SMTL ID : 4f6t.1

The crystal structure of the molybdenum storage protein (MoSto) from Azotobacter vinelandii loaded with various polyoxometalates

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-3-3-mer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: K.40, G.42, G.43, Q.44, S.45, G.75, A.76, G.77, T.167, D.168, K.187, D.188, E.189, G.191, L.192, Y.193, A.195, N.196, P.197, K.198, S.222, I.223 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.43, A:Q.44, A:S.45, A:A.76, A:T.167, A:D.188, A:Y.193, A:Y.193, A:N.196, A:K.198 Water bridges: A:K.40, A:G.77, A:G.77, A:R.166, A:R.166, A:T.167, A:D.168, A:K.198 Salt bridges: A:K.40, A:K.40, A:K.187, A:K.187 ATP.6: 23 residues within 4Å: Chain A: S.14 Chain B: K.13, G.15, G.16, R.17, G.47, A.48, G.49, R.53, E.158, N.159, V.160, G.162, I.163, Y.164, A.166, D.167, P.168, N.169, P.193, L.194, P.195 Ligands: MG.7 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:G.16, B:R.17, B:V.18, B:A.48, B:G.49, B:R.53, B:N.159, B:N.159, B:Y.164, B:Y.164, B:N.169 Water bridges: B:K.13, B:K.13, B:K.13, B:K.13, B:R.17, B:D.139 Salt bridges: B:K.13, B:K.13 ATP.11: 22 residues within 4Å: Chain C: K.40, G.42, G.43, Q.44, S.45, G.75, A.76, G.77, T.167, D.168, K.187, D.188, E.189, G.191, L.192, Y.193, A.195, N.196, P.197, K.198, S.222, I.223 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:G.43, C:Q.44, C:S.45, C:A.76, C:T.167, C:D.188, C:Y.193, C:Y.193, C:N.196, C:K.198 Water bridges: C:K.40, C:G.77, C:G.77, C:R.166, C:R.166, C:T.167, C:D.168, C:K.198 Salt bridges: C:K.40, C:K.40, C:K.187, C:K.187 ATP.16: 23 residues within 4Å: Chain C: S.14 Chain D: K.13, G.15, G.16, R.17, G.47, A.48, G.49, R.53, E.158, N.159, V.160, G.162, I.163, Y.164, A.166, D.167, P.168, N.169, P.193, L.194, P.195 Ligands: MG.17 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:G.16, D:R.17, D:V.18, D:A.48, D:G.49, D:R.53, D:N.159, D:N.159, D:Y.164, D:Y.164, D:N.169 Water bridges: D:K.13, D:K.13, D:K.13, D:K.13, D:R.17, D:D.139 Salt bridges: D:K.13, D:K.13 ATP.21: 22 residues within 4Å: Chain E: K.40, G.42, G.43, Q.44, S.45, G.75, A.76, G.77, T.167, D.168, K.187, D.188, E.189, G.191, L.192, Y.193, A.195, N.196, P.197, K.198, S.222, I.223 22 PLIP interactions: 22 interactions with chain E Hydrogen bonds: E:G.43, E:Q.44, E:S.45, E:A.76, E:T.167, E:D.188, E:Y.193, E:Y.193, E:N.196, E:K.198 Water bridges: E:K.40, E:G.77, E:G.77, E:R.166, E:R.166, E:T.167, E:D.168, E:K.198 Salt bridges: E:K.40, E:K.40, E:K.187, E:K.187 ATP.26: 23 residues within 4Å: Chain E: S.14 Chain F: K.13, G.15, G.16, R.17, G.47, A.48, G.49, R.53, E.158, N.159, V.160, G.162, I.163, Y.164, A.166, D.167, P.168, N.169, P.193, L.194, P.195 Ligands: MG.27 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:G.16, F:R.17, F:V.18, F:A.48, F:G.49, F:R.53, F:N.159, F:N.159, F:Y.164, F:Y.164, F:N.169 Water bridges: F:K.13, F:K.13, F:K.13, F:K.13, F:R.17, F:D.139 Salt bridges: F:K.13, F:K.13

6 x 8M0: bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)(Non-covalent)

8M0.2: 19 residues within 4Å: Chain A: V.124, G.125, G.126, A.127, G.128, F.144, S.145, M.147, P.148, P.149, L.174, F.178 Chain B: Y.123, H.124, H.125, H.126 Ligands: MG.4, 6M0.5, 8M0.8 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.126, A:A.127, A:G.128, A:S.145, A:M.147, B:H.124, B:H.125, B:H.125, B:H.126 Water bridges: A:S.102, A:L.129, A:S.145 8M0.8: 17 residues within 4Å: Chain B: P.71, A.74, S.75, G.78, Q.79, H.82, Y.95, E.97, H.98, P.99, S.118, P.121, P.122, H.124 Ligands: 8M0.2, PO4.10, 6M0.25 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.79, B:Y.95, B:H.98, B:H.98, B:H.98, B:S.118, B:H.124 Water bridges: B:S.75, B:S.75, B:Q.79 8M0.12: 19 residues within 4Å: Chain C: V.124, G.125, G.126, A.127, G.128, F.144, S.145, M.147, P.148, P.149, L.174, F.178 Chain D: Y.123, H.124, H.125, H.126 Ligands: MG.14, 6M0.15, 8M0.18 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.126, C:A.127, C:G.128, C:S.145, D:H.124, D:H.125, D:H.125, D:H.126 Water bridges: C:S.102, C:L.129, C:S.145 8M0.18: 17 residues within 4Å: Chain D: P.71, A.74, S.75, G.78, Q.79, H.82, Y.95, E.97, H.98, P.99, S.118, P.121, P.122, H.124 Ligands: 6M0.5, 8M0.12, PO4.20 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:Q.79, D:Y.95, D:H.98, D:H.98, D:H.98, D:S.118, D:H.124 Water bridges: D:S.75, D:S.75, D:Q.79 8M0.22: 19 residues within 4Å: Chain E: V.124, G.125, G.126, A.127, G.128, F.144, S.145, M.147, P.148, P.149, L.174, F.178 Chain F: Y.123, H.124, H.125, H.126 Ligands: MG.24, 6M0.25, 8M0.28 11 PLIP interactions: 4 interactions with chain F, 7 interactions with chain E Hydrogen bonds: F:H.124, F:H.125, F:H.125, F:H.126, E:G.126, E:A.127, E:G.128, E:S.145 Water bridges: E:S.102, E:L.129, E:S.145 8M0.28: 17 residues within 4Å: Chain F: P.71, A.74, S.75, G.78, Q.79, H.82, Y.95, E.97, H.98, P.99, S.118, P.121, P.122, H.124 Ligands: 6M0.15, 8M0.22, PO4.30 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:Q.79, F:Y.95, F:H.98, F:H.98, F:H.98, F:S.118, F:H.124 Water bridges: F:S.75, F:S.75, F:Q.79

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

PO4.3: 4 residues within 4Å: Chain A: R.208, E.240, H.260, I.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.240 Salt bridges: A:R.208, A:H.260 PO4.10: 3 residues within 4Å: Chain B: P.71, A.74 Ligands: 8M0.8 No protein-ligand interaction detected (PLIP) PO4.13: 4 residues within 4Å: Chain C: R.208, E.240, H.260, I.264 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.240 Salt bridges: C:R.208, C:H.260 PO4.20: 3 residues within 4Å: Chain D: P.71, A.74 Ligands: 8M0.18 No protein-ligand interaction detected (PLIP) PO4.23: 4 residues within 4Å: Chain E: R.208, E.240, H.260, I.264 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.240 Salt bridges: E:R.208, E:H.260 PO4.30: 3 residues within 4Å: Chain F: P.71, A.74 Ligands: 8M0.28 No protein-ligand interaction detected (PLIP)

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: S.145, M.147 Ligands: 8M0.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.145, A:M.147, H2O.10 MG.7: 4 residues within 4Å: Chain B: D.139, E.158, P.195 Ligands: ATP.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.158, B:P.195, H2O.12, H2O.12 MG.14: 3 residues within 4Å: Chain C: S.145, M.147 Ligands: 8M0.12 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.145, C:M.147, H2O.30 MG.17: 4 residues within 4Å: Chain D: D.139, E.158, P.195 Ligands: ATP.16 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.158, D:P.195, H2O.32, H2O.33 MG.24: 3 residues within 4Å: Chain E: S.145, M.147 Ligands: 8M0.22 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:S.145, E:M.147, H2O.51 MG.27: 4 residues within 4Å: Chain F: D.139, E.158, P.195 Ligands: ATP.26 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.158, F:P.195, H2O.53, H2O.53

3 x 6M0: MO(6)-O(26) Cluster(Non-covalent)

6M0.5: 5 residues within 4Å: Chain A: D.106, K.151 Chain B: P.99 Ligands: 8M0.2, 8M0.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.151 Water bridges: A:D.106, A:D.106 6M0.15: 5 residues within 4Å: Chain C: D.106, K.151 Chain D: P.99 Ligands: 8M0.12, 8M0.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.151 Water bridges: C:D.106, C:D.106 6M0.25: 5 residues within 4Å: Chain E: D.106, K.151 Chain F: P.99 Ligands: 8M0.8, 8M0.22 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.151 Water bridges: E:D.106, E:D.106

3 x MO: MOLYBDENUM ATOM(Non-covalent)

MO.9: 5 residues within 4Å: Chain B: H.108 Chain F: Q.104, H.108 Ligands: MO.19, MO.29 Ligand excluded by PLIP MO.19: 5 residues within 4Å: Chain B: Q.104, H.108 Chain D: H.108 Ligands: MO.9, MO.29 Ligand excluded by PLIP MO.29: 5 residues within 4Å: Chain D: Q.104, H.108 Chain F: H.108 Ligands: MO.9, MO.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kowalewski, B. et al., Nature's Polyoxometalate Chemistry: X-ray Structure of the Mo Storage Protein Loaded with Discrete Polynuclear Mo-O Clusters. J.Am.Chem.Soc. (2012)

Release Date

2012-07-18

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
B

E
B

B
A

D
A

F
A

Molybdenum storage protein subunit beta

Molybdenum storage protein subunit alpha