SMTL ID : 7ady.1

CO-removed state of the active site of vanadium nitrogenase VFe protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x D6N: FeV(Non-covalent)

D6N.1: 15 residues within 4Å: Chain A: V.57, K.83, Q.176, F.211, I.213, C.257, S.260, G.336, P.338, R.339, K.361, F.362, H.423 Ligands: HCA.2, BCT.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions, Metal complexes: A:C.257, H2O.1 D6N.15: 15 residues within 4Å: Chain D: V.57, K.83, Q.176, F.211, I.213, C.257, S.260, G.336, P.338, R.339, K.361, F.362, H.423 Ligands: HCA.16, BCT.17 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.257, H2O.49

2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)

HCA.2: 9 residues within 4Å: Chain A: C.52, L.56, K.83, Q.176, K.361, P.406, H.423 Chain B: F.59 Ligands: D6N.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.56, A:H.423 Hydrogen bonds: A:T.82, A:Q.176, A:K.361 Water bridges: A:K.83, A:K.83, A:G.405, A:G.405, A:R.407 Salt bridges: A:K.83, A:K.361, A:H.423, A:H.423 HCA.16: 9 residues within 4Å: Chain D: C.52, L.56, K.83, Q.176, K.361, P.406, H.423 Chain E: F.59 Ligands: D6N.15 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.56, D:H.423 Hydrogen bonds: D:Q.176, D:K.361, D:K.361, D:H.423 Water bridges: D:K.83, D:K.83, D:G.405, D:R.407, D:R.407, D:R.407, D:H.423 Salt bridges: D:K.83, D:K.361, D:H.423, D:H.423

2 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.3: 6 residues within 4Å: Chain A: T.335, G.336, G.337, P.338, R.339 Ligands: D6N.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.335, A:G.337, A:R.339 BCT.17: 6 residues within 4Å: Chain D: T.335, G.336, G.337, P.338, R.339 Ligands: D6N.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.335, D:G.336, D:G.337

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.4: 5 residues within 4Å: Chain A: R.47, G.48, S.175, Q.176, F.362 No protein-ligand interaction detected (PLIP) H2S.18: 5 residues within 4Å: Chain D: R.47, G.48, S.175, Q.176, F.362 No protein-ligand interaction detected (PLIP)

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 2 residues within 4Å: Chain A: V.107, V.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.107 TRS.6: 5 residues within 4Å: Chain A: F.92, Y.96, M.126, D.128 Chain B: W.391 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:E.394, A:Y.96, A:Y.96, A:Y.96 TRS.19: 5 residues within 4Å: Chain D: F.92, Y.96, M.126, I.129 Chain E: W.391 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Water bridges: E:N.398, D:Y.96, D:Y.96

2 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)

CLF.7: 19 residues within 4Å: Chain A: C.49, F.51, P.72, G.74, C.75, D.78, T.137, C.138, G.170 Chain B: C.31, P.33, G.53, Q.54, G.55, C.56, F.59, T.114, C.115, S.153 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, Salt bridges: A:D.78 Metal complexes: A:C.49, A:C.75, A:C.75, A:C.138, B:C.31, B:C.56, B:C.56, B:C.115 CLF.20: 19 residues within 4Å: Chain D: C.49, F.51, P.72, G.74, C.75, D.78, T.137, C.138, G.170 Chain E: C.31, P.33, G.53, Q.54, G.55, C.56, F.59, T.114, C.115, S.153 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain D, Metal complexes: E:C.31, E:C.56, E:C.56, E:C.115, D:C.49, D:C.75, D:C.75, D:C.138 Salt bridges: D:D.78

4 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 2 residues within 4Å: Chain B: E.70 Chain E: D.314 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: E:D.314, B:E.70, H2O.25, H2O.26, H2O.32, H2O.86 MG.9: 2 residues within 4Å: Chain B: D.314 Chain E: E.70 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: E:E.70, B:D.314, H2O.24, H2O.36, H2O.73, H2O.81 MG.13: 1 residues within 4Å: Chain C: E.14 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain F: E.14 No protein-ligand interaction detected (PLIP)

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 6 residues within 4Å: Chain B: R.256, L.276, V.277, N.278, P.369, R.370 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.256, B:R.370 Water bridges: B:L.276, B:D.336 EDO.11: 7 residues within 4Å: Chain B: H.177, G.178, K.179, G.180, A.243, D.244, N.247 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.247 EDO.12: 6 residues within 4Å: Chain B: N.132, L.135, E.136, R.142, K.143, I.144 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.136, B:K.143, B:I.144 Water bridges: B:R.142 EDO.14: 7 residues within 4Å: Chain A: R.276 Chain C: F.22, N.31, V.35, L.57, F.58, D.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.276 EDO.21: 7 residues within 4Å: Chain E: H.177, G.178, K.179, G.180, A.243, D.244, N.247 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.244, E:N.247 EDO.22: 6 residues within 4Å: Chain E: R.256, L.276, V.277, N.278, P.369, R.370 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.256, E:R.370 Water bridges: E:R.256, E:L.276 EDO.23: 6 residues within 4Å: Chain E: N.132, L.135, E.136, R.142, K.143, I.144 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.143, E:I.144 Water bridges: E:R.142 EDO.24: 6 residues within 4Å: Chain E: Q.32, H.150, P.152, K.155, T.160, E.164 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.32, E:T.160 Water bridges: E:T.160, E:T.160 EDO.26: 8 residues within 4Å: Chain D: R.276 Chain F: W.19, F.22, N.31, V.35, L.57, F.58, D.61 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:D.61, D:R.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rohde, M. et al., CO Binding to the FeV Cofactor of CO-Reducing Vanadium Nitrogenase at Atomic Resolution. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2020-09-30

Peptides

Nitrogenase vanadium-iron protein alpha chain: AD
Nitrogenase vanadium-iron protein beta chain: BE
Nitrogenase vanadium-iron protein delta chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Nitrogenase vanadium-iron protein alpha chain

Nitrogenase vanadium-iron protein beta chain

Nitrogenase vanadium-iron protein delta chain

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