SMTL ID : 6mrj.1

Crystal structure of H.pylori NikR in complex with DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: H.99, H.101, C.107 Chain D: I.84, H.88 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Metal complexes: A:H.99, A:H.101, A:C.107, D:H.88 NI.3: 6 residues within 4Å: Chain A: I.84, H.88 Chain D: H.99, I.100, H.101, C.107 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:H.99, D:H.101, D:C.107, A:H.88 NI.4: 6 residues within 4Å: Chain B: H.99, I.100, H.101, C.107 Chain C: I.84, H.88 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:H.99, B:H.101, B:C.107, C:H.88 NI.5: 5 residues within 4Å: Chain B: I.84, H.88 Chain C: H.99, H.101, C.107 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.99, C:H.101, C:C.107, B:H.88

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: G.128, L.130, V.133 Chain B: E.39, D.43 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.39, B:D.43, A:L.130, A:V.133 MG.6: 6 residues within 4Å: Chain C: E.39, D.43 Chain D: G.128, G.129, L.130, V.133 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:E.39, C:D.43, D:G.128, D:L.130, D:V.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pozharski, E. et al., Crystal structure of H.pylori NikR in complex with DNA. To Be Published

Release Date

2019-11-20

Peptides

Nickel-responsive regulator: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Nickel-responsive regulator

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