SMTL ID : 2vxx.1

X-ray structure of DpsA from Thermosynechococcus elongatus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-12-mer

Ligands

24 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.51, H.63, Q.67 Chain B: H.78, E.82 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.78, B:E.82, A:H.51, H2O.7, H2O.7 ZN.2: 3 residues within 4Å: Chain A: H.63 Chain B: E.82 Chain K: H.164 4 PLIP interactions: 1 interactions with chain K, 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: K:H.164, A:H.63, B:E.82, H2O.7 ZN.3: 4 residues within 4Å: Chain A: E.82 Chain B: H.63 Chain F: H.164 Ligands: ZN.4 4 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: F:H.164, B:H.63, A:E.82, H2O.6 ZN.4: 5 residues within 4Å: Chain A: H.78, E.82 Chain B: H.51, H.63 Ligands: ZN.3 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.51, A:H.78, A:E.82, H2O.6 ZN.8: 5 residues within 4Å: Chain C: H.63 Chain D: E.82 Chain H: H.164 Ligands: ZN.9, PEG.11 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: H:H.164, C:H.63, D:E.82, H2O.13, H2O.15 ZN.9: 6 residues within 4Å: Chain C: H.51, H.63, Q.67 Chain D: H.78, E.82 Ligands: ZN.8 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:H.51, D:H.78, D:E.82, H2O.11, H2O.15 ZN.12: 4 residues within 4Å: Chain A: H.164 Chain C: E.82 Chain D: H.63 Ligands: ZN.13 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: A:H.164, C:E.82, D:H.63, H2O.4, H2O.15 ZN.13: 4 residues within 4Å: Chain C: H.78, E.82 Chain D: H.51 Ligands: ZN.12 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:H.51, C:H.78, C:E.82, H2O.15 ZN.15: 5 residues within 4Å: Chain E: H.51, H.63, Q.67 Chain F: H.78, E.82 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: E:H.51, F:H.78, F:E.82, H2O.24, H2O.24 ZN.16: 3 residues within 4Å: Chain C: H.164 Chain E: H.63 Chain F: E.82 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: E:H.63, F:E.82, C:H.164, H2O.24 ZN.17: 4 residues within 4Å: Chain E: E.82 Chain F: H.63 Chain J: H.164 Ligands: ZN.18 4 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: E:E.82, F:H.63, J:H.164, H2O.23 ZN.18: 5 residues within 4Å: Chain E: H.78, E.82 Chain F: H.51, H.63 Ligands: ZN.17 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:H.78, E:E.82, F:H.51, H2O.23 ZN.22: 5 residues within 4Å: Chain G: H.63 Chain H: E.82 Chain L: H.164 Ligands: ZN.23, PEG.25 5 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: G:H.63, H:E.82, L:H.164, H2O.30, H2O.32 ZN.23: 6 residues within 4Å: Chain G: H.51, H.63, Q.67 Chain H: H.78, E.82 Ligands: ZN.22 5 PLIP interactions: 2 interactions with chain H, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: H:H.78, H:E.82, G:H.51, H2O.28, H2O.32 ZN.26: 4 residues within 4Å: Chain E: H.164 Chain G: E.82 Chain H: H.63 Ligands: ZN.27 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: H:H.63, G:E.82, E:H.164, H2O.21, H2O.32 ZN.27: 4 residues within 4Å: Chain G: H.78, E.82 Chain H: H.51 Ligands: ZN.26 4 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: G:H.78, G:E.82, H:H.51, H2O.32 ZN.29: 5 residues within 4Å: Chain I: H.51, H.63, Q.67 Chain J: H.78, E.82 5 PLIP interactions: 1 interactions with chain I, 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: I:H.51, J:H.78, J:E.82, H2O.41, H2O.41 ZN.30: 3 residues within 4Å: Chain G: H.164 Chain I: H.63 Chain J: E.82 4 PLIP interactions: 1 interactions with chain G, 1 interactions with chain I, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: G:H.164, I:H.63, J:E.82, H2O.41 ZN.31: 4 residues within 4Å: Chain B: H.164 Chain I: E.82 Chain J: H.63 Ligands: ZN.32 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain I, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: B:H.164, I:E.82, J:H.63, H2O.41 ZN.32: 5 residues within 4Å: Chain I: H.78, E.82 Chain J: H.51, H.63 Ligands: ZN.31 4 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: I:H.78, I:E.82, J:H.51, H2O.40 ZN.36: 5 residues within 4Å: Chain D: H.164 Chain K: H.63 Chain L: E.82 Ligands: ZN.37, PEG.39 5 PLIP interactions: 1 interactions with chain K, 1 interactions with chain D, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: K:H.63, D:H.164, L:E.82, H2O.47, H2O.49 ZN.37: 6 residues within 4Å: Chain K: H.51, H.63, Q.67 Chain L: H.78, E.82 Ligands: ZN.36 5 PLIP interactions: 1 interactions with chain K, 2 interactions with chain L, 2 Ligand-Water interactions Metal complexes: K:H.51, L:H.78, L:E.82, H2O.45, H2O.49 ZN.40: 4 residues within 4Å: Chain I: H.164 Chain K: E.82 Chain L: H.63 Ligands: ZN.41 5 PLIP interactions: 1 interactions with chain I, 1 interactions with chain L, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: I:H.164, L:H.63, K:E.82, H2O.38, H2O.49 ZN.41: 4 residues within 4Å: Chain K: H.78, E.82 Chain L: H.51 Ligands: ZN.40 4 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: L:H.51, K:H.78, K:E.82, H2O.49

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

FE.5: 5 residues within 4Å: Chain D: E.140 Chain H: E.140 Chain L: E.140 Ligands: FE.19, FE.33 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain L, 1 interactions with chain D Metal complexes: H:E.140, L:E.140, D:E.140 FE.10: 3 residues within 4Å: Chain A: E.140 Chain C: E.140 Chain F: E.140 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C, 1 interactions with chain A Metal complexes: F:E.140, C:E.140, A:E.140 FE.19: 5 residues within 4Å: Chain D: E.140 Chain H: E.140 Chain L: E.140 Ligands: FE.5, FE.33 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain D, 1 interactions with chain H Metal complexes: L:E.140, D:E.140, H:E.140 FE.24: 3 residues within 4Å: Chain E: E.140 Chain G: E.140 Chain J: E.140 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G, 1 interactions with chain J Metal complexes: E:E.140, G:E.140, J:E.140 FE.33: 5 residues within 4Å: Chain D: E.140 Chain H: E.140 Chain L: E.140 Ligands: FE.5, FE.19 3 PLIP interactions: 1 interactions with chain L, 1 interactions with chain D, 1 interactions with chain H Metal complexes: L:E.140, D:E.140, H:E.140 FE.38: 3 residues within 4Å: Chain B: E.140 Chain I: E.140 Chain K: E.140 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain K, 1 interactions with chain I Metal complexes: B:E.140, K:E.140, I:E.140

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 9 residues within 4Å: Chain B: F.65, D.68, C.69, Q.72, K.157, E.160, R.161, H.164 Chain J: Y.60 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.72, B:K.157 PG4.20: 9 residues within 4Å: Chain B: Y.60 Chain F: F.65, D.68, C.69, Q.72, K.157, E.160, R.161, H.164 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:Q.72, F:K.157, B:Y.60 PG4.34: 9 residues within 4Å: Chain F: Y.60 Chain J: F.65, D.68, C.69, Q.72, K.157, E.160, R.161, H.164 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain J Hydrogen bonds: F:Y.60, J:Q.72, J:K.157

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 4 residues within 4Å: Chain B: C.102, C.103, F.104, T.105 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.105 PEG.11: 5 residues within 4Å: Chain C: H.63, Q.64, Q.67, D.68 Ligands: ZN.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.68 PEG.14: 2 residues within 4Å: Chain D: R.35, A.100 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.35, D:L.101 PEG.21: 4 residues within 4Å: Chain F: C.102, C.103, F.104, T.105 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.105 PEG.25: 5 residues within 4Å: Chain G: H.63, Q.64, Q.67, D.68 Ligands: ZN.22 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.68 PEG.28: 2 residues within 4Å: Chain H: R.35, A.100 2 PLIP interactions: 2 interactions with chain H Water bridges: H:R.35, H:L.101 PEG.35: 4 residues within 4Å: Chain J: C.102, C.103, F.104, T.105 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:T.105 PEG.39: 5 residues within 4Å: Chain K: H.63, Q.64, Q.67, D.68 Ligands: ZN.36 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:D.68 PEG.42: 2 residues within 4Å: Chain L: R.35, A.100 2 PLIP interactions: 2 interactions with chain L Water bridges: L:R.35, L:L.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alaleona, F. et al., Thermosynechococcus Elongatus Dpsa Binds Zn(II) at a Unique Three Histidine-Containing Ferroxidase Center and Utilizes O2 as Iron Oxidant with Very High Efficiency, Unlike the Typical Dps Proteins. FEBS J. (2010)

Release Date

2009-11-17

Peptides

STARVATION INDUCED DNA BINDING 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

STARVATION INDUCED DNA BINDING PROTEIN