SMTL ID : 2bj8.1

NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH AND LOW-AFFINITY SITES

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: H.89, H.91, C.97 Chain D: L.74, H.78 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Metal complexes: A:H.89, A:H.91, A:C.97, D:H.78 NI.4: 5 residues within 4Å: Chain B: H.89, H.91, C.97 Chain C: L.74, H.78 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.89, B:H.91, B:C.97, C:H.78 NI.5: 3 residues within 4Å: Chain B: H.64, D.65 Chain C: D.75 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Metal complexes: C:D.75, B:H.64, B:D.65, B:D.65 NI.6: 3 residues within 4Å: Chain B: D.75 Chain C: H.64, D.65 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.64, C:D.65, C:D.65, B:D.75, H2O.141 NI.7: 3 residues within 4Å: Chain B: E.32, D.36, R.39 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.32, B:D.36, B:D.36 NI.10: 1 residues within 4Å: Chain B: E.53 No protein-ligand interaction detected (PLIP) NI.11: 5 residues within 4Å: Chain B: L.74, H.78 Chain C: H.89, H.91, C.97 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.89, C:H.91, C:C.97, B:H.78 NI.14: 5 residues within 4Å: Chain A: L.74, H.78 Chain D: H.89, H.91, C.97 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Metal complexes: A:H.78, D:H.89, D:H.91, D:C.97 NI.15: 3 residues within 4Å: Chain A: D.75 Chain D: H.64, D.65 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Metal complexes: A:D.75, D:H.64, D:D.65, D:D.65 NI.16: 3 residues within 4Å: Chain A: H.64, D.65 Chain D: D.75 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:H.64, A:D.65, A:D.65, D:D.75, H2O.36 NI.17: 3 residues within 4Å: Chain D: E.32, D.36, R.39 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.32, D:D.36, D:D.36 NI.20: 1 residues within 4Å: Chain D: E.53 No protein-ligand interaction detected (PLIP)

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 6 residues within 4Å: Chain A: D.19, I.22, E.23, Y.27, E.28, R.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.23 PG4.12: 6 residues within 4Å: Chain C: D.19, I.22, E.23, Y.27, E.28, R.30 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.23

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 2 residues within 4Å: Chain A: F.6, S.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.5, A:S.7 Water bridges: B:R.5 EPE.13: 2 residues within 4Å: Chain C: F.6, S.7 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:R.5 Hydrogen bonds: C:R.5, C:S.7

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain A: F.6 Chain B: R.30 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: F.6 Chain D: R.30 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 3 residues within 4Å: Chain B: K.124, H.125, G.126 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.125, B:G.126, B:G.126 EDO.19: 3 residues within 4Å: Chain D: K.124, H.125, G.126 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.126, D:G.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chivers, P.T. et al., Structure of Pyrococcus Horikoshii Nikr: Nickel Sensing and Implications for the Regulation of DNA Recognition. J.Mol.Biol. (2005)

Release Date

2005-04-08

Peptides

NICKEL RESPONSIVE REGULATOR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

NICKEL RESPONSIVE REGULATOR

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