SMTL ID : 5koh.1

Nitrogenase MoFeP from Gluconacetobacter diazotrophicus in dithionite reduced state

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: 8 residues within 4Å: Chain A: A.81, R.112, Q.207, G.440, I.441, K.442, H.458 Ligands: ICS.2 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A Water bridges: B:R.104, B:R.104, A:E.396, A:E.396, A:K.442, A:K.442, A:K.442 Hydrophobic interactions: A:H.458 Hydrogen bonds: A:Q.207, A:I.441 Salt bridges: A:K.442, A:H.458, A:H.458 HCA.8: 8 residues within 4Å: Chain C: A.81, R.112, Q.207, G.440, I.441, K.442, H.458 Ligands: ICS.9 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:H.458 Hydrogen bonds: C:Q.207, C:I.441 Water bridges: C:Q.111, C:R.113, C:K.442, C:K.442, C:K.442, C:Q.456, C:Q.456, C:S.459, D:Y.97, D:R.104, 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.9: 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.8 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.396 Metal complexes: C:C.291

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 11 residues within 4Å: Chain A: M.73, G.422, L.425, E.426, K.442, E.443, P.446, M.450 Chain B: R.99, Y.265, M.267 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.425, A:E.443, A:P.446 Hydrogen bonds: A:K.442, B:R.99 MRD.4: 7 residues within 4Å: Chain A: E.312, Y.313, Q.320, A.323, S.324, K.327, Y.409 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.323 Hydrogen bonds: A:Q.320 Water bridges: A:Y.409

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

CLF.5: 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 9 PLIP interactions: 5 interactions with chain A, 4 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:C.152 CLF.11: 18 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, S.91, G.93, C.94, Y.97, Y.98, T.151, C.152, A.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.78, C:C.104, C:C.104, C:C.170 Salt bridges: C:E.169

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

FE.6: 5 residues within 4Å: Chain B: D.348, D.352 Chain D: K.107, E.108, R.469 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Metal complexes: B:D.348, B:D.352, D:K.107, D:E.108 FE.7: 5 residues within 4Å: Chain B: K.107, E.108, R.469 Chain D: D.348, D.352 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:D.348, D:D.352, B:K.107, B:E.108, H2O.58

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.10: 10 residues within 4Å: Chain C: M.73, G.422, L.425, E.426, K.442, E.443, P.446, M.450 Chain D: R.99, M.267 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.425, C:E.443, C:P.446 Hydrogen bonds: C:K.442, D:R.99

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

2016-09-21

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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