SMTL ID : 2ogx.1

The crystal structure of the molybdenum storage protein from Azotobacter vinelandii loaded with polyoxotungstates (WSto)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-3-3-mer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.45, D.171, E.190, P.227 Ligands: ATP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.190, A:P.227, H2O.8 MG.29: 5 residues within 4Å: Chain C: K.45, D.171, E.190, P.227 Ligands: ATP.31 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.190, C:P.227, H2O.23 MG.57: 5 residues within 4Å: Chain E: K.45, D.171, E.190, P.227 Ligands: ATP.59 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.190, E:P.227, H2O.38

3 x WO3: TRI-TUNGSTEN(VI) OXIDE COMPLEX(Non-covalent)

WO3.2: 8 residues within 4Å: Chain A: T.132, H.140 Chain C: H.140 Chain E: Q.136, I.139, H.140 Ligands: WO3.30, WO3.58 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Metal complexes: A:H.140 Hydrogen bonds: E:Q.136 WO3.30: 8 residues within 4Å: Chain A: Q.136, I.139, H.140 Chain C: T.132, H.140 Chain E: H.140 Ligands: WO3.2, WO3.58 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.140 Hydrogen bonds: A:Q.136 WO3.58: 8 residues within 4Å: Chain A: H.140 Chain C: Q.136, I.139, H.140 Chain E: T.132, H.140 Ligands: WO3.2, WO3.30 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Metal complexes: E:H.140 Hydrogen bonds: C:Q.136

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 23 residues within 4Å: Chain A: K.45, G.47, G.48, R.49, G.79, A.80, G.81, R.85, E.190, N.191, V.192, G.194, I.195, Y.196, A.198, D.199, P.200, N.201, P.225, L.226, P.227 Chain B: S.16 Ligands: MG.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.48, A:R.49, A:A.80, A:G.81, A:R.85, A:N.191, A:N.191, A:Y.196, A:Y.196, A:N.201, A:N.201 Water bridges: A:K.45, A:K.45, A:R.49, A:D.171 Salt bridges: A:K.45, A:K.45 ATP.31: 23 residues within 4Å: Chain C: K.45, G.47, G.48, R.49, G.79, A.80, G.81, R.85, E.190, N.191, V.192, G.194, I.195, Y.196, A.198, D.199, P.200, N.201, P.225, L.226, P.227 Chain D: S.16 Ligands: MG.29 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:G.48, C:R.49, C:A.80, C:G.81, C:R.85, C:N.191, C:N.191, C:Y.196, C:Y.196, C:N.201, C:N.201 Water bridges: C:K.45, C:K.45, C:R.49, C:D.171 Salt bridges: C:K.45, C:K.45 ATP.59: 23 residues within 4Å: Chain E: K.45, G.47, G.48, R.49, G.79, A.80, G.81, R.85, E.190, N.191, V.192, G.194, I.195, Y.196, A.198, D.199, P.200, N.201, P.225, L.226, P.227 Chain F: S.16 Ligands: MG.57 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:G.48, E:R.49, E:A.80, E:G.81, E:R.85, E:N.191, E:N.191, E:Y.196, E:Y.196, E:N.201, E:N.201 Water bridges: E:K.45, E:K.45, E:R.49, E:D.171 Salt bridges: E:K.45, E:K.45

69 x W: TUNGSTEN ION(Non-covalent)(Non-functional Binders)(Covalent)

W.4: 6 residues within 4Å: Chain A: H.156, H.157, H.158 Ligands: W.5, W.16, W.17 Ligand excluded by PLIP W.5: 4 residues within 4Å: Chain A: H.157 Ligands: W.4, W.17, W.18 Ligand excluded by PLIP W.6: 4 residues within 4Å: Chain A: E.129 Ligands: W.7, W.9, W.11 Ligand excluded by PLIP W.7: 8 residues within 4Å: Chain A: Y.127, E.129, H.130 Ligands: W.6, W.8, W.9, W.10, W.11 Ligand excluded by PLIP W.8: 3 residues within 4Å: Chain A: E.129 Ligands: W.7, W.10 Ligand excluded by PLIP W.9: 5 residues within 4Å: Chain A: A.106, H.130 Ligands: W.6, W.7, W.10 Ligand excluded by PLIP W.10: 3 residues within 4Å: Ligands: W.7, W.8, W.9 Ligand excluded by PLIP W.11: 3 residues within 4Å: Chain A: E.129 Ligands: W.6, W.7 Ligand excluded by PLIP W.12: 1 residues within 4Å: Ligands: W.13 Ligand excluded by PLIP W.13: 3 residues within 4Å: Chain A: H.157 Chain F: A.112 Ligands: W.12 Ligand excluded by PLIP W.16: 4 residues within 4Å: Chain A: H.158 Ligands: W.4, W.17, W.19 Ligand excluded by PLIP W.17: 8 residues within 4Å: Chain B: G.128, A.129 Ligands: W.4, W.5, W.16, W.18, W.19, W.20 Ligand excluded by PLIP W.18: 5 residues within 4Å: Chain B: G.128, A.129 Ligands: W.5, W.17, W.20 Ligand excluded by PLIP W.19: 6 residues within 4Å: Chain B: G.128, G.130, L.176 Ligands: W.16, W.17, W.20 Ligand excluded by PLIP W.20: 7 residues within 4Å: Chain A: H.157 Chain B: G.128, A.129, G.130 Ligands: W.17, W.18, W.19 Ligand excluded by PLIP W.21: 7 residues within 4Å: Chain B: S.132 Ligands: W.22, W.23, W.26, W.50, W.51, W.79 Ligand excluded by PLIP W.22: 8 residues within 4Å: Chain B: S.132, V.134 Ligands: W.21, W.23, W.28, W.51, W.77, W.79 Ligand excluded by PLIP W.23: 8 residues within 4Å: Ligands: W.21, W.22, W.49, W.50, W.51, W.77, W.78, W.79 Ligand excluded by PLIP W.24: 3 residues within 4Å: Chain B: D.108, S.147 Ligands: W.25 Ligand excluded by PLIP W.25: 2 residues within 4Å: Chain B: D.108 Ligands: W.24 Ligand excluded by PLIP W.26: 5 residues within 4Å: Ligands: W.21, W.27, W.28, W.56, W.83 Ligand excluded by PLIP W.27: 5 residues within 4Å: Ligands: W.26, W.54, W.55, W.56, W.83 Ligand excluded by PLIP W.28: 4 residues within 4Å: Ligands: W.22, W.26, W.82, W.83 Ligand excluded by PLIP W.32: 6 residues within 4Å: Chain C: H.156, H.157, H.158 Ligands: W.33, W.44, W.45 Ligand excluded by PLIP W.33: 4 residues within 4Å: Chain C: H.157 Ligands: W.32, W.45, W.46 Ligand excluded by PLIP W.34: 4 residues within 4Å: Chain C: E.129 Ligands: W.35, W.37, W.39 Ligand excluded by PLIP W.35: 8 residues within 4Å: Chain C: Y.127, E.129, H.130 Ligands: W.34, W.36, W.37, W.38, W.39 Ligand excluded by PLIP W.36: 3 residues within 4Å: Chain C: E.129 Ligands: W.35, W.38 Ligand excluded by PLIP W.37: 5 residues within 4Å: Chain C: A.106, H.130 Ligands: W.34, W.35, W.38 Ligand excluded by PLIP W.38: 3 residues within 4Å: Ligands: W.35, W.36, W.37 Ligand excluded by PLIP W.39: 3 residues within 4Å: Chain C: E.129 Ligands: W.34, W.35 Ligand excluded by PLIP W.40: 1 residues within 4Å: Ligands: W.41 Ligand excluded by PLIP W.41: 3 residues within 4Å: Chain B: A.112 Chain C: H.157 Ligands: W.40 Ligand excluded by PLIP W.44: 4 residues within 4Å: Chain C: H.158 Ligands: W.32, W.45, W.47 Ligand excluded by PLIP W.45: 8 residues within 4Å: Chain D: G.128, A.129 Ligands: W.32, W.33, W.44, W.46, W.47, W.48 Ligand excluded by PLIP W.46: 5 residues within 4Å: Chain D: G.128, A.129 Ligands: W.33, W.45, W.48 Ligand excluded by PLIP W.47: 6 residues within 4Å: Chain D: G.128, G.130, L.176 Ligands: W.44, W.45, W.48 Ligand excluded by PLIP W.48: 7 residues within 4Å: Chain C: H.157 Chain D: G.128, A.129, G.130 Ligands: W.45, W.46, W.47 Ligand excluded by PLIP W.49: 7 residues within 4Å: Chain D: S.132 Ligands: W.23, W.50, W.51, W.54, W.78, W.79 Ligand excluded by PLIP W.50: 8 residues within 4Å: Chain D: S.132, V.134 Ligands: W.21, W.23, W.49, W.51, W.56, W.79 Ligand excluded by PLIP W.51: 8 residues within 4Å: Ligands: W.21, W.22, W.23, W.49, W.50, W.77, W.78, W.79 Ligand excluded by PLIP W.52: 3 residues within 4Å: Chain D: D.108, S.147 Ligands: W.53 Ligand excluded by PLIP W.53: 2 residues within 4Å: Chain D: D.108 Ligands: W.52 Ligand excluded by PLIP W.54: 5 residues within 4Å: Ligands: W.27, W.49, W.55, W.56, W.84 Ligand excluded by PLIP W.55: 5 residues within 4Å: Ligands: W.27, W.54, W.82, W.83, W.84 Ligand excluded by PLIP W.56: 4 residues within 4Å: Ligands: W.26, W.27, W.50, W.54 Ligand excluded by PLIP W.60: 6 residues within 4Å: Chain E: H.156, H.157, H.158 Ligands: W.61, W.72, W.73 Ligand excluded by PLIP W.61: 4 residues within 4Å: Chain E: H.157 Ligands: W.60, W.73, W.74 Ligand excluded by PLIP W.62: 4 residues within 4Å: Chain E: E.129 Ligands: W.63, W.65, W.67 Ligand excluded by PLIP W.63: 8 residues within 4Å: Chain E: Y.127, E.129, H.130 Ligands: W.62, W.64, W.65, W.66, W.67 Ligand excluded by PLIP W.64: 3 residues within 4Å: Chain E: E.129 Ligands: W.63, W.66 Ligand excluded by PLIP W.65: 5 residues within 4Å: Chain E: A.106, H.130 Ligands: W.62, W.63, W.66 Ligand excluded by PLIP W.66: 3 residues within 4Å: Ligands: W.63, W.64, W.65 Ligand excluded by PLIP W.67: 3 residues within 4Å: Chain E: E.129 Ligands: W.62, W.63 Ligand excluded by PLIP W.68: 1 residues within 4Å: Ligands: W.69 Ligand excluded by PLIP W.69: 3 residues within 4Å: Chain D: A.112 Chain E: H.157 Ligands: W.68 Ligand excluded by PLIP W.72: 4 residues within 4Å: Chain E: H.158 Ligands: W.60, W.73, W.75 Ligand excluded by PLIP W.73: 8 residues within 4Å: Chain F: G.128, A.129 Ligands: W.60, W.61, W.72, W.74, W.75, W.76 Ligand excluded by PLIP W.74: 5 residues within 4Å: Chain F: G.128, A.129 Ligands: W.61, W.73, W.76 Ligand excluded by PLIP W.75: 6 residues within 4Å: Chain F: G.128, G.130, L.176 Ligands: W.72, W.73, W.76 Ligand excluded by PLIP W.76: 7 residues within 4Å: Chain E: H.157 Chain F: G.128, A.129, G.130 Ligands: W.73, W.74, W.75 Ligand excluded by PLIP W.77: 7 residues within 4Å: Chain F: S.132 Ligands: W.22, W.23, W.51, W.78, W.79, W.82 Ligand excluded by PLIP W.78: 8 residues within 4Å: Chain F: S.132, V.134 Ligands: W.23, W.49, W.51, W.77, W.79, W.84 Ligand excluded by PLIP W.79: 8 residues within 4Å: Ligands: W.21, W.22, W.23, W.49, W.50, W.51, W.77, W.78 Ligand excluded by PLIP W.80: 3 residues within 4Å: Chain F: D.108, S.147 Ligands: W.81 Ligand excluded by PLIP W.81: 2 residues within 4Å: Chain F: D.108 Ligands: W.80 Ligand excluded by PLIP W.82: 5 residues within 4Å: Ligands: W.28, W.55, W.77, W.83, W.84 Ligand excluded by PLIP W.83: 5 residues within 4Å: Ligands: W.26, W.27, W.28, W.55, W.82 Ligand excluded by PLIP W.84: 4 residues within 4Å: Ligands: W.54, W.55, W.78, W.82 Ligand excluded by PLIP

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.14: 9 residues within 4Å: Chain B: K.42, G.44, G.45, Q.46, S.47, G.77, G.79, K.189 Ligands: PO4.15 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.45, B:Q.46, B:S.47, B:A.78 Water bridges: B:G.79 Salt bridges: B:K.42, B:K.189 PO4.15: 6 residues within 4Å: Chain B: G.77, A.78, G.79, R.168, T.169 Ligands: PO4.14 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:A.78, B:G.79, B:T.169, B:T.169, B:T.169 Water bridges: B:D.170 Salt bridges: B:K.42, B:R.168 PO4.42: 9 residues within 4Å: Chain D: K.42, G.44, G.45, Q.46, S.47, G.77, G.79, K.189 Ligands: PO4.43 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.45, D:Q.46, D:S.47, D:A.78 Water bridges: D:G.79 Salt bridges: D:K.42, D:K.189 PO4.43: 6 residues within 4Å: Chain D: G.77, A.78, G.79, R.168, T.169 Ligands: PO4.42 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:A.78, D:G.79, D:T.169, D:T.169, D:T.169 Water bridges: D:D.170 Salt bridges: D:K.42, D:R.168 PO4.70: 9 residues within 4Å: Chain F: K.42, G.44, G.45, Q.46, S.47, G.77, G.79, K.189 Ligands: PO4.71 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.45, F:Q.46, F:S.47, F:A.78 Water bridges: F:G.79 Salt bridges: F:K.42, F:K.189 PO4.71: 6 residues within 4Å: Chain F: G.77, A.78, G.79, R.168, T.169 Ligands: PO4.70 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:A.78, F:G.79, F:T.169, F:T.169, F:T.169 Water bridges: F:D.170 Salt bridges: F:K.42, F:R.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schemberg, J. et al., Towards Biological Supramolecular Chemistry: A Variety of Pocket-Templated, Individual Metal Oxide Cluster Nucleations in the Cavity of a Mo/W-Storage Protein. Angew.Chem.Int.Ed.Engl. (2007)

Release Date

2007-04-24

Peptides

Molybdenum storage protein subunit alpha: ACE
Molybdenum storage protein subunit beta: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

Molybdenum storage protein subunit alpha

Molybdenum storage protein subunit beta

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