SMTL ID : 4wn9.1

Structure of the Nitrogenase MoFe Protein from Clostridium pasteurianum Pressurized with Xenon

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)

HCA.1: 9 residues within 4Å: Chain A: A.54, R.85, Q.180, G.462, I.463, K.464, H.480 Chain B: Y.51 Ligands: ICS.2 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.480 Hydrogen bonds: A:Q.180, A:I.463 Water bridges: A:G.84, A:R.86, A:K.464, A:K.464, A:K.464, A:K.464, A:K.464, B:Y.51, B:Y.51, B:R.58 Salt bridges: A:K.464, A:H.480, A:H.480 HCA.10: 8 residues within 4Å: Chain C: R.85, Q.180, G.462, I.463, K.464, Q.478, H.480 Ligands: ICS.11 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:H.480 Hydrogen bonds: C:Q.180, C:I.463 Water bridges: C:G.84, C:K.464, C:K.464, C:K.464, D:S.50, D:Y.51, D:R.58 Salt bridges: C:K.464, C:H.480, C:H.480

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

ICS.2: 16 residues within 4Å: Chain A: V.59, R.85, H.184, Y.214, I.216, C.260, S.263, V.341, G.342, G.343, S.344, R.345, E.366, F.367, H.480 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.366 Metal complexes: A:C.260 ICS.11: 15 residues within 4Å: Chain C: V.59, R.85, H.184, Y.214, I.216, C.260, S.263, V.341, G.342, G.343, S.344, R.345, F.367, H.480 Ligands: HCA.10 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.366 Metal complexes: C:C.260

6 x XE: XENON(Non-covalent)

XE.3: 4 residues within 4Å: Chain A: D.254, C.300, F.301, I.407 No protein-ligand interaction detected (PLIP) XE.4: 5 residues within 4Å: Chain A: K.477, Y.488, F.497, E.500, L.501 No protein-ligand interaction detected (PLIP) XE.6: 4 residues within 4Å: Chain B: R.12, A.14, L.15, R.16 No protein-ligand interaction detected (PLIP) XE.12: 5 residues within 4Å: Chain C: K.477, Y.488, F.497, E.500, L.501 No protein-ligand interaction detected (PLIP) XE.13: 4 residues within 4Å: Chain C: D.254, C.300, F.301, V.406 No protein-ligand interaction detected (PLIP) XE.15: 4 residues within 4Å: Chain D: R.12, A.14, L.15, R.16 No protein-ligand interaction detected (PLIP)

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

CLF.5: 19 residues within 4Å: Chain A: C.51, Y.53, P.74, I.75, G.76, C.77, T.142, C.143, G.174 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.51, A:C.77, A:C.77, A:C.143 CLF.14: 19 residues within 4Å: Chain C: C.51, Y.53, P.74, I.75, G.76, C.77, T.142, C.143, G.174 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: 4 interactions with chain C, 5 interactions with chain D, Metal complexes: C:C.51, C:C.77, C:C.77, C:C.143, D:C.23, D:C.48, D:C.48, D:C.106, D:S.141

2 x PRO: PROLINE(Non-covalent)

PRO.7: 8 residues within 4Å: Chain B: Y.30, H.59, F.60, F.178, V.179, G.180, F.411, K.424 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.30, B:F.178, B:F.178 Hydrogen bonds: B:G.180, B:D.183 Water bridges: B:H.59, B:G.410, P.7 Salt bridges: B:H.59, B:K.424 PRO.16: 9 residues within 4Å: Chain D: Y.30, H.59, F.60, F.178, V.179, G.180, G.410, F.411, K.424 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:Y.30, D:F.60, D:F.411 Hydrogen bonds: D:G.180 Water bridges: D:H.59, D:G.410, D:G.410, D:F.411 Salt bridges: D:H.59, D:K.424

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

FE.8: 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.28, H2O.45 FE.9: 4 residues within 4Å: Chain B: K.61, E.62 Chain D: D.301, D.305 6 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:D.301, D:D.305, B:K.61, B:E.62, H2O.15, H2O.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morrison, C.N. et al., Substrate Pathways in the Nitrogenase MoFe Protein by Experimental Identification of Small Molecule Binding Sites. Biochemistry (2015)

Release Date

2015-03-18

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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