SMTL ID : 1m1y.2 (1 other biounit)

Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-2-2-4-mer

Ligands

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

HCA.1: 7 residues within 4Å: Chain A: A.64, Q.190, G.423, I.424, K.425, H.441 Ligands: CFM.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.441 Hydrogen bonds: A:Q.190, A:I.424 Salt bridges: A:K.425, A:H.441, A:H.441 HCA.5: 7 residues within 4Å: Chain C: A.64, Q.190, G.423, I.424, K.425, H.441 Ligands: CFM.6 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:H.441 Hydrogen bonds: C:Q.190, C:I.424 Salt bridges: C:K.425, C:H.441, C:H.441

2 x CFM: FE-MO-S CLUSTER(Non-covalent)

CFM.2: 15 residues within 4Å: Chain A: V.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 CFM.6: 15 residues within 4Å: Chain C: V.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.5 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.379 Metal complexes: C:C.274

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain B: D.352, D.356 Chain C: K.432 Chain D: R.107, E.108 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Metal complexes: D:R.107, D:E.108, B:D.352, B:D.352, B:D.356 CA.8: 5 residues within 4Å: Chain A: K.432 Chain B: R.107, E.108 Chain D: D.352, D.356 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Metal complexes: B:R.107, B:E.108, D:D.352, D:D.352, D:D.356

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

CLF.4: 16 residues within 4Å: Chain A: C.61, Y.63, P.84, G.86, C.87, Y.90, E.152, C.153 Chain B: C.69, P.71, S.91, G.93, C.94, T.151, C.152, S.187 12 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, 2 Ligand-Ligand interactions Salt bridges: A:E.152 Metal complexes: A:C.61, A:C.87, A:C.87, A:C.153, B:C.69, B:C.94, B:C.94, B:C.152, B:S.187, CLF.4, CLF.4 CLF.7: 16 residues within 4Å: Chain C: C.61, Y.63, P.84, G.86, C.87, Y.90, C.153, G.184 Chain D: C.69, P.71, S.91, G.93, C.94, T.151, C.152, S.187 12 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C, 2 Ligand-Ligand interactions Metal complexes: D:C.69, D:C.94, D:C.94, D:C.152, D:S.187, C:C.61, C:C.87, C:C.87, C:C.153, CLF.7, CLF.7 Salt bridges: C:E.152

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.9: 11 residues within 4Å: Chain E: C.97, A.98, C.132, G.133, G.134 Chain F: C.97, A.98, G.99, C.132, G.133, G.134 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F, Metal complexes: E:C.97, E:C.132, F:C.97, F:C.132 pi-Cation interactions: F:F.135 SF4.10: 9 residues within 4Å: Chain G: C.97, A.98, C.132, G.133, G.134 Chain H: C.97, A.98, C.132, G.134 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain H, Metal complexes: G:C.97, G:C.132, H:C.97, H:C.132 pi-Cation interactions: H:F.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmid, B. et al., Biochemical and Structural Characterization of the Crosslinked Complex of Nitrogenase: Comparison to the ADP-AlF4- Stabilized Structure. Biochemistry (2002)

Release Date

2003-02-11

Peptides

Nitrogenase molybdenum-iron protein alpha chain: AC
Nitrogenase molybdenum-iron protein beta chain: BD
nitrogenase IRON protein 1: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

C
K

B
J

D
L

E
M

F
N

G
O

H
P

Nitrogenase molybdenum-iron protein alpha chain

Nitrogenase molybdenum-iron protein beta chain

nitrogenase IRON protein 1

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