SMTL ID : 8p8g.1

Nitrogenase MoFe protein from A. vinelandii beta double mutant D353G/D357G

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: K.154 Chain B: E.33, K.34, Y.35 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: K.349, Y.350, R.353, R.469 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: K.277, K.323, F.324 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain B: R.59, E.60, A.61, L.62, G.424, H.429 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain B: F.15, L.16, K.21, L.24 Chain D: A.514, Y.517 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain B: T.360, W.361 Chain C: D.453, Y.454, S.455, R.469 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain B: L.80, P.110, V.111, S.112, V.260, F.269, M.271 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: T.148 Chain B: L.55, Q.58, R.59 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain B: N.317, A.405, A.408, I.409 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain B: P.295, E.299, K.302, R.401 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: D.323, D.326, E.327, M.330 Chain C: P.486 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: E.128, V.132 Chain B: E.156, F.189 Ligand excluded by PLIP EDO.18: 11 residues within 4Å: Chain A: K.441 Chain B: E.109, D.262, T.263, P.264, A.265, R.481 Chain D: G.349, R.350, G.353, M.354 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: K.349, Y.350, R.353, R.469 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: K.277, L.278, P.301, K.323, F.324 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain C: G.414, F.417, E.418, I.438, F.439 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain C: L.201, H.204, I.205, D.208 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain C: A.348, K.349 Ligand excluded by PLIP EDO.30: 2 residues within 4Å: Chain C: Y.298, G.299 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain C: V.347, A.348, R.351, P.352 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain D: Q.136, E.172, G.173, F.174 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: L.456 Chain D: E.507, E.508, G.511, T.515 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain D: D.41, F.44, H.457 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain D: A.123, V.124, F.125, G.126 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain D: P.295, W.296, E.299 Ligands: EDO.37 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain D: P.295, W.296, K.315, L.316, N.317 Ligands: EDO.36 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain D: L.80, P.110, V.111, S.112, V.260, F.269, M.271 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain D: P.182, F.183, G.203, R.206, Y.207 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain B: A.514, Y.517 Chain C: I.109 Chain D: F.15, L.16, K.21, L.24 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain D: R.59, E.60, A.61, L.62, G.424, H.429 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain A: D.453, Y.454, R.469 Chain D: T.360, W.361 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain D: R.238, R.242, E.488 Ligand excluded by PLIP EDO.45: 8 residues within 4Å: Chain B: R.350, G.353, M.354 Chain C: K.441 Chain D: E.109, D.262, T.263 Ligands: EDO.46 Ligand excluded by PLIP EDO.46: 11 residues within 4Å: Chain B: G.349, R.350, G.353, M.354 Chain C: K.441 Chain D: E.109, D.262, T.263, P.264, A.265 Ligands: EDO.45 Ligand excluded by PLIP EDO.47: 1 residues within 4Å: Chain D: Y.207 Ligand excluded by PLIP

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: R.101, T.112, T.119, M.120 Chain B: F.450, R.453 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain C: R.101, T.112, T.119, M.120 Chain D: F.450, R.453 Ligand excluded by PLIP

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

HCA.3: 7 residues within 4Å: Chain A: A.73, R.104, Q.199, G.432, I.433, H.450 Ligands: ICS.4 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A Water bridges: B:Y.98, B:R.105, A:K.434, A:K.434, A:K.434, A:K.434, A:H.450 Hydrophobic interactions: A:H.450 Hydrogen bonds: A:Q.199, A:I.433 Salt bridges: A:K.434, A:H.450, A:H.450 HCA.23: 7 residues within 4Å: Chain C: A.73, R.104, Q.199, G.432, I.433, H.450 Ligands: ICS.24 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:H.450 Hydrogen bonds: C:Q.199, C:I.433 Water bridges: C:G.103, C:K.434, C:K.434, C:K.434, C:Q.448, C:Q.448, D:R.105 Salt bridges: C:K.434, C:H.450, C:H.450

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

ICS.4: 15 residues within 4Å: Chain A: V.78, R.104, H.203, Y.237, I.239, C.283, S.286, I.363, G.364, G.365, L.366, R.367, F.389, H.450 Ligands: HCA.3 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.388 Metal complexes: A:C.283 ICS.24: 14 residues within 4Å: Chain C: V.78, R.104, H.203, Y.237, I.239, C.283, S.286, G.364, G.365, L.366, R.367, F.389, H.450 Ligands: HCA.23 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.388 Metal complexes: C:C.283

2 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.14: 3 residues within 4Å: Chain B: N.399, K.400, R.401 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.400 DIO.43: 3 residues within 4Å: Chain D: N.399, K.400, R.401 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.400, D:R.401, D:R.401

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 1 residues within 4Å: Chain B: P.36 No protein-ligand interaction detected (PLIP)

2 x 1CL: FE(8)-S(7) CLUSTER, OXIDIZED(Non-covalent)

1CL.19: 19 residues within 4Å: Chain A: C.70, Y.72, P.93, G.95, C.96, Y.99, E.161, C.162, G.193 Chain B: C.70, P.72, S.92, G.94, C.95, Y.98, T.152, C.153, S.188 Ligands: CLF.20 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Salt bridges: A:E.161 Metal complexes: A:C.70, A:C.96, A:C.96, A:C.162, B:C.70, B:C.95, B:C.95, B:C.153, B:S.188 1CL.48: 19 residues within 4Å: Chain C: C.70, Y.72, P.93, G.95, C.96, Y.99, E.161, C.162, G.193 Chain D: C.70, P.72, S.92, G.94, C.95, Y.98, T.152, C.153, S.188 Ligands: CLF.49 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C, Metal complexes: D:C.70, D:C.95, D:C.95, D:C.153, D:S.188, C:C.70, C:C.96, C:C.96, C:C.162 Salt bridges: C:E.161

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

CLF.20: 19 residues within 4Å: Chain A: C.70, Y.72, P.93, G.95, C.96, Y.99, E.161, C.162, G.193 Chain B: C.70, P.72, S.92, G.94, C.95, Y.98, T.152, C.153, S.188 Ligands: 1CL.19 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, Salt bridges: A:E.161 Metal complexes: A:C.70, A:C.96, A:C.96, A:C.162, B:C.70, B:C.95, B:C.95, B:C.153 CLF.49: 19 residues within 4Å: Chain C: C.70, Y.72, P.93, G.95, C.96, Y.99, E.161, C.162, G.193 Chain D: C.70, P.72, S.92, G.94, C.95, Y.98, T.152, C.153, S.188 Ligands: 1CL.48 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C, Metal complexes: D:C.70, D:C.95, D:C.95, D:C.153, C:C.70, C:C.96, C:C.96, C:C.162 Salt bridges: C:E.161

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

NA.22: 2 residues within 4Å: Chain C: D.130, K.138 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.138

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cadoux, C. et al., The Mononuclear Metal-Binding Site of Mo-Nitrogenase Is Not Required for Activity. Jacs Au (2023)

Release Date

2023-12-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Nitrogenase protein alpha chain

Nitrogenase molybdenum-iron protein beta chain