SMTL ID : 1q5y.1

Nickel-Bound C-terminal Regulatory Domain of NikR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-tetramer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: H.39, H.41, C.47 Chain C: V.24, H.28 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.39, A:H.41, A:C.47, C:H.28 NI.2: 5 residues within 4Å: Chain A: V.24, H.28 Chain C: H.39, H.41, C.47 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.39, C:H.41, C:C.47, A:H.28 NI.8: 5 residues within 4Å: Chain B: H.39, H.41, C.47 Chain D: V.24, H.28 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Metal complexes: D:H.28, B:H.39, B:H.41, B:C.47 NI.9: 5 residues within 4Å: Chain B: V.24, H.28 Chain D: H.39, H.41, C.47 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Metal complexes: D:H.39, D:H.41, D:C.47, B:H.28

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

EDO.3: 4 residues within 4Å: Chain A: R.17 Chain C: R.17, D.18, S.21 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.21 Water bridges: C:S.21, C:S.21 EDO.4: 4 residues within 4Å: Chain C: I.68, G.76, H.77, L.78 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.77, C:L.78 EDO.5: 6 residues within 4Å: Chain C: I.68, V.73, R.74, H.75, G.76 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.73, C:G.76 EDO.6: 4 residues within 4Å: Chain C: V.73, R.74, H.75 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.75, C:H.75 EDO.7: 5 residues within 4Å: Chain C: H.77, L.78, Q.79 Chain D: G.76, H.77 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:L.78, D:G.76 Water bridges: C:C.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schreiter, E.R. et al., Crystal Structure of the Nickel-Responsive Transcription Factor NikR. Nat.Struct.Biol. (2003)

Release Date

2003-09-30

Peptides

Nickel responsive regulator: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Nickel responsive regulator