SMTL ID : 4wes.1

Nitrogenase molybdenum-iron protein from Clostridium pasteurianum at 1.08 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.08 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.56, R.87, Q.182, G.464, I.465, K.466, H.482 Ligands: ICS.2 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.482 Hydrogen bonds: A:Q.182, A:I.465 Water bridges: A:G.86, A:K.466, A:K.466, A:K.466, A:K.466, B:Y.51, B:Y.51, B:R.58 Salt bridges: A:K.466, A:H.482, A:H.482 HCA.7: 8 residues within 4Å: Chain C: A.56, R.87, Q.182, G.464, I.465, K.466, H.482 Ligands: ICS.8 15 PLIP interactions: 2 interactions with chain D, 13 interactions with chain C Water bridges: D:S.50, D:R.58, C:R.88, C:E.368, C:K.466, C:K.466, C:K.466, C:Q.480, C:Q.480 Hydrophobic interactions: C:H.482 Hydrogen bonds: C:Q.182, C:I.465 Salt bridges: C:K.466, C:H.482, C:H.482

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

ICS.2: 15 residues within 4Å: Chain A: V.61, R.87, H.186, Y.216, I.218, C.262, S.265, V.343, G.344, G.345, S.346, R.347, F.369, H.482 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.368 Metal complexes: A:C.262 ICS.8: 15 residues within 4Å: Chain C: V.61, R.87, H.186, Y.216, I.218, C.262, S.265, V.343, G.344, G.345, S.346, R.347, F.369, H.482 Ligands: HCA.7 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.368 Metal complexes: C:C.262

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

MPD.3: 5 residues within 4Å: Chain A: D.256, C.302, F.303, V.408, I.409 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.303, A:F.303

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

CLF.4: 19 residues within 4Å: Chain A: C.53, Y.55, P.76, I.77, G.78, C.79, T.144, C.145, G.176 Chain B: C.23, P.25, S.45, G.47, C.48, Y.51, H.52, T.105, C.106, S.141 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A, Metal complexes: B:C.23, B:C.48, B:C.48, B:C.106, B:S.141, A:C.53, A:C.79, A:C.79, A:C.145 CLF.9: 19 residues within 4Å: Chain C: C.53, Y.55, P.76, I.77, G.78, C.79, T.144, C.145, G.176 Chain D: C.23, P.25, S.45, G.47, C.48, Y.51, H.52, T.105, C.106, S.141 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C, Metal complexes: D:C.23, D:C.48, D:C.48, D:C.106, D:S.141, C:C.53, C:C.79, C:C.79, C:C.145

2 x FE2: FE (II) ION(Non-covalent)

FE2.5: 4 residues within 4Å: Chain B: D.301, D.305 Chain D: K.61, E.62 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.301, B:D.305, D:K.61, D:E.62, H2O.42, H2O.92 FE2.6: 4 residues within 4Å: Chain B: K.61, E.62 Chain D: D.301, D.305 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:K.61, B:E.62, D:D.301, D:D.305, H2O.42, H2O.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L.M. et al., Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 angstrom resolution: comparison with the Azotobacter vinelandii MoFe protein. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-02-11

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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