SMTL ID : 5ww4.1

Crystal structure of the second DNA-Binding protein under starvation from Mycobacterium smegmatis soaked with iron in the ratio of 48 iron atoms per dodecamer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-12-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: D.68, E.72 Chain B: K.38, H.41, D.57 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.4 FE.4: 5 residues within 4Å: Chain A: K.38, H.41, D.57 Chain B: D.68, E.72 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.41, B:D.68, B:D.68, B:E.72, H2O.1 FE.9: 4 residues within 4Å: Chain C: D.68, E.72 Chain D: H.41, D.57 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:D.68, C:E.72, D:H.41, H2O.9, H2O.10 FE.10: 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.7 FE.13: 5 residues within 4Å: Chain E: D.68, E.72 Chain F: K.38, H.41, D.57 5 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:H.41, E:D.68, E:D.68, E:E.72, H2O.16 FE.16: 5 residues within 4Å: Chain E: K.38, H.41, D.57 Chain F: D.68, E.72 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:D.68, F:D.68, F:E.72, E:H.41, H2O.13 FE.21: 4 residues within 4Å: Chain G: D.68, E.72 Chain H: H.41, D.57 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: G:D.68, G:E.72, H:H.41, H2O.22, H2O.23 FE.22: 5 residues within 4Å: Chain G: K.38, H.41, D.57 Chain H: D.68, E.72 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: H:D.68, H:D.68, H:E.72, G:H.41, H2O.19 FE.25: 5 residues within 4Å: Chain I: D.68, E.72 Chain J: K.38, H.41, D.57 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.29 FE.28: 5 residues within 4Å: Chain I: K.38, H.41, D.57 Chain J: D.68, E.72 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: J:D.68, J:D.68, J:E.72, I:H.41, H2O.26 FE.33: 4 residues within 4Å: Chain K: D.68, E.72 Chain L: H.41, D.57 5 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K, 2 Ligand-Water interactions Metal complexes: L:H.41, K:D.68, K:E.72, H2O.34, H2O.35 FE.34: 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.32

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: N.48, D.51 Chain E: N.48, D.51 Chain I: N.48, D.51 Ligands: MG.14, MG.26 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 1 interactions with chain I Metal complexes: A:D.51, E:D.51, I:D.51 MG.7: 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 C, 1 interactions with chain L, 1 interactions with chain B Metal complexes: C:D.51, L:D.51, B:D.51 MG.14: 8 residues within 4Å: Chain A: N.48, D.51 Chain E: N.48, D.51 Chain I: N.48, D.51 Ligands: MG.2, MG.26 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E, 1 interactions with chain I Metal complexes: A:D.51, E:D.51, I:D.51 MG.19: 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.26: 8 residues within 4Å: Chain A: N.48, D.51 Chain E: N.48, D.51 Chain I: N.48, D.51 Ligands: MG.2, MG.14 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain I, 1 interactions with chain A Metal complexes: E:D.51, I:D.51, A:D.51 MG.31: 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 J, 1 interactions with chain H, 1 interactions with chain K Metal complexes: J:D.51, H:D.51, K:D.51

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

CL.3: 8 residues within 4Å: Chain A: R.50, L.54 Chain E: R.50, L.54 Chain I: R.50, L.54 Ligands: CL.15, CL.27 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: R.50, L.54 Chain C: R.50, L.54 Chain L: R.50, L.54 Ligand excluded by PLIP CL.15: 8 residues within 4Å: Chain A: R.50, L.54 Chain E: R.50, L.54 Chain I: R.50, L.54 Ligands: CL.3, CL.27 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain D: R.50, L.54 Chain F: R.50, L.54 Chain G: R.50, L.54 Ligand excluded by PLIP CL.27: 8 residues within 4Å: Chain A: R.50, L.54 Chain E: R.50, L.54 Chain I: R.50, L.54 Ligands: CL.3, CL.15 Ligand excluded by PLIP CL.32: 6 residues within 4Å: Chain H: R.50, L.54 Chain J: R.50, L.54 Chain K: R.50, L.54 Ligand excluded by PLIP

12 x FE2: FE (II) ION(Non-functional Binders)(Non-covalent)

FE2.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE2.6: 1 residues within 4Å: Chain B: D.138 No protein-ligand interaction detected (PLIP) FE2.11: 2 residues within 4Å: Ligands: FE2.23, FE2.35 No protein-ligand interaction detected (PLIP) FE2.12: 2 residues within 4Å: Ligands: FE2.24, FE2.36 No protein-ligand interaction detected (PLIP) FE2.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE2.18: 1 residues within 4Å: Chain F: D.138 No protein-ligand interaction detected (PLIP) FE2.23: 2 residues within 4Å: Ligands: FE2.11, FE2.35 No protein-ligand interaction detected (PLIP) FE2.24: 2 residues within 4Å: Ligands: FE2.12, FE2.36 No protein-ligand interaction detected (PLIP) FE2.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FE2.30: 1 residues within 4Å: Chain J: D.138 No protein-ligand interaction detected (PLIP) FE2.35: 2 residues within 4Å: Ligands: FE2.11, FE2.23 No protein-ligand interaction detected (PLIP) FE2.36: 2 residues within 4Å: Ligands: FE2.12, FE2.24 No protein-ligand interaction detected (PLIP)

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

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