SMTL ID : 6op3.1

Selenium incorporated FeMo-cofactor of nitrogenase from Azotobacter vinelandii with low concentration of selenium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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 13 PLIP interactions: 12 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:K.423, A:E.437, B:R.104 Salt bridges: A:K.423, A:H.439, A:H.439 HCA.13: 8 residues within 4Å: Chain C: A.62, R.93, Q.188, G.421, I.422, K.423, H.439 Ligands: ICS.14 14 PLIP interactions: 12 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, 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, 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, SE.5 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.377 Metal complexes: A:C.272 ICS.14: 15 residues within 4Å: Chain C: V.67, R.93, Y.226, I.228, C.272, S.275, I.352, G.353, G.354, L.355, R.356, F.378, H.439 Ligands: HCA.13, SE.16 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.377 Metal complexes: C:C.272

12 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: 6 residues within 4Å: Chain A: R.93, R.94, N.95, Y.96, Y.97, T.108 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A Water bridges: D:L.520, A:N.95 Hydrogen bonds: A:N.95 IMD.7: 7 residues within 4Å: Chain B: 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:S.481, B:Q.491 Water bridges: B:Y.232 IMD.8: 5 residues within 4Å: Chain A: G.154, L.155, F.183 Chain B: E.119, A.122 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.119 Water bridges: A:R.184 IMD.10: 5 residues within 4Å: Chain B: L.252, D.255, G.274, T.275, E.279 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.255 Water bridges: B:K.240, B:K.240, B:L.252, B:D.255, B:G.274 IMD.11: 6 residues within 4Å: Chain B: Q.512, A.513 Chain C: I.98 Chain D: F.14, L.15, L.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.513 IMD.15: 2 residues within 4Å: Chain C: E.284, W.291 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.291 Water bridges: C:W.291 pi-Stacking: C:W.291, C:W.291 IMD.17: 7 residues within 4Å: Chain B: D.519 Chain C: R.93, R.94, N.95, Y.96, Y.97, T.108 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.95, C:N.95, C:N.95 IMD.19: 5 residues within 4Å: Chain C: G.154, L.155, F.183 Chain D: E.119, A.122 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.184 IMD.21: 7 residues within 4Å: Chain D: I.468, S.481, T.482, T.483, Q.491, I.492, T.495 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.482, D:T.495 Water bridges: D:S.481 IMD.22: 5 residues within 4Å: Chain D: L.252, D.255, G.274, T.275, E.279 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.255, D:E.279 Water bridges: D:L.252, D:E.257 IMD.24: 4 residues within 4Å: Chain A: I.98 Chain B: L.23 Chain D: Q.512, A.513 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.14

2 x SE: SELENIUM ATOM(Non-covalent)

SE.5: 4 residues within 4Å: Chain A: V.67, H.192, F.378 Ligands: ICS.2 No protein-ligand interaction detected (PLIP) SE.16: 4 residues within 4Å: Chain C: V.67, H.192, F.378 Ligands: ICS.14 No protein-ligand interaction detected (PLIP)

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

CLF.6: 19 residues within 4Å: Chain A: C.59, Y.61, P.82, G.84, C.85, Y.88, E.150, C.151, G.182 Chain B: 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 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.20: 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: 4 interactions with chain D, 5 interactions with chain C, Metal complexes: D:C.69, D:C.94, D:C.94, D:C.152, C:C.59, C:C.85, C:C.85, C:C.151 Salt bridges: C:E.150

2 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 1 residues within 4Å: Chain B: K.364 No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain D: K.8, P.12 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.12: 4 residues within 4Å: Chain B: D.352, D.356 Chain D: R.107, E.108 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:R.107, D:E.108, B:D.352, B:D.356, H2O.21, H2O.72 CA.18: 2 residues within 4Å: Chain C: I.325, K.329 No protein-ligand interaction detected (PLIP) CA.25: 8 residues within 4Å: Chain A: F.426, Q.429, K.430 Chain B: R.107, E.108 Chain D: D.352, D.356 Ligands: CA.26 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Metal complexes: D:D.352, D:D.352, D:D.356, B:R.107 CA.26: 5 residues within 4Å: Chain B: R.107, E.108 Chain D: D.352, D.356 Ligands: CA.25 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:D.352, D:D.356, B:R.107, B:E.108, H2O.31

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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