SMTL ID : 6ug0.1

N2-bound Nitrogenase MoFe-protein from Azotobacter vinelandii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

hetero-2-2-mer

Ligands

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

HCA.1: 7 residues within 4Å: Chain A: A.65, R.96, Q.191, G.424, I.425, H.442 Ligands: ICE.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.442 Hydrogen bonds: A:Q.191, A:I.425 Water bridges: A:K.426, A:K.426, A:K.426, A:K.426, A:E.440, B:R.105 Salt bridges: A:K.426, A:H.442, A:H.442 HCA.17: 9 residues within 4Å: Chain C: A.65, R.96, Q.191, G.424, I.425, K.426, H.442 Ligands: ICZ.18, GOL.29 14 PLIP interactions: 2 interactions with chain D, 12 interactions with chain C Water bridges: D:Y.98, D:R.105, C:E.380, C:K.426, C:K.426, C:K.426, C:E.440, C:E.440 Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.191, C:I.425 Salt bridges: C:K.426, C:H.442, C:H.442

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

ICE.2: 15 residues within 4Å: Chain A: V.70, R.96, 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, HDZ.3 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.380 Metal complexes: A:C.275 ICE.18: 15 residues within 4Å: Chain C: V.70, R.96, H.195, Y.229, C.275, S.278, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.17, HDZ.19, HDZ.26 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275

3 x HDZ: NITROGEN MOLECULE(Non-covalent)

HDZ.3: 4 residues within 4Å: Chain A: V.70, H.195, F.381 Ligands: ICE.2 No protein-ligand interaction detected (PLIP) HDZ.19: 7 residues within 4Å: Chain C: I.355, G.356, G.357, L.358, R.359, P.360 Ligands: ICZ.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.356, C:G.357, C:L.358, C:R.359 HDZ.26: 5 residues within 4Å: Chain C: R.96, Y.229, I.231, R.359 Ligands: ICZ.18 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.96 Water bridges: C:R.96, C:Y.229, C:R.359, C:H.442

6 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.4: 1 residues within 4Å: Chain A: D.204 No protein-ligand interaction detected (PLIP) H2S.9: 6 residues within 4Å: Chain A: R.93, T.104, T.111, M.112 Chain B: F.450, R.453 No protein-ligand interaction detected (PLIP) H2S.10: 1 residues within 4Å: Chain B: Y.251 No protein-ligand interaction detected (PLIP) H2S.20: 2 residues within 4Å: Chain C: D.204, W.205 No protein-ligand interaction detected (PLIP) H2S.21: 6 residues within 4Å: Chain C: R.93, T.104, T.111, M.112 Chain D: F.450, R.453 No protein-ligand interaction detected (PLIP) H2S.30: 1 residues within 4Å: Chain D: Y.251 No protein-ligand interaction detected (PLIP)

8 x MO: MOLYBDENUM ATOM(Non-covalent)

MO.5: 1 residues within 4Å: Chain A: W.294 Ligand excluded by PLIP MO.6: 3 residues within 4Å: Chain A: N.29, L.32, C.45 Ligand excluded by PLIP MO.7: 3 residues within 4Å: Chain A: P.37, A.38, V.39 Ligand excluded by PLIP MO.11: 2 residues within 4Å: Chain B: E.258, E.259 Ligand excluded by PLIP MO.22: 1 residues within 4Å: Chain C: W.294 Ligand excluded by PLIP MO.23: 4 residues within 4Å: Chain C: N.29, K.30, L.32, C.45 Ligand excluded by PLIP MO.24: 3 residues within 4Å: Chain C: P.37, A.38, V.39 Ligand excluded by PLIP MO.31: 2 residues within 4Å: Chain D: E.258, E.259 Ligand excluded by PLIP

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

1CL.8: 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 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Salt bridges: A:E.153 Metal complexes: A:C.62, A:C.88, A:C.88, A:C.154, B:C.70, B:C.95, B:C.95, B:C.153, B:S.188 1CL.27: 19 residues within 4Å: Chain C: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, 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 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D, Salt bridges: C:E.153 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, D:S.188

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

FE.12: 4 residues within 4Å: Chain B: D.353, D.357 Chain D: R.108, E.109 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.353, D:R.108, D:E.109, H2O.6, H2O.22 FE.15: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:D.353, D:D.357, D:D.357, B:E.109, H2O.7

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 8 residues within 4Å: Chain B: F.230, E.231, T.232, Y.233, D.372, F.375, G.470, F.471 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.231, B:T.232 Water bridges: B:N.236 GOL.16: 8 residues within 4Å: Chain B: T.360, W.361 Chain C: D.445, Y.446, S.447, R.461, M.465 Chain D: A.10 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.445, C:R.461, B:T.360 Water bridges: C:S.447, C:S.447 GOL.25: 2 residues within 4Å: Chain C: F.125, K.129 No protein-ligand interaction detected (PLIP) GOL.28: 7 residues within 4Å: Chain A: I.101 Chain B: F.15, L.16, K.21, L.24 Chain D: Q.513, A.514 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:A.514, B:F.15 GOL.29: 8 residues within 4Å: Chain C: Y.91, S.92, G.95, R.96 Chain D: Y.98, S.101, R.105 Ligands: HCA.17 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:S.92, D:S.101, D:S.101, D:R.105, D:R.105 Water bridges: C:G.95 GOL.32: 7 residues within 4Å: Chain D: F.230, E.231, T.232, Y.233, F.375, G.470, F.471 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.231, D:T.232, D:T.232, D:Y.233 Water bridges: D:N.236

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.14: 5 residues within 4Å: Chain B: E.347, R.350, E.488, Q.492 Chain D: R.481 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.350, B:Q.492, D:R.481

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, W. et al., Structural evidence for a dynamic metallocofactor during N2reduction by Mo-nitrogenase. Science (2020)

Release Date

2020-06-24

Peptides

Nitrogenase molybdenum-iron 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 molybdenum-iron protein alpha chain

Nitrogenase molybdenum-iron protein beta chain

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