SMTL ID : 3od2.1

E. coli NikR soaked with excess nickel ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: H.87, H.89, C.95 Chain D: V.72, H.76 Ligand excluded by PLIP NI.2: 1 residues within 4Å: Chain A: M.1 Ligand excluded by PLIP NI.3: 2 residues within 4Å: Chain A: H.125 Chain B: H.125 Ligand excluded by PLIP NI.4: 3 residues within 4Å: Chain A: H.78, H.110, D.114 Ligand excluded by PLIP NI.5: 2 residues within 4Å: Chain A: H.79 Chain D: H.92 Ligand excluded by PLIP NI.6: 3 residues within 4Å: Chain A: H.123 Chain B: P.130, E.132 Ligand excluded by PLIP NI.8: 5 residues within 4Å: Chain B: H.87, H.89, C.95 Chain C: V.72, H.76 Ligand excluded by PLIP NI.9: 3 residues within 4Å: Chain B: H.78, H.110, D.114 Ligand excluded by PLIP NI.10: 1 residues within 4Å: Chain B: H.123 Ligand excluded by PLIP NI.11: 3 residues within 4Å: Chain B: H.79, D.80 Chain C: H.92 Ligand excluded by PLIP NI.12: 2 residues within 4Å: Chain B: M.1, Q.2 Ligand excluded by PLIP NI.13: 5 residues within 4Å: Chain B: V.72, H.76 Chain C: H.87, H.89, C.95 Ligand excluded by PLIP NI.14: 1 residues within 4Å: Chain C: M.1 Ligand excluded by PLIP NI.15: 2 residues within 4Å: Chain C: H.125 Chain D: H.125 Ligand excluded by PLIP NI.16: 3 residues within 4Å: Chain C: H.78, H.110, D.114 Ligand excluded by PLIP NI.17: 2 residues within 4Å: Chain B: H.92 Chain C: H.79 Ligand excluded by PLIP NI.18: 3 residues within 4Å: Chain C: H.123 Chain D: P.130, E.132 Ligand excluded by PLIP NI.20: 5 residues within 4Å: Chain A: V.72, H.76 Chain D: H.87, H.89, C.95 Ligand excluded by PLIP NI.21: 3 residues within 4Å: Chain D: H.78, H.110, D.114 Ligand excluded by PLIP NI.22: 1 residues within 4Å: Chain D: H.123 Ligand excluded by PLIP NI.23: 3 residues within 4Å: Chain A: H.92 Chain D: H.79, D.80 Ligand excluded by PLIP NI.24: 2 residues within 4Å: Chain D: M.1, Q.2 Ligand excluded by PLIP

2 x 3CM: 3-CYCLOHEXYLPROPYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE(Non-covalent)

3CM.7: 10 residues within 4Å: Chain A: L.19, S.20, R.23, Y.25, I.35 Chain B: Q.42, E.43, G.124, H.125, L.126 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.19, A:Y.25, A:I.35, B:E.43 Hydrogen bonds: A:R.23, B:Q.42, B:G.124, B:L.126 Salt bridges: A:R.23 3CM.19: 10 residues within 4Å: Chain C: L.19, S.20, R.23, Y.25, I.35 Chain D: Q.42, E.43, G.124, H.125, L.126 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:E.43, C:L.19, C:Y.25, C:I.35 Hydrogen bonds: D:Q.42, D:G.124, D:L.126, C:R.23 Salt bridges: C:R.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, C.M. et al., Structural basis of low-affinity nickel binding to the nickel-responsive transcription factor NikR from Escherichia coli. Biochemistry (2010)

Release Date

2010-09-08

Peptides

Nickel-responsive regulatory protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Nickel-responsive regulatory protein

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