SMTL ID : 2isz.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

NI.1: 3 residues within 4Å: Chain C: H.79, E.83, H.98 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.79, C:E.83, C:H.98, H2O.3 NI.2: 4 residues within 4Å: Chain C: M.10, C.102, E.105, H.106 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.102, C:C.102, C:E.105, C:H.106, H2O.3 NI.3: 2 residues within 4Å: Chain C: D.59, H.61 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.61 NI.5: 3 residues within 4Å: Chain D: H.79, E.83, H.98 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.79, D:E.83, D:H.98, H2O.4 NI.6: 4 residues within 4Å: Chain D: M.10, C.102, E.105, H.106 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.102, D:C.102, D:E.105, D:H.106, H2O.4 NI.7: 2 residues within 4Å: Chain D: D.59, H.61 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.61, H2O.4, H2O.4, H2O.4 NI.8: 3 residues within 4Å: Chain E: H.79, E.83, H.98 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.79, E:E.83, E:H.98, H2O.5 NI.9: 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.5 NI.10: 2 residues within 4Å: Chain E: D.59, H.61 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:H.61, H2O.5, H2O.5, H2O.5 NI.12: 3 residues within 4Å: Chain F: H.79, E.83, H.98 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.79, F:E.83, F:H.98, H2O.6 NI.13: 5 residues within 4Å: Chain F: M.10, R.13, C.102, E.105, H.106 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:C.102, F:E.105, F:H.106, H2O.5 NI.14: 2 residues within 4Å: Chain F: D.59, H.61 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.61, H2O.6, H2O.6

3 x NA: SODIUM ION(Non-functional Binders)

NA.4: 1 residues within 4Å: Chain B: C.19 No protein-ligand interaction detected (PLIP) NA.11: 1 residues within 4Å: Chain A: C.16 4 PLIP interactions: 4 interactions with chain E Water bridges: E:D.35, E:D.35, E:D.35, E:Q.36 NA.15: 1 residues within 4Å: Chain B: C.24 No protein-ligand interaction detected (PLIP)

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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