SMTL ID : 2bj7.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

8 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.6: 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.7: 3 residues within 4Å: Chain B: H.64, D.65 Chain C: D.75 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.64, B:D.65, B:D.65, C:D.75 NI.8: 3 residues within 4Å: Chain B: D.75 Chain C: H.64, D.65 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:H.64, C:D.65, B:D.75, H2O.6, H2O.6 NI.10: 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.15: 5 residues within 4Å: Chain A: L.74, H.78 Chain D: H.89, H.91, C.97 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:H.89, D:H.91, D:C.97, A:H.78 NI.16: 3 residues within 4Å: Chain A: D.75 Chain D: H.64, D.65 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:H.64, D:D.65, D:D.65, A:D.75 NI.17: 3 residues within 4Å: Chain A: H.64, D.65 Chain D: D.75 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: D:D.75, A:H.64, A:D.65, H2O.1, H2O.1

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

EDO.2: 2 residues within 4Å: Chain A: F.6, S.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:R.5 Hydrogen bonds: A:S.7 EDO.9: 4 residues within 4Å: Chain A: L.137 Chain B: K.124, H.125, G.126 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:L.137, B:H.125, B:G.126, B:G.126 EDO.11: 2 residues within 4Å: Chain C: F.6, S.7 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Water bridges: D:R.5 Hydrogen bonds: C:S.7 EDO.18: 4 residues within 4Å: Chain C: L.137 Chain D: K.124, H.125, G.126 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.126, D:G.126, C:L.137

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

PG4.3: 10 residues within 4Å: Chain A: F.41, H.45, K.111, D.115, L.118, H.125, G.126, L.128 Chain B: I.25, Y.27 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.115, A:G.126, B:D.36 PG4.4: 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: 10 residues within 4Å: Chain C: F.41, H.45, K.111, D.115, L.118, H.125, G.126, L.128 Chain D: I.25, Y.27 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.126, D:Y.27 Water bridges: C:H.45, C:H.45 PG4.13: 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 CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: F.6 Chain B: R.30 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: F.6 Chain D: R.30 Ligand excluded by PLIP

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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