SMTL ID : 5koj.1

Nitrogenase MoFeP protein in the IDS oxidized state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 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.81, Q.207, G.440, I.441, H.458 Chain B: Y.97 Ligands: ICS.2 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.458 Hydrogen bonds: A:Q.207, A:I.441, B:Y.97, B:Y.97 Water bridges: A:Q.111, B:R.104 Salt bridges: A:K.442, A:H.458, A:H.458 HCA.5: 9 residues within 4Å: Chain C: A.81, R.112, Q.207, G.440, I.441, Q.456, H.458 Chain D: R.104 Ligands: ICS.6 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:H.458 Hydrogen bonds: C:Q.207, C:I.441 Water bridges: C:Q.111, C:K.442, D:Y.97, D:R.104 Salt bridges: C:K.442, C:H.458, C:H.458

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

ICS.2: 15 residues within 4Å: Chain A: V.86, R.112, H.211, Y.245, I.247, C.291, S.294, V.371, G.372, G.373, L.374, R.375, F.397, H.458 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.396 Metal complexes: A:C.291 ICS.6: 15 residues within 4Å: Chain C: V.86, R.112, H.211, Y.245, I.247, C.291, S.294, V.371, G.372, G.373, L.374, R.375, F.397, H.458 Ligands: HCA.5 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.396 Metal complexes: C:C.291

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

CLF.3: 18 residues within 4Å: Chain A: C.78, Y.80, P.101, G.103, C.104, Y.107, E.169, C.170, G.201 Chain B: C.69, S.91, G.93, C.94, Y.97, Y.98, T.151, C.152, A.187 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Salt bridges: A:E.169 Metal complexes: A:C.78, A:C.104, A:C.104, A:C.170, B:C.69, B:C.94, B:C.94, B:Y.98, B:C.152 CLF.7: 19 residues within 4Å: Chain C: C.78, Y.80, P.101, G.103, C.104, Y.107, E.169, C.170, G.201 Chain D: C.69, P.71, S.91, G.93, C.94, Y.97, Y.98, T.151, C.152, A.187 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D, Salt bridges: C:E.169 Metal complexes: C:C.78, C:C.104, C:C.104, C:C.170, D:C.69, D:C.94, D:C.94, D:Y.98, D:C.152

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

FE.4: 5 residues within 4Å: Chain B: D.348, D.352 Chain C: K.449 Chain D: K.107, E.108 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Metal complexes: B:D.348, B:D.352, B:D.352, D:K.107, D:E.108 FE.8: 5 residues within 4Å: Chain A: K.449 Chain B: K.107, E.108 Chain D: D.348, D.352 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Metal complexes: D:D.348, D:D.352, D:D.352, B:K.107, B:E.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Owens, C.P. et al., Tyrosine-Coordinated P-Cluster in G. diazotrophicus Nitrogenase: Evidence for the Importance of O-Based Ligands in Conformationally Gated Electron Transfer. J.Am.Chem.Soc. (2016)

Release Date

2016-09-14

Peptides

Nitrogenase protein alpha chain: AC
Nitrogenase FeMo beta subunit protein NifK: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Nitrogenase protein alpha chain

Nitrogenase FeMo beta subunit protein NifK

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