SMTL ID : 6sev.1

Structure of Dps from Listeria innocua soaked with 10 mM zinc for 120 minutes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-12-mer

Ligands

42 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: D.52, E.56 Chain D: H.25, H.37, D.41 Ligands: ZN.2, ZN.3 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Metal complexes: D:H.25, A:D.52, A:D.52, A:E.56 ZN.2: 5 residues within 4Å: Chain A: E.56 Chain B: K.135 Chain D: H.25, H.37 Ligands: ZN.1 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Metal complexes: D:H.37, A:E.56 ZN.3: 4 residues within 4Å: Chain A: D.52 Chain D: H.22, D.41 Ligands: ZN.1 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.41 ZN.4: 4 residues within 4Å: Chain A: D.115, N.123 Chain F: D.115, D.120 No protein-ligand interaction detected (PLIP) ZN.5: 4 residues within 4Å: Chain A: D.124 Chain B: D.124 Chain F: D.124 Ligands: ZN.6 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F, 2 interactions with chain B Metal complexes: A:D.124, F:D.124, F:D.124, B:D.124, B:D.124 ZN.6: 4 residues within 4Å: Chain A: D.124 Chain B: D.124 Chain F: D.124 Ligands: ZN.5 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F, 1 interactions with chain B Metal complexes: A:D.124, F:D.124, B:D.124 ZN.7: 4 residues within 4Å: Chain B: E.56 Chain E: H.37 Chain F: K.135 Ligands: ZN.8 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.37, H2O.4 ZN.8: 6 residues within 4Å: Chain B: D.52, E.56 Chain E: H.25, H.37, D.41 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: B:D.52, B:D.52, B:E.56, E:H.25, H2O.4 ZN.9: 3 residues within 4Å: Chain B: H.31 Chain C: N.32 Ligands: ZN.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.31 ZN.10: 4 residues within 4Å: Chain B: H.25, H.37 Chain E: E.56 Ligands: ZN.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.56 ZN.11: 6 residues within 4Å: Chain C: H.25, H.37, D.41 Chain I: D.52, E.56 Ligands: ZN.14 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain C Metal complexes: I:D.52, I:D.52, I:E.56, C:H.25 ZN.12: 3 residues within 4Å: Chain C: H.31 Ligands: ZN.9, ZN.17 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.31 ZN.13: 3 residues within 4Å: Chain C: D.124 Chain E: D.124 Chain J: D.124 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain J, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: E:D.124, J:D.124, C:D.124, H2O.4 ZN.14: 5 residues within 4Å: Chain C: H.25, H.37 Chain D: K.135 Chain I: E.56 Ligands: ZN.11 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain I Metal complexes: C:H.37, I:E.56, I:E.56 ZN.15: 5 residues within 4Å: Chain A: H.25, D.41 Chain D: D.52, E.56 Ligands: ZN.16 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:D.52, D:D.52, D:E.56, A:H.25 ZN.16: 4 residues within 4Å: Chain A: H.25, H.37 Chain D: E.56 Ligands: ZN.15 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Metal complexes: D:E.56, A:H.37 ZN.17: 2 residues within 4Å: Chain D: H.31 Ligands: ZN.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.31 ZN.18: 4 residues within 4Å: Chain B: H.25 Chain E: D.52, E.56 Ligands: ZN.10 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain B Metal complexes: E:D.52, E:D.52, E:E.56, B:H.25 ZN.19: 3 residues within 4Å: Chain C: D.124 Chain E: D.124 Chain J: D.124 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain J, 1 interactions with chain C Metal complexes: E:D.124, J:D.124, C:D.124 ZN.20: 5 residues within 4Å: Chain F: H.25, D.41 Chain L: D.52, E.56 Ligands: ZN.21 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain F Metal complexes: L:D.52, L:D.52, L:E.56, F:H.25 ZN.21: 4 residues within 4Å: Chain F: H.25, H.37 Chain L: E.56 Ligands: ZN.20 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.56 ZN.22: 7 residues within 4Å: Chain G: D.52, E.56 Chain J: H.25, H.37, D.41 Ligands: ZN.23, ZN.24 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain G Metal complexes: J:H.25, G:D.52, G:D.52, G:E.56 ZN.23: 5 residues within 4Å: Chain G: E.56 Chain H: K.135 Chain J: H.25, H.37 Ligands: ZN.22 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain G Metal complexes: J:H.37, G:E.56 ZN.24: 4 residues within 4Å: Chain G: D.52 Chain J: H.22, D.41 Ligands: ZN.22 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.41 ZN.25: 4 residues within 4Å: Chain G: D.115, N.123 Chain L: D.115, D.120 No protein-ligand interaction detected (PLIP) ZN.26: 4 residues within 4Å: Chain G: D.124 Chain H: D.124 Chain L: D.124 Ligands: ZN.27 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain G, 2 interactions with chain H Metal complexes: L:D.124, L:D.124, G:D.124, H:D.124, H:D.124 ZN.27: 4 residues within 4Å: Chain G: D.124 Chain H: D.124 Chain L: D.124 Ligands: ZN.26 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain G, 1 interactions with chain H Metal complexes: L:D.124, G:D.124, H:D.124 ZN.28: 4 residues within 4Å: Chain H: E.56 Chain K: H.37 Chain L: K.135 Ligands: ZN.29 2 PLIP interactions: 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:H.37, H2O.8 ZN.29: 6 residues within 4Å: Chain H: D.52, E.56 Chain K: H.25, H.37, D.41 Ligands: ZN.28 5 PLIP interactions: 1 interactions with chain K, 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: K:H.25, H:D.52, H:D.52, H:E.56, H2O.8 ZN.30: 3 residues within 4Å: Chain H: H.31 Chain I: N.32 Ligands: ZN.33 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:H.31 ZN.31: 4 residues within 4Å: Chain H: H.25, H.37 Chain K: E.56 Ligands: ZN.39 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.56 ZN.32: 6 residues within 4Å: Chain C: D.52, E.56 Chain I: H.25, H.37, D.41 Ligands: ZN.35 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain C Metal complexes: I:H.25, C:D.52, C:D.52, C:E.56 ZN.33: 3 residues within 4Å: Chain I: H.31 Ligands: ZN.30, ZN.38 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:H.31 ZN.34: 3 residues within 4Å: Chain D: D.124 Chain I: D.124 Chain K: D.124 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain D, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: K:D.124, D:D.124, I:D.124, H2O.8 ZN.35: 5 residues within 4Å: Chain C: E.56 Chain I: H.25, H.37 Chain J: K.135 Ligands: ZN.32 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain C Metal complexes: I:H.37, C:E.56, C:E.56 ZN.36: 5 residues within 4Å: Chain G: H.25, D.41 Chain J: D.52, E.56 Ligands: ZN.37 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain G Metal complexes: J:D.52, J:D.52, J:E.56, G:H.25 ZN.37: 4 residues within 4Å: Chain G: H.25, H.37 Chain J: E.56 Ligands: ZN.36 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain J Metal complexes: G:H.37, J:E.56 ZN.38: 2 residues within 4Å: Chain J: H.31 Ligands: ZN.33 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:H.31 ZN.39: 4 residues within 4Å: Chain H: H.25 Chain K: D.52, E.56 Ligands: ZN.31 4 PLIP interactions: 1 interactions with chain H, 3 interactions with chain K Metal complexes: H:H.25, K:D.52, K:D.52, K:E.56 ZN.40: 3 residues within 4Å: Chain D: D.124 Chain I: D.124 Chain K: D.124 3 PLIP interactions: 1 interactions with chain K, 1 interactions with chain D, 1 interactions with chain I Metal complexes: K:D.124, D:D.124, I:D.124 ZN.41: 5 residues within 4Å: Chain F: D.52, E.56 Chain L: H.25, D.41 Ligands: ZN.42 4 PLIP interactions: 1 interactions with chain L, 3 interactions with chain F Metal complexes: L:H.25, F:D.52, F:D.52, F:E.56 ZN.42: 4 residues within 4Å: Chain F: E.56 Chain L: H.25, H.37 Ligands: ZN.41 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeth, K. et al., Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps. Inorg.Chem. (2019)

Release Date

2019-09-25

Peptides

DNA starvation/stationary phase protection protein: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

DNA starvation/stationary phase protection protein