SMTL ID : 1g20.1

MGATP-BOUND AND NUCLEOTIDE-FREE STRUCTURES OF A NITROGENASE PROTEIN COMPLEX BETWEEN LEU127DEL-FE PROTEIN AND THE MOFE PROTEIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-4-mer

Ligands

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

HCA.1: 9 residues within 4Å: Chain A: A.65, R.96, Q.191, G.424, I.425, K.426, E.440, H.442 Ligands: CFM.2 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:H.442 Hydrogen bonds: A:Q.191, A:I.425, A:E.440 Water bridges: A:G.95, A:K.426, A:K.426, A:K.426, A:H.442, B:Y.98, B:Y.98, B:R.105, B:R.105 Salt bridges: A:K.426, A:H.442, A:H.442 HCA.5: 10 residues within 4Å: Chain C: A.65, G.95, R.96, Q.191, G.424, I.425, K.426, E.440, H.442 Ligands: CFM.6 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:H.442 Hydrogen bonds: C:Q.191, C:I.425 Water bridges: C:G.95, C:R.97, C:K.426, C:K.426, D:R.105 Salt bridges: C:K.426, C:H.442, C:H.442

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

CFM.2: 15 residues within 4Å: Chain A: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.380 Metal complexes: A:C.275 CFM.6: 15 residues within 4Å: Chain C: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442 Ligands: HCA.5 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.380 Metal complexes: C:C.275

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain B: D.353, D.357 Chain D: R.108, E.109 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:D.353, B:D.357, D:R.108, D:E.109, H2O.25 CA.7: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:R.108, B:E.109, D:D.353, D:D.357, H2O.9

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

CLF.4: 18 residues within 4Å: Chain A: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 Chain B: C.70, P.72, S.92, G.94, C.95, Y.98, T.152, C.153, S.188 12 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: B:C.70, B:C.95, B:C.95, B:C.153, B:S.188, A:C.62, A:C.88, A:C.88, A:C.154, CLF.4, CLF.4 Salt bridges: A:E.153 CLF.8: 18 residues within 4Å: Chain C: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185 Chain D: C.70, P.72, S.92, G.94, C.95, Y.98, T.152, C.153, S.188 12 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D, 2 Ligand-Ligand interactions Salt bridges: C:E.153 Metal complexes: C:C.62, C:C.88, C:C.88, C:C.154, D:C.70, D:C.95, D:C.95, D:C.153, D:S.188, CLF.8, CLF.8

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

SF4.9: 11 residues within 4Å: Chain A: L.158 Chain B: V.157, I.158 Chain E: C.98, A.99, G.100, C.132 Chain F: C.98, A.99, G.100, C.132 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E, Metal complexes: F:C.98, F:C.132, E:C.98, E:C.132 SF4.10: 11 residues within 4Å: Chain C: L.158 Chain D: V.157, I.158 Chain G: C.98, A.99, G.100, C.132 Chain H: C.98, A.99, G.100, C.132 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain G, Metal complexes: H:C.98, H:C.132, G:C.98, G:C.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chiu, H. et al., MgATP-Bound and nucleotide-free structures of a nitrogenase protein complex between the Leu 127 Delta-Fe-protein and the MoFe-protein. Biochemistry (2001)

Release Date

2001-01-31

Peptides

NITROGENASE MOLYBDENUM-IRON PROTEIN ALPHA CHAIN: AC
NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN: BD
NITROGENASE IRON PROTEIN: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

G
G

H
H

NITROGENASE MOLYBDENUM-IRON PROTEIN ALPHA CHAIN

NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN

NITROGENASE IRON PROTEIN

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