SMTL ID : 5i4j.1

Dps4 from Nostoc punctiforme in complex with Zn ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-12-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.73, E.77 Chain B: H.46, H.58 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.46, A:H.73, A:E.77 ZN.3: 4 residues within 4Å: Chain A: H.46, H.58 Chain B: H.73, E.77 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.46, B:H.73, B:E.77 ZN.4: 4 residues within 4Å: Chain C: H.73, E.77 Chain D: H.46, H.58 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:H.73, C:E.77, D:H.46, H2O.2 ZN.5: 4 residues within 4Å: Chain C: H.46, H.58 Chain D: H.73, E.77 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:H.73, C:H.46, H2O.3 ZN.6: 4 residues within 4Å: Chain E: H.73, E.77 Chain F: H.46, H.58 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Metal complexes: E:H.73, E:E.77, F:H.46 ZN.8: 4 residues within 4Å: Chain E: H.46, H.58 Chain F: H.73, E.77 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Metal complexes: E:H.46, F:H.73, F:E.77 ZN.9: 4 residues within 4Å: Chain G: H.73, E.77 Chain H: H.46, H.58 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: G:H.73, G:E.77, H:H.46, H2O.5 ZN.10: 4 residues within 4Å: Chain G: H.46, H.58 Chain H: H.73, E.77 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: H:H.73, G:H.46, H2O.6 ZN.11: 4 residues within 4Å: Chain I: H.73, E.77 Chain J: H.46, H.58 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J Metal complexes: I:H.73, I:E.77, J:H.46 ZN.13: 4 residues within 4Å: Chain I: H.46, H.58 Chain J: H.73, E.77 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I Metal complexes: J:H.73, J:E.77, I:H.46 ZN.14: 4 residues within 4Å: Chain K: H.73, E.77 Chain L: H.46, H.58 4 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: L:H.46, K:H.73, K:E.77, H2O.8 ZN.15: 4 residues within 4Å: Chain K: H.46, H.58 Chain L: H.73, E.77 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: L:H.73, K:H.46, H2O.8

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 7 residues within 4Å: Chain A: Y.10, D.11, N.12, L.15, L.16, D.17, R.18 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.11, A:N.12 Water bridges: A:L.15 Salt bridges: A:R.18 EPE.7: 7 residues within 4Å: Chain E: Y.10, D.11, N.12, L.15, L.16, D.17, R.18 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.11, E:N.12 Water bridges: E:L.15 Salt bridges: E:R.18 EPE.12: 7 residues within 4Å: Chain I: Y.10, D.11, N.12, L.15, L.16, D.17, R.18 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:D.11, I:N.12 Water bridges: I:L.15 Salt bridges: I:R.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Howe, C. et al., On the trail of iron into Dps4 from N. punctiforme. To Be Published

Release Date

2017-02-01

Peptides

Ferritin, Dps family protein: 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

Ferritin, Dps family protein