SMTL ID : 6op4.1

Selenium-incorporated, carbon monoxide-inhibited, reactivated FeMo-cofactor of nitrogenase from Azotobacter vinelandii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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.62, R.93, Q.188, G.421, I.422, K.423, H.439 Ligands: ICS.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.439 Hydrogen bonds: A:Q.188, A:I.422 Water bridges: A:R.94, A:K.423, A:K.423, A:K.423, A:E.437, B:R.104 Salt bridges: A:K.423, A:H.439, A:H.439 HCA.12: 8 residues within 4Å: Chain C: A.62, R.93, Q.188, G.421, I.422, K.423, H.439 Ligands: ICS.13 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:H.439 Hydrogen bonds: C:Q.188, C:I.422 Water bridges: C:G.92, C:K.423, C:K.423, C:K.423, C:E.437, C:E.437, C:S.440, D:Y.97, D:R.104 Salt bridges: C:K.423, C:H.439, C:H.439

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

ICS.2: 15 residues within 4Å: Chain A: V.67, R.93, H.192, Y.226, I.228, C.272, S.275, I.352, G.353, G.354, L.355, R.356, F.378, H.439 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.377 Metal complexes: A:C.272 ICS.13: 15 residues within 4Å: Chain C: V.67, R.93, H.192, Y.226, I.228, C.272, S.275, I.352, G.353, G.354, L.355, R.356, F.378, H.439 Ligands: HCA.12 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.377 Metal complexes: C:C.272

9 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 2 residues within 4Å: Chain A: E.284, W.291 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.291 pi-Stacking: A:W.291, A:W.291 IMD.4: 7 residues within 4Å: Chain A: A.91, R.93, R.94, N.95, Y.96, Y.97, T.108 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.95 Water bridges: A:N.95, D:L.520 IMD.7: 8 residues within 4Å: Chain B: Y.232, I.468, S.481, T.482, T.483, Q.491, I.492, T.495 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.232, B:S.481, B:Q.491 IMD.8: 4 residues within 4Å: Chain A: G.154, F.183 Chain B: E.119, A.122 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.119, B:E.119 IMD.10: 5 residues within 4Å: Chain B: L.252, D.255, G.274, T.275, E.279 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.252 IMD.14: 1 residues within 4Å: Chain C: W.291 1 PLIP interactions: 1 interactions with chain C pi-Stacking: C:W.291 IMD.16: 4 residues within 4Å: Chain C: G.154, F.183 Chain D: E.119, A.122 No protein-ligand interaction detected (PLIP) IMD.17: 8 residues within 4Å: Chain D: Y.232, I.468, S.481, T.482, T.483, Q.491, I.492, T.495 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.482, D:T.495 IMD.18: 5 residues within 4Å: Chain D: L.252, D.255, G.274, T.275, E.279 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.240, D:E.279

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

CLF.5: 17 residues within 4Å: Chain A: C.59, Y.61, P.82, G.84, C.85, Y.88, C.151, G.182 Chain B: C.69, P.71, S.91, G.93, C.94, Y.97, T.151, C.152, S.187 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, Salt bridges: A:E.150 Metal complexes: A:C.59, A:C.85, A:C.85, A:C.151, B:C.69, B:C.94, B:C.94, B:C.152 CLF.15: 19 residues within 4Å: Chain C: C.59, Y.61, P.82, G.84, C.85, Y.88, E.150, C.151, G.182 Chain D: C.69, P.71, S.91, G.93, C.94, Y.97, F.98, T.151, C.152, S.187 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D, Salt bridges: C:E.150 Metal complexes: C:C.59, C:C.85, C:C.85, C:C.151, D:C.69, D:C.94, D:C.94, D:C.152

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain B: D.352, D.356 Chain D: R.107, E.108 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.352, B:D.356, D:R.107, D:E.108, H2O.7, H2O.24 CA.11: 4 residues within 4Å: Chain B: R.107, E.108 Chain D: D.352, D.356 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:D.352, D:D.356, B:R.107, H2O.10, H2O.22

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain D: K.8, P.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henthorn, J.T. et al., Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-Edge High Resolution X-ray Absorption Spectroscopy. J.Am.Chem.Soc. (2019)

Release Date

2019-08-14

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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