SMTL ID : 1tjo.1

Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-12-mer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 6 residues within 4Å: Chain A: H.150, R.153 Chain C: H.150, R.153 Chain H: H.150, R.153 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 2 interactions with chain H Salt bridges: A:H.150, A:R.153, C:H.150, C:R.153, H:H.150, H:R.153 SO4.5: 8 residues within 4Å: Chain B: H.150, R.153 Chain F: H.150, R.153 Chain J: H.150, R.153 Ligands: SO4.19, SO4.33 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F, 2 interactions with chain J Salt bridges: B:H.150, B:R.153, F:H.150, F:R.153, J:H.150, J:R.153 SO4.15: 6 residues within 4Å: Chain E: H.150, R.153 Chain G: H.150, R.153 Chain L: H.150, R.153 6 PLIP interactions: 2 interactions with chain G, 2 interactions with chain E, 2 interactions with chain L Salt bridges: G:H.150, G:R.153, E:H.150, E:R.153, L:H.150, L:R.153 SO4.19: 8 residues within 4Å: Chain B: H.150, R.153 Chain F: H.150, R.153 Chain J: H.150, R.153 Ligands: SO4.5, SO4.33 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain J, 2 interactions with chain B Salt bridges: F:H.150, F:R.153, J:H.150, J:R.153, B:H.150, B:R.153 SO4.29: 6 residues within 4Å: Chain D: H.150, R.153 Chain I: H.150, R.153 Chain K: H.150, R.153 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain K, 2 interactions with chain I Salt bridges: D:H.150, D:R.153, K:H.150, K:R.153, I:H.150, I:R.153 SO4.33: 8 residues within 4Å: Chain B: H.150, R.153 Chain F: H.150, R.153 Chain J: H.150, R.153 Ligands: SO4.5, SO4.19 6 PLIP interactions: 2 interactions with chain F, 2 interactions with chain J, 2 interactions with chain B Salt bridges: F:H.150, F:R.153, J:H.150, J:R.153, B:H.150, B:R.153

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

FE.2: 3 residues within 4Å: Chain A: D.79, E.83 Chain B: H.52 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.52, A:D.79, A:E.83, H2O.3, H2O.6 FE.3: 3 residues within 4Å: Chain A: E.154 Chain C: E.154 Chain H: E.154 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain H, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:E.154, H:E.154, A:E.154, H2O.6, H2O.21, H2O.22 FE.6: 3 residues within 4Å: Chain A: H.52 Chain B: D.79, E.83 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.79, B:E.83, A:H.52, H2O.8, H2O.15 FE.7: 5 residues within 4Å: Chain B: E.154 Chain F: E.154 Chain J: E.154 Ligands: FE.21, FE.35 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain J, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: B:E.154, J:E.154, F:E.154, H2O.11, H2O.41, H2O.72 FE.9: 3 residues within 4Å: Chain C: D.79, E.83 Chain D: H.52 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:H.52, C:D.79, C:E.83, H2O.17, H2O.21 FE.12: 3 residues within 4Å: Chain C: H.52 Chain D: D.79, E.83 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:H.52, D:D.79, D:E.83, H2O.20, H2O.29 FE.16: 3 residues within 4Å: Chain E: D.79, E.83 Chain F: H.52 5 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: F:H.52, E:D.79, E:E.83, H2O.34, H2O.37 FE.17: 3 residues within 4Å: Chain E: E.154 Chain G: E.154 Chain L: E.154 6 PLIP interactions: 1 interactions with chain L, 1 interactions with chain E, 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: L:E.154, E:E.154, G:E.154, H2O.37, H2O.52, H2O.53 FE.20: 3 residues within 4Å: Chain E: H.52 Chain F: D.79, E.83 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: E:H.52, F:D.79, F:E.83, H2O.39, H2O.45 FE.21: 5 residues within 4Å: Chain B: E.154 Chain F: E.154 Chain J: E.154 Ligands: FE.7, FE.35 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 1 interactions with chain J, 3 Ligand-Water interactions Metal complexes: B:E.154, F:E.154, J:E.154, H2O.11, H2O.41, H2O.72 FE.23: 3 residues within 4Å: Chain G: D.79, E.83 Chain H: H.52 5 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: G:D.79, G:E.83, H:H.52, H2O.48, H2O.52 FE.26: 3 residues within 4Å: Chain G: H.52 Chain H: D.79, E.83 5 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: G:H.52, H:D.79, H:E.83, H2O.51, H2O.60 FE.30: 3 residues within 4Å: Chain I: D.79, E.83 Chain J: H.52 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: I:D.79, I:E.83, J:H.52, H2O.65, H2O.67 FE.31: 3 residues within 4Å: Chain D: E.154 Chain I: E.154 Chain K: E.154 6 PLIP interactions: 1 interactions with chain I, 1 interactions with chain D, 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: I:E.154, D:E.154, K:E.154, H2O.67, H2O.82, H2O.84 FE.34: 3 residues within 4Å: Chain I: H.52 Chain J: D.79, E.83 5 PLIP interactions: 2 interactions with chain J, 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: J:D.79, J:E.83, I:H.52, H2O.70, H2O.76 FE.35: 5 residues within 4Å: Chain B: E.154 Chain F: E.154 Chain J: E.154 Ligands: FE.7, FE.21 6 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B, 1 interactions with chain J, 3 Ligand-Water interactions Metal complexes: F:E.154, B:E.154, J:E.154, H2O.11, H2O.41, H2O.72 FE.37: 3 residues within 4Å: Chain K: D.79, E.83 Chain L: H.52 5 PLIP interactions: 2 interactions with chain K, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: K:D.79, K:E.83, L:H.52, H2O.78, H2O.82 FE.40: 3 residues within 4Å: Chain K: H.52 Chain L: D.79, E.83 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: L:D.79, L:E.83, K:H.52, H2O.82, H2O.91

12 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: H.168 Chain C: Q.86 Chain D: E.56 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: D:E.56, A:H.168, H2O.21, H2O.28, H2O.30 MG.8: 3 residues within 4Å: Chain B: H.168 Chain E: E.56 Chain F: Q.86 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: B:H.168, E:E.56, H2O.12, H2O.14, H2O.15 MG.10: 3 residues within 4Å: Chain C: H.168 Chain G: E.56 Chain H: Q.86 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: C:H.168, G:E.56, H2O.20, H2O.21, H2O.21 MG.13: 3 residues within 4Å: Chain D: H.168 Chain I: Q.86 Chain J: E.56 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: J:E.56, D:H.168, H2O.26, H2O.29, H2O.30 MG.18: 3 residues within 4Å: Chain E: H.168 Chain G: Q.86 Chain H: E.56 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: H:E.56, E:H.168, H2O.52, H2O.59, H2O.61 MG.22: 3 residues within 4Å: Chain F: H.168 Chain I: E.56 Chain J: Q.86 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: F:H.168, I:E.56, H2O.43, H2O.45, H2O.45 MG.24: 3 residues within 4Å: Chain G: H.168 Chain K: E.56 Chain L: Q.86 5 PLIP interactions: 1 interactions with chain G, 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: G:H.168, K:E.56, H2O.50, H2O.52, H2O.52 MG.27: 3 residues within 4Å: Chain A: Q.86 Chain B: E.56 Chain H: H.168 5 PLIP interactions: 1 interactions with chain H, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: H:H.168, B:E.56, H2O.57, H2O.60, H2O.61 MG.32: 3 residues within 4Å: Chain I: H.168 Chain K: Q.86 Chain L: E.56 5 PLIP interactions: 1 interactions with chain L, 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: L:E.56, I:H.168, H2O.82, H2O.90, H2O.91 MG.36: 3 residues within 4Å: Chain A: E.56 Chain B: Q.86 Chain J: H.168 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: J:H.168, A:E.56, H2O.73, H2O.75, H2O.76 MG.38: 3 residues within 4Å: Chain C: E.56 Chain D: Q.86 Chain K: H.168 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: C:E.56, K:H.168, H2O.81, H2O.82, H2O.83 MG.41: 3 residues within 4Å: Chain E: Q.86 Chain F: E.56 Chain L: H.168 5 PLIP interactions: 1 interactions with chain L, 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: L:H.168, F:E.56, H2O.87, H2O.91, H2O.91

6 x NA: SODIUM ION(Non-functional Binders)

NA.11: 8 residues within 4Å: Chain C: E.59, V.176 Chain G: E.59, V.176 Chain K: E.59, V.176 Ligands: NA.25, NA.39 4 PLIP interactions: 1 interactions with chain K, 2 interactions with chain G, 1 interactions with chain C Hydrogen bonds: K:E.59, G:E.59, G:E.59, C:E.59 NA.14: 4 residues within 4Å: Chain A: E.59 Chain D: E.59 Chain J: E.59, V.176 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain J, 1 interactions with chain A Hydrogen bonds: D:E.59, J:E.59, A:E.59 NA.25: 8 residues within 4Å: Chain C: E.59, V.176 Chain G: E.59, V.176 Chain K: E.59, V.176 Ligands: NA.11, NA.39 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain K, 2 interactions with chain G Hydrogen bonds: C:E.59, K:E.59, G:E.59, G:E.59 NA.28: 4 residues within 4Å: Chain B: E.59, V.176 Chain E: E.59 Chain H: E.59 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:E.59, B:E.59, B:E.59 NA.39: 8 residues within 4Å: Chain C: E.59, V.176 Chain G: E.59, V.176 Chain K: E.59, V.176 Ligands: NA.11, NA.25 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain K, 2 interactions with chain G Hydrogen bonds: C:E.59, K:E.59, G:E.59, G:E.59 NA.42: 4 residues within 4Å: Chain F: E.59, V.176 Chain I: E.59 Chain L: E.59 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain I Hydrogen bonds: F:E.59, F:E.59, I:E.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeth, K. et al., Iron-oxo clusters biomineralizing on protein surfaces: structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states. Proc.Natl.Acad.Sci.USA (2004)

Release Date

2004-10-19

Peptides

Iron-rich dpsA-homolog 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

Iron-rich dpsA-homolog protein

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