SMTL ID : 5ww9.1

Crystal structure of R73E mutant of the second DNA-Binding protein under starvation from Mycobacterium smegmatis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-12-mer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: N.48, D.51 Chain E: N.48, D.51 Chain I: N.48, D.51 Ligands: MG.9, MG.17 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain I Metal complexes: E:D.51, A:D.51, I:D.51 MG.7: 6 residues within 4Å: Chain D: N.48, D.51 Chain F: N.48, D.51 Chain G: N.48, D.51 3 PLIP interactions: 1 interactions with chain G, 1 interactions with chain D, 1 interactions with chain F Metal complexes: G:D.51, D:D.51, F:D.51 MG.9: 8 residues within 4Å: Chain A: N.48, D.51 Chain E: N.48, D.51 Chain I: N.48, D.51 Ligands: MG.1, MG.17 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain I Metal complexes: E:D.51, A:D.51, I:D.51 MG.15: 6 residues within 4Å: Chain H: N.48, D.51 Chain J: N.48, D.51 Chain K: N.48, D.51 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain H, 1 interactions with chain J Metal complexes: K:D.51, H:D.51, J:D.51 MG.17: 8 residues within 4Å: Chain A: N.48, D.51 Chain E: N.48, D.51 Chain I: N.48, D.51 Ligands: MG.1, MG.9 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain E, 1 interactions with chain A Metal complexes: I:D.51, E:D.51, A:D.51 MG.23: 6 residues within 4Å: Chain B: N.48, D.51 Chain C: N.48, D.51 Chain L: N.48, D.51 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain L, 1 interactions with chain C Metal complexes: B:D.51, L:D.51, C:D.51

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

CL.2: 8 residues within 4Å: Chain A: R.50, L.54 Chain E: R.50, L.54 Chain I: R.50, L.54 Ligands: CL.10, CL.18 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain B: R.50, L.54 Chain C: R.50 Chain L: R.50, L.54 Ligand excluded by PLIP CL.10: 8 residues within 4Å: Chain A: R.50, L.54 Chain E: R.50, L.54 Chain I: R.50, L.54 Ligands: CL.2, CL.18 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain D: R.50, L.54 Chain F: R.50, L.54 Chain G: R.50 Ligand excluded by PLIP CL.18: 8 residues within 4Å: Chain A: R.50, L.54 Chain E: R.50, L.54 Chain I: R.50, L.54 Ligands: CL.2, CL.10 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain H: R.50, L.54 Chain J: R.50, L.54 Chain K: R.50 Ligand excluded by PLIP

12 x FE: FE (III) ION(Non-covalent)

FE.3: 4 residues within 4Å: Chain A: D.68, E.72 Chain B: K.38, H.41 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.68, A:D.68, A:E.72, B:H.41, H2O.6 FE.5: 5 residues within 4Å: Chain A: K.38, H.41, W.42 Chain B: D.68, E.72 No protein-ligand interaction detected (PLIP) FE.6: 5 residues within 4Å: Chain C: D.68, E.72 Chain D: K.38, H.41, D.57 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:H.41, C:D.68, C:D.68, C:E.72, H2O.16 FE.8: 5 residues within 4Å: Chain C: K.38, H.41, D.57 Chain D: D.68, E.72 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:D.68, D:D.68, D:E.72, C:H.41, H2O.11 FE.11: 4 residues within 4Å: Chain E: D.68, E.72 Chain F: K.38, H.41 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:D.68, E:D.68, E:E.72, F:H.41, H2O.26 FE.13: 5 residues within 4Å: Chain E: K.38, H.41, W.42 Chain F: D.68, E.72 No protein-ligand interaction detected (PLIP) FE.14: 5 residues within 4Å: Chain G: D.68, E.72 Chain H: K.38, H.41, D.57 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: G:D.68, G:D.68, G:E.72, H:H.41, H2O.36 FE.16: 5 residues within 4Å: Chain G: K.38, H.41, D.57 Chain H: D.68, E.72 5 PLIP interactions: 1 interactions with chain G, 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: G:H.41, H:D.68, H:D.68, H:E.72, H2O.31 FE.19: 4 residues within 4Å: Chain I: D.68, E.72 Chain J: K.38, H.41 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: I:D.68, I:D.68, I:E.72, J:H.41, H2O.46 FE.21: 5 residues within 4Å: Chain I: K.38, H.41, W.42 Chain J: D.68, E.72 No protein-ligand interaction detected (PLIP) FE.22: 5 residues within 4Å: Chain K: D.68, E.72 Chain L: K.38, H.41, D.57 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: K:D.68, K:D.68, K:E.72, L:H.41, H2O.55 FE.24: 5 residues within 4Å: Chain K: K.38, H.41, D.57 Chain L: D.68, E.72 5 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: K:H.41, L:D.68, L:D.68, L:E.72, H2O.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, S.M. et al., Flexible aspartates propel iron to the ferroxidation sites along pathways stabilized by a conserved arginine in Dps proteins from Mycobacterium smegmatis. Metallomics (2017)

Release Date

2017-08-09

Peptides

Putative starvation-induced DNA protecting protein/Ferritin and Dps: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Putative starvation-induced DNA protecting protein/Ferritin and Dps