SMTL ID : 2it0.1

Crystal structure of a two-domain IdeR-DNA complex crystal form II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

NI.1: 4 residues within 4Å: Chain C: H.79, E.83, H.98 Ligands: ACT.4 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.79, C:E.83, C:H.98, ACT.4 NI.2: 5 residues within 4Å: Chain C: M.10, R.13, C.102, E.105, H.106 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.102, C:C.102, C:E.105, C:H.106 NI.3: 5 residues within 4Å: Chain C: D.59, H.61, E.63 Ligands: ACT.5, ACT.6 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Ligand interactions Metal complexes: C:H.61, ACT.5, ACT.6 NI.7: 4 residues within 4Å: Chain D: H.79, E.83, H.98 Ligands: ACT.10 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.79, D:E.83, D:H.98, ACT.10 NI.8: 5 residues within 4Å: Chain D: M.10, R.13, C.102, E.105, H.106 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.102, D:C.102, D:E.105, D:H.106 NI.9: 4 residues within 4Å: Chain D: D.59, H.61, E.63 Ligands: ACT.11 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.61, ACT.11 NI.12: 4 residues within 4Å: Chain E: H.79, E.83, H.98 Ligands: ACT.15 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:H.79, E:E.83, E:H.98, ACT.15 NI.13: 4 residues within 4Å: Chain E: M.10, C.102, E.105, H.106 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:C.102, E:C.102, E:E.105, E:H.106, H2O.2 NI.14: 5 residues within 4Å: Chain E: D.59, H.61, E.63 Ligands: ACT.16, ACT.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:H.61 NI.18: 4 residues within 4Å: Chain F: H.79, E.83, H.98 Ligands: ACT.21 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.79, F:E.83, F:H.98, ACT.21 NI.19: 5 residues within 4Å: Chain F: M.10, R.13, C.102, E.105, H.106 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.102, F:C.102, F:E.105, F:H.106 NI.20: 4 residues within 4Å: Chain F: D.59, H.61, E.63 Ligands: ACT.22 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.61, ACT.22

10 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 6 residues within 4Å: Chain C: H.79, R.80, E.83, H.98, N.130 Ligands: NI.1 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:H.79, C:R.80, C:H.98 ACT.5: 4 residues within 4Å: Chain C: H.61, E.63 Ligands: NI.3, ACT.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.63 Salt bridges: C:H.61 ACT.6: 6 residues within 4Å: Chain C: A.57, D.59, H.61, E.63 Ligands: NI.3, ACT.5 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.61 ACT.10: 6 residues within 4Å: Chain D: H.79, R.80, E.83, H.98, N.130 Ligands: NI.7 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:H.79, D:R.80, D:H.98 ACT.11: 3 residues within 4Å: Chain D: H.61, E.63 Ligands: NI.9 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.61 ACT.15: 6 residues within 4Å: Chain E: H.79, R.80, E.83, H.98, N.130 Ligands: NI.12 3 PLIP interactions: 3 interactions with chain E Salt bridges: E:H.79, E:R.80, E:H.98 ACT.16: 4 residues within 4Å: Chain E: P.25, H.61, E.63 Ligands: NI.14 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:H.61 ACT.17: 5 residues within 4Å: Chain E: A.57, D.59, H.61, E.63 Ligands: NI.14 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.63 Salt bridges: E:H.61 ACT.21: 5 residues within 4Å: Chain F: H.79, R.80, E.83, H.98 Ligands: NI.18 3 PLIP interactions: 3 interactions with chain F Salt bridges: F:H.79, F:R.80, F:H.98 ACT.22: 5 residues within 4Å: Chain F: A.57, D.59, H.61, E.63 Ligands: NI.20 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:H.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wisedchaisri, G. et al., Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis. Biochemistry (2007)

Release Date

2007-02-13

Peptides

Iron-dependent repressor ideR: CDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
D

Iron-dependent repressor ideR

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