SMTL ID : 3k1a.1

Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70Ile MoFe protein variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 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.64, R.95, Q.190, G.423, I.424, K.425, H.441 Ligands: CFN.2 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.441 Hydrogen bonds: A:Q.190, A:I.424 Water bridges: A:E.379, A:E.379, A:K.425, A:K.425, A:E.439, B:Y.97 Salt bridges: A:K.425, A:H.441, A:H.441 HCA.6: 8 residues within 4Å: Chain C: A.64, R.95, Q.190, G.423, I.424, K.425, H.441 Ligands: CFN.5 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:H.441 Hydrogen bonds: C:Q.190, C:I.424 Water bridges: C:G.94, C:K.425, C:K.425, C:K.425, C:K.425, D:R.104 Salt bridges: C:K.425, C:H.441, C:H.441

2 x CFN: FE(7)-MO-S(9)-N CLUSTER(Non-covalent)

CFN.2: 15 residues within 4Å: Chain A: I.69, R.95, H.194, Y.228, I.230, C.274, S.277, I.354, G.355, G.356, L.357, R.358, F.380, H.441 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.379 Metal complexes: A:C.274 CFN.5: 15 residues within 4Å: Chain C: I.69, R.95, H.194, Y.228, I.230, C.274, S.277, I.354, G.355, G.356, L.357, R.358, F.380, H.441 Ligands: HCA.6 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.379 Metal complexes: C:C.274

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

CLF.3: 15 residues within 4Å: Chain A: C.61, P.84, G.86, C.87, E.152, C.153, G.184 Chain B: C.69, S.91, G.93, C.94, Y.97, T.151, C.152, S.187 9 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Salt bridges: A:E.152 Metal complexes: A:C.61, A:C.87, A:C.87, A:C.153, B:C.94, B:C.94, B:C.152, CLF.3 CLF.8: 15 residues within 4Å: Chain C: C.61, P.84, G.86, C.87, E.152, C.153, G.184 Chain D: C.69, S.91, G.93, C.94, Y.97, T.151, C.152, S.187 9 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D, 1 Ligand-Ligand interactions Salt bridges: C:E.152 Metal complexes: C:C.61, C:C.87, C:C.87, C:C.153, D:C.94, D:C.94, D:C.152, CLF.8

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain B: D.352, D.356 Chain D: R.107, E.108 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:D.352, B:D.356, D:R.107, D:E.108, H2O.16 CA.7: 4 residues within 4Å: Chain B: R.107, E.108 Chain D: D.352, D.356 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.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sarma, R. et al., Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70(Ile) MoFe protein variant. J.Inorg.Biochem. (2010)

Release Date

2010-02-16

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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