SMTL ID : 2ux1.1

Identification of two zinc-binding sites in the Streptococcus suis Dpr protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-12-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: H.33, H.37 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.33, A:H.37, H2O.5, H2O.5 ZN.2: 4 residues within 4Å: Chain A: D.67, E.71 Chain C: H.40, H.52 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.40, A:D.67, A:E.71, H2O.5, H2O.5 ZN.3: 4 residues within 4Å: Chain B: D.67, E.71 Chain D: H.40, H.52 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:H.40, B:D.67, B:E.71, H2O.8, H2O.8 ZN.4: 2 residues within 4Å: Chain B: H.33, H.37 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.33, B:H.37, H2O.8 ZN.5: 4 residues within 4Å: Chain A: H.40, H.52 Chain C: D.67, E.71 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:D.67, C:E.71, A:H.40, H2O.12, H2O.12 ZN.6: 2 residues within 4Å: Chain C: H.33, H.37 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.33, C:H.37, H2O.12 ZN.8: 2 residues within 4Å: Chain D: H.33, H.37 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.33, D:H.37, H2O.17, H2O.17 ZN.9: 4 residues within 4Å: Chain B: H.40, H.52 Chain D: D.67, E.71 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:H.40, D:D.67, D:E.71, H2O.17, H2O.17 ZN.11: 4 residues within 4Å: Chain E: D.67, E.71 Chain G: H.40, H.52 5 PLIP interactions: 1 interactions with chain G, 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: G:H.40, E:D.67, E:E.71, H2O.20, H2O.20 ZN.12: 2 residues within 4Å: Chain E: H.33, H.37 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.33, E:H.37, H2O.20 ZN.13: 2 residues within 4Å: Chain F: H.33, H.37 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.33, F:H.37, H2O.24 ZN.14: 4 residues within 4Å: Chain F: D.67, E.71 Chain H: H.40, H.52 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: F:D.67, F:E.71, H:H.40, H2O.24, H2O.24 ZN.15: 2 residues within 4Å: Chain G: H.33, H.37 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.33, G:H.37 ZN.16: 4 residues within 4Å: Chain E: H.40, H.52 Chain G: D.67, E.71 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: G:D.67, G:E.71, E:H.40, H2O.28, H2O.28 ZN.19: 2 residues within 4Å: Chain H: H.33, H.37 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:H.33, H:H.37, H2O.31, H2O.31 ZN.20: 4 residues within 4Å: Chain F: H.40, H.52 Chain H: D.67, E.71 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: H:D.67, H:E.71, F:H.40, H2O.32, H2O.32 ZN.23: 2 residues within 4Å: Chain I: H.33, H.37 4 PLIP interactions: 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:H.33, I:H.37, H2O.35, H2O.35 ZN.24: 3 residues within 4Å: Chain I: D.67, E.71 Chain K: H.40 5 PLIP interactions: 1 interactions with chain K, 2 interactions with chain I, 2 Ligand-Water interactions Metal complexes: K:H.40, I:D.67, I:E.71, H2O.35, H2O.39 ZN.26: 2 residues within 4Å: Chain J: H.33, H.37 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:H.33, J:H.37, H2O.39 ZN.27: 4 residues within 4Å: Chain J: D.67, E.71 Chain L: H.40, H.52 5 PLIP interactions: 2 interactions with chain J, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: J:D.67, J:E.71, L:H.40, H2O.39, H2O.39 ZN.30: 2 residues within 4Å: Chain K: H.33, H.37 4 PLIP interactions: 2 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:H.33, K:H.37, H2O.42, H2O.42 ZN.31: 3 residues within 4Å: Chain I: H.40 Chain K: D.67, E.71 5 PLIP interactions: 1 interactions with chain I, 2 interactions with chain K, 2 Ligand-Water interactions Metal complexes: I:H.40, K:D.67, K:E.71, H2O.43, H2O.43 ZN.33: 4 residues within 4Å: Chain J: H.40, H.52 Chain L: D.67, E.71 5 PLIP interactions: 1 interactions with chain J, 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: J:H.40, L:D.67, L:E.71, H2O.46, H2O.46 ZN.34: 2 residues within 4Å: Chain L: H.33, H.37 3 PLIP interactions: 2 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:H.33, L:H.37, H2O.46

4 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.18: 1 residues within 4Å: Chain H: N.101 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:N.101, H2O.28, H2O.42 CA.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.29: 2 residues within 4Å: Chain K: D.17, E.132 4 PLIP interactions: 2 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:D.17, K:E.132, H2O.42, H2O.42

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

EPE.10: 8 residues within 4Å: Chain C: R.46, G.47, I.50 Chain E: R.46, G.47 Chain L: R.46, G.47, I.50 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain E Water bridges: L:G.47, E:G.47 EPE.21: 7 residues within 4Å: Chain D: R.46, G.47 Chain G: G.47, I.50 Chain I: R.46, G.47, I.50 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain D Water bridges: I:R.46, I:G.47, D:R.46, D:G.47 EPE.25: 5 residues within 4Å: Chain B: R.46, G.47 Chain F: R.46, G.47 Chain J: G.47 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain J, 2 interactions with chain F Water bridges: B:R.46, B:G.47, J:R.46, F:R.46, F:G.47 Hydrogen bonds: J:G.47 EPE.28: 7 residues within 4Å: Chain A: R.46, G.47 Chain H: R.46, G.47 Chain K: R.46, G.47, I.50 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain H, 2 interactions with chain A Hydrogen bonds: K:E.105 Water bridges: H:G.47, A:R.46, A:G.47

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

CL.17: 4 residues within 4Å: Chain H: R.44, G.45, T.103, I.104 Ligand excluded by PLIP CL.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Havukainen, H. et al., Structural Basis of the Zinc- and Terbium-Mediated Inhibition of Ferroxidase Activity in Dps Ferritin- Like Proteins. Protein Sci. (2008)

Release Date

2008-05-27

Peptides

DNA PROTECTION DURING STARVATION PROTEIN: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

DNA PROTECTION DURING STARVATION PROTEIN

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