SMTL ID : 4m34.1

Crystal structure of gated-pore mutant D138H of second DNA-Binding protein under starvation from Mycobacterium smegmatis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-12-mer

Ligands

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

FE2.1: 5 residues within 4Å: Chain A: D.75, E.79 Chain B: K.45, H.48, D.64 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.75, A:E.79, B:H.48, H2O.4, H2O.7 FE2.6: 5 residues within 4Å: Chain A: K.45, H.48, D.64 Chain B: D.75, E.79 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:D.75, B:D.75, B:E.79, A:H.48, H2O.4 FE2.8: 4 residues within 4Å: Chain C: D.75, E.79 Chain D: H.48, D.64 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:D.75, C:E.79, D:H.48, H2O.9, H2O.13 FE2.9: 5 residues within 4Å: Chain C: K.45, H.48, D.64 Chain D: D.75, E.79 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:D.75, D:E.79, C:H.48, H2O.9, H2O.13 FE2.13: 5 residues within 4Å: Chain E: D.75, E.79 Chain F: K.45, H.48, D.64 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: E:D.75, E:E.79, F:H.48, H2O.16, H2O.19 FE2.18: 5 residues within 4Å: Chain E: K.45, H.48, D.64 Chain F: D.75, E.79 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:D.75, F:D.75, F:E.79, E:H.48, H2O.16 FE2.20: 4 residues within 4Å: Chain G: D.75, E.79 Chain H: H.48, D.64 5 PLIP interactions: 1 interactions with chain H, 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: H:H.48, G:D.75, G:E.79, H2O.22, H2O.25 FE2.21: 5 residues within 4Å: Chain G: K.45, H.48, D.64 Chain H: D.75, E.79 5 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: G:H.48, H:D.75, H:E.79, H2O.22, H2O.25 FE2.25: 5 residues within 4Å: Chain I: D.75, E.79 Chain J: K.45, H.48, D.64 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: I:D.75, I:E.79, J:H.48, H2O.29, H2O.32 FE2.30: 5 residues within 4Å: Chain I: K.45, H.48, D.64 Chain J: D.75, E.79 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: J:D.75, J:D.75, J:E.79, I:H.48, H2O.29 FE2.32: 4 residues within 4Å: Chain K: D.75, E.79 Chain L: H.48, D.64 5 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K, 2 Ligand-Water interactions Metal complexes: L:H.48, K:D.75, K:E.79, H2O.35, H2O.38 FE2.33: 5 residues within 4Å: Chain K: K.45, H.48, D.64 Chain L: D.75, E.79 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: L:D.75, L:E.79, K:H.48, H2O.35, H2O.38

18 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 8 residues within 4Å: Chain A: N.55, D.58 Chain E: N.55, D.58 Chain I: N.55, D.58 Ligands: MG.14, MG.26 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain I Metal complexes: E:D.58, A:D.58, I:D.58 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: H.148 Chain C: H.148 Chain F: H.148 No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain B: N.55, D.58 Chain C: N.55, D.58 Chain L: N.55, D.58 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain L Metal complexes: B:D.58, C:D.58, L:D.58 MG.10: 3 residues within 4Å: Chain D: D.137 Ligands: MG.22, MG.34 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain D: H.148 Chain H: H.148 Chain L: H.148 Ligands: MG.23, MG.35 No protein-ligand interaction detected (PLIP) MG.14: 8 residues within 4Å: Chain A: N.55, D.58 Chain E: N.55, D.58 Chain I: N.55, D.58 Ligands: MG.2, MG.26 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A, 1 interactions with chain I Metal complexes: E:D.58, A:D.58, I:D.58 MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain E: H.148 Chain G: H.148 Chain J: H.148 No protein-ligand interaction detected (PLIP) MG.19: 6 residues within 4Å: Chain D: N.55, D.58 Chain F: N.55, D.58 Chain G: N.55, D.58 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain G Metal complexes: D:D.58, F:D.58, G:D.58 MG.22: 3 residues within 4Å: Chain H: D.137 Ligands: MG.10, MG.34 No protein-ligand interaction detected (PLIP) MG.23: 5 residues within 4Å: Chain D: H.148 Chain H: H.148 Chain L: H.148 Ligands: MG.11, MG.35 No protein-ligand interaction detected (PLIP) MG.26: 8 residues within 4Å: Chain A: N.55, D.58 Chain E: N.55, D.58 Chain I: N.55, D.58 Ligands: MG.2, MG.14 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain A, 1 interactions with chain E Metal complexes: I:D.58, A:D.58, E:D.58 MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain B: H.148 Chain I: H.148 Chain K: H.148 No protein-ligand interaction detected (PLIP) MG.31: 6 residues within 4Å: Chain H: N.55, D.58 Chain J: N.55, D.58 Chain K: N.55, D.58 3 PLIP interactions: 1 interactions with chain J, 1 interactions with chain K, 1 interactions with chain H Metal complexes: J:D.58, K:D.58, H:D.58 MG.34: 3 residues within 4Å: Chain L: D.137 Ligands: MG.10, MG.22 No protein-ligand interaction detected (PLIP) MG.35: 5 residues within 4Å: Chain D: H.148 Chain H: H.148 Chain L: H.148 Ligands: MG.11, MG.23 No protein-ligand interaction detected (PLIP)

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

CL.5: 7 residues within 4Å: Chain A: R.57 Chain E: R.57, L.61 Chain I: R.57, L.61 Ligands: CL.17, CL.29 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain D: R.57, L.61 Chain F: R.57, L.61 Chain G: R.57, L.61 Ligand excluded by PLIP CL.17: 7 residues within 4Å: Chain A: R.57, L.61 Chain E: R.57 Chain I: R.57, L.61 Ligands: CL.5, CL.29 Ligand excluded by PLIP CL.24: 6 residues within 4Å: Chain H: R.57, L.61 Chain J: R.57, L.61 Chain K: R.57, L.61 Ligand excluded by PLIP CL.29: 7 residues within 4Å: Chain A: R.57, L.61 Chain E: R.57, L.61 Chain I: R.57 Ligands: CL.5, CL.17 Ligand excluded by PLIP CL.36: 6 residues within 4Å: Chain B: R.57, L.61 Chain C: R.57, L.61 Chain L: R.57, L.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, S.M. et al., A histidine aspartate ionic lock gates the iron passage in miniferritins from Mycobacterium smegmatis. J.Biol.Chem. (2014)

Release Date

2014-03-05

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