SMTL ID : 7uta.1

CryoEM structure of Azotobacter vinelandii nitrogenase complex (2:1 FeP:MoFeP) inhibited by BeFx during catalytic N2 reduction

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-4-mer

Ligands

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

HCA.1: 7 residues within 4Å: Chain A: G.95, R.96, Q.191, G.424, I.425, H.442 Ligands: ICS.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.442 Hydrogen bonds: A:Q.191, A:I.425 Salt bridges: A:K.426, A:H.442 HCA.6: 7 residues within 4Å: Chain C: G.95, R.96, Q.191, G.424, I.425, H.442 Ligands: ICS.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.191, C:I.425, C:H.442 Salt bridges: C:K.426, C:H.442

2 x ICS: iron-sulfur-molybdenum cluster with interstitial carbon(Non-covalent)

ICS.2: 15 residues within 4Å: Chain A: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.380 Metal complexes: A:C.275 ICS.7: 15 residues within 4Å: Chain C: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.6 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275

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

CLF.3: 19 residues within 4Å: Chain A: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 Chain B: C.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A, Metal complexes: B:C.70, B:C.95, B:C.95, B:C.153, A:C.62, A:C.88, A:C.88, A:C.154 CLF.8: 18 residues within 4Å: Chain C: C.62, Y.64, P.85, G.87, C.88, Y.91, C.154, G.185 Chain D: C.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D, Metal complexes: C:C.62, C:C.88, C:C.88, C:C.154, D:C.70, D:C.95, D:C.95, D:C.153

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

FE.4: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Metal complexes: B:R.108, B:E.109, D:D.353, D:D.357 FE.5: 4 residues within 4Å: Chain B: D.353, D.357 Chain D: R.108, E.109 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:R.108, D:E.109, B:D.353, B:D.357

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.9: 13 residues within 4Å: Chain A: L.158 Chain B: V.157, I.158 Chain E: C.98, A.99, G.100, V.132, C.133 Chain F: C.98, A.99, G.100, V.132, C.133 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E, Metal complexes: F:C.98, F:C.133, E:C.98, E:C.133 SF4.16: 13 residues within 4Å: Chain C: L.158, I.159 Chain D: V.157, I.158 Chain G: C.98, A.99, G.100, C.133 Chain H: C.98, A.99, G.100, V.132, C.133 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H, Metal complexes: G:C.98, G:C.133, H:C.98, H:C.133

4 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain E: S.17, D.40, D.44 Ligands: ADP.11, 0BE.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.17 MG.13: 3 residues within 4Å: Chain F: S.17 Ligands: ADP.14, 0BE.15 No protein-ligand interaction detected (PLIP) MG.17: 6 residues within 4Å: Chain G: S.17, D.40, D.44, D.126 Ligands: ADP.18, 0BE.19 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.17 MG.20: 3 residues within 4Å: Chain H: S.17 Ligands: ADP.21, 0BE.22 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.17

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.11: 19 residues within 4Å: Chain E: G.13, I.14, G.15, K.16, S.17, T.18, N.186, V.212, P.213, R.214, D.215, V.218, E.222, Y.241 Chain F: K.11, E.155, M.157 Ligands: MG.10, 0BE.12 19 PLIP interactions: 14 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:G.13, E:I.14, E:G.15, E:K.16, E:S.17, E:S.17, E:T.18, E:T.18, E:N.186, E:P.213, E:D.215, E:E.222, F:E.155, F:M.156, F:M.157 Salt bridges: E:K.16, F:K.11, F:K.11 pi-Cation interactions: E:R.214 ADP.14: 22 residues within 4Å: Chain E: K.11, E.155, M.157 Chain F: K.11, G.13, I.14, G.15, K.16, S.17, T.18, T.19, N.186, V.212, P.213, R.214, D.215, V.218, E.222, Q.237, Y.241 Ligands: MG.13, 0BE.15 16 PLIP interactions: 3 interactions with chain E, 13 interactions with chain F Hydrogen bonds: E:M.157, F:G.13, F:I.14, F:G.15, F:K.16, F:S.17, F:T.18, F:T.18, F:N.186, F:P.213, F:D.215, F:E.222, F:Q.237 Salt bridges: E:K.11, E:K.11, F:K.16 ADP.18: 21 residues within 4Å: Chain G: K.11, G.13, I.14, G.15, K.16, S.17, T.18, N.186, V.212, P.213, R.214, D.215, V.218, Q.219, E.222, Q.237 Chain H: K.11, E.155, M.157 Ligands: MG.17, 0BE.19 18 PLIP interactions: 15 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:G.13, G:I.14, G:G.15, G:K.16, G:S.17, G:T.18, G:T.18, G:N.186, G:P.213, G:D.215, G:E.222, G:Q.237, H:M.157 Salt bridges: G:K.16, H:K.11, H:K.11 pi-Cation interactions: G:R.214, G:R.214 ADP.21: 20 residues within 4Å: Chain G: K.11, E.155, M.157, R.188 Chain H: K.11, G.13, I.14, G.15, K.16, S.17, T.18, N.186, P.213, R.214, D.215, V.218, Q.219, Q.237 Ligands: MG.20, 0BE.22 16 PLIP interactions: 12 interactions with chain H, 4 interactions with chain G Hydrogen bonds: H:K.11, H:G.13, H:I.14, H:G.15, H:K.16, H:S.17, H:T.18, H:T.18, H:N.186, H:P.213, H:D.215, G:M.157, G:R.188 Salt bridges: H:K.16, G:K.11, G:K.11

4 x 0BE: BERYLLIUM(Non-covalent)

0BE.12: 5 residues within 4Å: Chain E: K.16, K.42 Chain F: K.11 Ligands: MG.10, ADP.11 No protein-ligand interaction detected (PLIP) 0BE.15: 5 residues within 4Å: Chain E: K.11 Chain F: G.13, K.16 Ligands: MG.13, ADP.14 No protein-ligand interaction detected (PLIP) 0BE.19: 4 residues within 4Å: Chain G: K.16 Chain H: K.11 Ligands: MG.17, ADP.18 No protein-ligand interaction detected (PLIP) 0BE.22: 6 residues within 4Å: Chain G: K.11 Chain H: G.12, G.13, K.16 Ligands: MG.20, ADP.21 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rutledge, H.L. et al., Structures of the nitrogenase complex prepared under catalytic turnover conditions. Science (2022)

Release Date

2022-08-17

Peptides

Nitrogenase molybdenum-iron protein alpha chain: AC
Nitrogenase molybdenum-iron protein beta chain: BD
Nitrogenase iron protein gamma chain: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

G
G

H
H

Nitrogenase molybdenum-iron protein alpha chain

Nitrogenase molybdenum-iron protein beta chain

Nitrogenase iron protein gamma chain

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