SMTL ID : 3eyy.1

Structural basis for the specialization of Nur, a nickel-specific Fur homologue, in metal sensing and DNA recognition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

NI.1: 5 residues within 4Å: Chain A: H.70, H.72, H.126 Ligands: EDO.6, MLI.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.70, A:H.72, A:H.126 NI.10: 5 residues within 4Å: Chain B: H.70, H.72, H.126 Ligands: EDO.14, MLI.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.70, B:H.72, B:H.126

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.33, H.86, H.88, H.90, E.101 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.33, A:H.86, A:H.88, A:H.90 ZN.11: 5 residues within 4Å: Chain B: H.33, H.86, H.88, H.90, E.101 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.33, B:H.86, B:H.88, B:H.90

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: D.5, K.7, S.8 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: D.29, E.32 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: T.4, D.5, K.7, S.8 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: V.28, D.29, E.32 Ligand excluded by PLIP

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

EDO.6: 6 residues within 4Å: Chain A: H.70, H.72, Y.80 Chain B: H.75 Ligands: NI.1, MLI.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.80, A:Y.80, B:H.75 EDO.7: 2 residues within 4Å: Chain A: R.13, Y.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.13 Water bridges: A:Y.15, A:Y.15 EDO.14: 6 residues within 4Å: Chain A: H.75 Chain B: H.70, H.72, Y.80 Ligands: NI.10, MLI.16 No protein-ligand interaction detected (PLIP) EDO.15: 1 residues within 4Å: Chain B: R.13 No protein-ligand interaction detected (PLIP)

3 x MLI: MALONATE ION(Non-functional Binders)

MLI.8: 9 residues within 4Å: Chain A: H.70, H.72, H.126, F.127 Chain B: G.74, H.75, F.130 Ligands: NI.1, EDO.6 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.130 Hydrogen bonds: B:H.75 Water bridges: B:H.75 Salt bridges: B:H.75, B:H.75, A:H.70, A:H.72, A:H.126, A:H.126 MLI.9: 3 residues within 4Å: Chain A: E.63, E.64, G.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.63 MLI.16: 9 residues within 4Å: Chain A: G.74, H.75, F.130 Chain B: H.70, H.72, H.126, F.127 Ligands: NI.10, EDO.14 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.130 Hydrogen bonds: A:H.75 Water bridges: A:H.75 Salt bridges: A:H.75, A:H.75, B:H.70, B:H.72, B:H.126, B:H.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

An, Y.J. et al., Structural basis for the specialization of Nur, a nickel-specific Fur homolog, in metal sensing and DNA recognition. Nucleic Acids Res. (2009)

Release Date

2009-06-09

Peptides

Putative iron uptake regulatory protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative iron uptake regulatory protein