SMTL ID : 7mci.1

MoFe protein from Azotobacter vinelandii with a sulfur-replenished cofactor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-2-2-mer

Ligands

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

HCA.1: 8 residues within 4Å: Chain A: A.65, R.96, Q.191, G.424, I.425, K.426, H.442 Ligands: ICS.2 14 PLIP interactions: 13 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:G.95, A:R.97, A:K.426, A:K.426, A:K.426, A:E.440, A:E.440, B:R.105 Salt bridges: A:K.426, A:H.442, A:H.442 HCA.14: 8 residues within 4Å: Chain C: A.65, R.96, Q.191, G.424, I.425, K.426, H.442 Ligands: ICS.15 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.191, C:I.425 Water bridges: C:R.97, C:K.426, C:K.426, C:K.426, C:K.426, C:E.440, D:R.105 Salt bridges: C:K.426, C:H.442, 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.15: 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.14 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275

2 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.3: 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.17: 5 residues within 4Å: Chain C: R.93, T.104, T.111 Chain D: F.450, R.453 No protein-ligand interaction detected (PLIP)

6 x MO: MOLYBDENUM ATOM(Non-covalent)

MO.4: 3 residues within 4Å: Chain A: N.29, L.32, C.45 Ligand excluded by PLIP MO.5: 2 residues within 4Å: Chain A: D.204, W.205 Ligand excluded by PLIP MO.6: 1 residues within 4Å: Chain A: W.294 Ligand excluded by PLIP MO.18: 3 residues within 4Å: Chain C: N.29, L.32, C.45 Ligand excluded by PLIP MO.19: 1 residues within 4Å: Chain C: W.294 Ligand excluded by PLIP MO.20: 2 residues within 4Å: Chain C: D.204, W.205 Ligand excluded by PLIP

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

CLF.7: 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 9 PLIP interactions: 5 interactions with chain A, 4 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 CLF.16: 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 9 PLIP interactions: 5 interactions with chain C, 4 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

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain B: P.182, F.183, G.203, R.206, Y.207 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.183, B:G.203, B:R.206 GOL.9: 7 residues within 4Å: Chain B: F.230, E.231, T.232, Y.233, F.375, G.470, F.471 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.231, B:T.232, B:Y.233 Water bridges: B:F.230, B:N.236, B:D.372 GOL.10: 7 residues within 4Å: Chain B: R.59, E.60, A.61, L.62, T.63, G.424, H.429 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.60 Water bridges: B:R.59, B:R.59, B:T.63, B:T.63, B:H.429, A:K.130 GOL.11: 7 residues within 4Å: Chain B: T.360, W.361 Chain C: D.445, S.447, R.461, M.465 Chain D: A.10 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.461, B:T.360 Water bridges: C:R.439, C:D.445, C:S.447, C:R.461, B:T.360 GOL.12: 4 residues within 4Å: Chain A: P.143 Chain B: E.42, V.43, W.46 No protein-ligand interaction detected (PLIP) GOL.22: 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:Y.233 Water bridges: D:N.236, D:Q.294 GOL.23: 8 residues within 4Å: Chain A: D.445, Y.446, S.447, R.461, M.465 Chain B: A.10 Chain D: T.360, W.361 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.461 Water bridges: A:R.439, A:S.447, A:R.461 GOL.24: 7 residues within 4Å: Chain B: Q.513, A.514 Chain C: I.101 Chain D: F.15, L.16, K.21, L.24 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:F.15, D:K.21, B:Q.513 Water bridges: B:Q.513 GOL.25: 6 residues within 4Å: Chain D: S.482, T.483, T.484, Q.492, I.493, T.496 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.482, D:T.483, D:T.496 GOL.26: 8 residues within 4Å: Chain C: K.130 Chain D: R.59, E.60, A.61, L.62, T.63, G.424, H.429 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.59, D:G.424, C:K.130, C:K.130 Water bridges: D:H.429 GOL.27: 5 residues within 4Å: Chain D: P.182, F.183, G.203, R.206, Y.207 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:F.183, D:G.203, D:R.206

2 x CA: CALCIUM ION(Non-covalent)

CA.13: 4 residues within 4Å: Chain B: D.353, D.357 Chain D: R.108, E.109 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.353, B:D.357, D:R.108, H2O.15, H2O.42 CA.21: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:D.353, D:D.357, B:R.108, B:E.109, H2O.17, H2O.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, C.C. et al., Evidence of substrate binding and product release via belt-sulfur mobilization of the nitrogenase cofactor. Nat Catal (2022)

Release Date

2022-05-18

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

Related Entries With Identical Sequence