: SO4.63 Ligand excluded by PLIP SO4.65: 9 residues within 4Å: Chain E: L.210, T.213, Y.235, I.243, R.247, A.253, L.254, Y.255, S.256 Ligand excluded by PLIP SO4.66: 5 residues within 4Å: Chain E: R.17, R.38, N.200 Chain F: R.326, Y.335 Ligand excluded by PLIP SO4.68: 5 residues within 4Å: Chain F: E.184, N.186, K.211, Y.212, K.232 Ligand excluded by PLIP SO4.69: 4 residues within 4Å: Chain F: R.139, S.156, R.415, S.419 Ligand excluded by PLIP SO4.70: 4 residues within 4Å: Chain F: K.431, R.433, V.434, K.435 Ligand excluded by PLIP SO4.71: 5 residues within 4Å: Chain F: R.15, Y.16, H.194, Y.242, R.245 Ligand excluded by PLIP SO4.72: 3 residues within 4Å: Chain F: V.434, K.435, R.442 Ligand excluded by PLIP SO4.73: 5 residues within 4Å: Chain F: K.89, K.92, L.93, L.94, E.95 Ligand excluded by PLIP SO4.74: 9 residues within 4Å: Chain F: L.210, T.213, Y.235, I.243, R.247, A.253, L.254, Y.255, S.256 Ligand excluded by PLIP SO4.75: 2 residues within 4Å: Chain F: K.8, N.251 Ligand excluded by PLIP SO4.76: 4 residues within 4Å: Chain F: R.137, Q.178, H.182 Ligands: SO4.84 Ligand excluded by PLIP SO4.77: 1 residues within 4Å: Chain F: R.7 Ligand excluded by PLIP SO4.78: 2 residues within 4Å: Chain F: K.175, E.240 Ligand excluded by PLIP SO4.79: 3 residues within 4Å: Chain F: H.13, Q.20, G.21 Ligand excluded by PLIP SO4.80: 3 residues within 4Å: Chain F: R.47, R.450 Ligands: SO4.83 Ligand excluded by PLIP SO4.81: 2 residues within 4Å: Chain F: R.161, R.163 Ligand excluded by PLIP SO4.82: 2 residues within 4Å: Chain F: S.156, R.161 Ligand excluded by PLIP SO4.83: 3 residues within 4Å: Chain F: S.448, T.449 Ligands: SO4.80 Ligand excluded by PLIP SO4.84: 5 residues within 4Å: Chain F: H.182, R.214, K.231, P.233 Ligands: SO4.76 Ligand excluded by PLIP SO4.85: 2 residues within 4Å: Chain F: N.365, H.366 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, D. et al., Structure of Escherichia coli dGTP Triphosphohydrolase: A HEXAMERIC ENZYME WITH DNA EFFECTOR MOLECULES. J.Biol.Chem. (2015)

Release Date

2015-02-25

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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