SMTL ID : 3qsi.2 (2 other biounits)

Nickel binding domain of NikR from Helicobacter pylori disclosing partial metal occupancy

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.08 Å

Oligo State

homo-tetramer

Ligands

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

NI.1: 3 residues within 4Å: Chain A: H.14, H.41 Chain D: H.28 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Metal complexes: A:H.14, A:H.41, D:H.28 NI.3: 5 residues within 4Å: Chain B: H.39, H.41, C.47 Chain C: I.24, H.28 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.39, B:H.41, B:C.47, C:H.28 NI.5: 4 residues within 4Å: Chain B: H.28 Chain C: H.14, H.41 Ligands: SO4.4 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.14, C:H.41, B:H.28 NI.6: 5 residues within 4Å: Chain A: I.24, H.28 Chain D: H.39, H.41, C.47 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:H.39, D:H.41, D:C.47, A:H.28

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

SO4.2: 1 residues within 4Å: Chain A: R.62 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.62 SO4.4: 7 residues within 4Å: Chain B: Q.27, H.28, T.32, H.33, V.34 Chain C: H.41 Ligands: NI.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.32, B:V.34 Salt bridges: B:H.28, C:H.41 SO4.7: 1 residues within 4Å: Chain D: R.17 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

West, A.L. et al., Ni(II) coordination to mixed sites modulates DNA binding of HpNikR via a long-range effect. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-04-04

Peptides

NikR nickel-responsive regulator: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
E

NikR nickel-responsive regulator

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