SMTL ID : 2bj9.1

NIKR WITH BOUND NICKEL AND PHOSPHATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

10 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: 1 interactions with chain D, 3 interactions with chain A Metal complexes: D:H.78, A:H.89, A:H.91, A:C.97 NI.2: 6 residues within 4Å: Chain A: L.118, S.119, L.120, V.123 Chain B: E.32, D.36 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:L.120, A:V.123, B:E.32, B:D.36 NI.5: 4 residues within 4Å: Chain B: H.89, H.91, C.97 Chain C: 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.6: 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.7: 4 residues within 4Å: Chain B: K.71, D.75 Chain C: H.64, D.65 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.64, C:D.65, C:D.65, B:D.75 NI.9: 5 residues within 4Å: Chain B: L.74, H.78 Chain C: H.89, H.91, C.97 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.78, C:H.89, C:H.91, C:C.97 NI.10: 6 residues within 4Å: Chain C: L.118, S.119, L.120, V.123 Chain D: E.32, D.36 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Metal complexes: D:E.32, D:D.36, C:L.120, C:V.123 NI.13: 4 residues within 4Å: Chain A: 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.14: 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.15: 4 residues within 4Å: Chain A: H.64, D.65 Chain D: K.71, D.75 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Metal complexes: A:H.64, A:D.65, A:D.65, D:D.75

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 3 residues within 4Å: Chain A: F.6, S.7 Chain B: R.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.5 Hydrogen bonds: A:S.7, A:S.7 PO4.8: 8 residues within 4Å: Chain A: E.66, K.121, G.122, K.124 Chain B: E.32, R.35, R.39, V.138 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.32, B:E.32, B:V.138, A:G.122 Salt bridges: B:R.35, B:R.39, A:K.121, A:K.124 PO4.11: 3 residues within 4Å: Chain C: F.6, S.7 Chain D: R.5 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.5 Hydrogen bonds: C:S.7, C:S.7 PO4.16: 8 residues within 4Å: Chain C: E.66, K.121, G.122, K.124 Chain D: E.32, R.35, R.39, V.138 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.122, D:E.32, D:E.32, D:V.138 Salt bridges: C:K.121, C:K.124, D:R.35, D:R.39

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

PG4.4: 7 residues within 4Å: Chain A: D.19, I.22, E.23, Y.27, E.28, N.29, R.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.19 PG4.12: 7 residues within 4Å: Chain C: D.19, I.22, E.23, Y.27, E.28, N.29, R.30 No protein-ligand interaction detected (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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