SMTL ID : 1g21.1

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 3.00 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: I.59, R.96, Q.191, G.424, I.425, K.426, E.427, H.442 Ligands: CFM.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.442 Hydrogen bonds: A:I.425 Salt bridges: A:K.426, A:K.426, A:H.442, A:H.442 HCA.5: 8 residues within 4Å: Chain C: A.65, R.96, Q.191, G.424, I.425, E.440, H.442 Ligands: CFM.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.425, C:E.440 Salt bridges: C:H.442, C:H.442

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

CFM.2: 16 residues within 4Å: Chain A: V.70, R.96, Q.191, 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: 16 residues within 4Å: Chain C: V.70, R.96, Q.191, 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 CLF: FE(8)-S(7) CLUSTER(Non-covalent)

CLF.3: 17 residues within 4Å: Chain A: C.62, Y.64, P.85, G.87, C.88, E.153, C.154, G.185 Chain B: C.70, P.72, S.92, C.95, Y.98, F.99, T.152, C.153, S.188 12 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, 2 Ligand-Ligand interactions Salt bridges: A:E.153 Metal complexes: A:C.62, A:C.88, A:C.88, A:C.154, B:C.70, B:C.95, B:C.95, B:C.153, B:S.188, CLF.3, CLF.3 CLF.8: 16 residues within 4Å: Chain C: C.62, Y.64, P.85, G.87, C.88, C.154, G.185 Chain D: C.70, P.72, S.92, C.95, Y.98, F.99, T.152, C.153, S.188 12 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C, 2 Ligand-Ligand interactions Metal complexes: D:C.70, D:C.95, D:C.95, D:C.153, D:S.188, C:C.62, C:C.88, C:C.88, C:C.154, CLF.8, CLF.8 Salt bridges: C:E.153

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain B: R.108, E.109 Chain D: D.353, D.357 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Metal complexes: D:D.353, D:D.357, B:R.108, B:E.109, B:E.109 CA.7: 4 residues within 4Å: Chain B: D.353, D.357 Chain D: R.108, E.109 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Metal complexes: D:R.108, D:E.109, B:D.353, B:D.357

4 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 5 residues within 4Å: Chain E: S.17, D.40, D.44, D.126 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.17 MG.11: 3 residues within 4Å: Chain F: S.17, D.126 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.17 MG.14: 4 residues within 4Å: Chain H: S.17, D.44, D.126 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.17 MG.17: 3 residues within 4Å: Chain G: S.17, D.126 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.17

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.10: 21 residues within 4Å: Chain E: G.12, G.13, I.14, G.15, K.16, S.17, T.18, D.40, K.42, R.47, N.185, V.211, P.212, R.213, D.214, V.217, E.221, Q.236 Chain F: K.11, M.156 Ligands: MG.9 23 PLIP interactions: 21 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.13, E:I.14, E:G.15, E:K.16, E:S.17, E:T.18, E:D.40, E:D.44, E:D.44, E:R.47, E:N.185, E:N.185, E:D.214, E:V.217, E:E.221, E:Q.236 Salt bridges: E:K.16, E:K.16, E:K.42, F:K.11, F:K.11 pi-Cation interactions: E:R.213, E:R.213 ATP.13: 21 residues within 4Å: Chain E: M.156 Chain F: G.12, G.13, I.14, G.15, K.16, S.17, T.18, D.40, K.42, N.185, R.187, P.212, R.213, D.214, V.217, Q.218, E.221, Q.236, Y.240 Ligands: MG.11 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:G.13, F:I.14, F:G.15, F:K.16, F:S.17, F:S.17, F:T.18, F:T.18, F:D.40, F:D.40, F:R.187, F:D.214, F:Q.218, F:E.221, F:Y.240, F:Y.240 Salt bridges: F:K.16, F:K.16, F:K.42 ATP.16: 21 residues within 4Å: Chain G: G.12, G.13, I.14, G.15, K.16, S.17, T.18, D.40, N.185, S.186, V.211, P.212, R.213, D.214, V.217, E.221, Q.236, Y.240 Chain H: K.11, M.156 Ligands: MG.17 15 PLIP interactions: 13 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:G.13, G:I.14, G:G.15, G:K.16, G:S.17, G:S.17, G:T.18, G:D.40, G:S.186, G:R.213, G:V.217, G:E.221 Salt bridges: G:K.16, H:K.11, H:K.11 ATP.18: 20 residues within 4Å: Chain G: M.156 Chain H: G.12, G.13, I.14, G.15, K.16, S.17, T.18, D.40, K.42, D.126, N.185, P.212, R.213, D.214, V.217, E.221, Q.236, Y.240 Ligands: MG.14 21 PLIP interactions: 18 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:G.13, H:I.14, H:G.15, H:K.16, H:S.17, H:S.17, H:T.18, H:T.18, H:D.40, H:D.40, H:N.185, H:D.214, H:E.221, H:Q.236, H:Y.240, H:Y.240, G:M.156 Salt bridges: H:K.16, H:K.16, G:K.11, G:K.11

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

SF4.12: 11 residues within 4Å: Chain A: L.158 Chain B: V.157 Chain E: C.98, A.99, G.100, C.132 Chain F: C.98, A.99, G.100, V.131, 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 SF4.15: 12 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, V.131, C.132 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H, Metal complexes: G:C.98, G:C.132, H:C.98, H: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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