SMTL ID : 1n2c.1

NITROGENASE COMPLEX FROM AZOTOBACTER VINELANDII STABILIZED BY ADP-TETRAFLUOROALUMINATE

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: 8 residues within 4Å: Chain A: A.64, Q.190, G.423, I.424, K.425, E.439, H.441 Ligands: CFM.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.441 Hydrogen bonds: A:Q.190, A:I.424, A:K.425, A:E.439 Salt bridges: A:H.441, A:H.441 HCA.5: 8 residues within 4Å: Chain C: A.64, Q.190, G.423, I.424, K.425, E.439, 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, C:K.425 Salt bridges: 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: 3 interactions with chain B, 2 interactions with chain D Metal complexes: B:D.352, B:D.352, B:D.356, D:R.107, D:E.108 CA.7: 5 residues within 4Å: Chain A: K.432 Chain B: R.107, E.108 Chain D: D.352, D.356 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Metal complexes: D:D.352, D:D.352, D:D.356, B:R.107, B:E.108

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

CLF.4: 19 residues within 4Å: Chain A: C.61, Y.63, P.84, V.85, G.86, C.87, Y.90, E.152, C.153, G.184 Chain B: C.69, P.71, S.91, G.93, C.94, Y.97, T.151, C.152, S.187 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A, Metal complexes: B:C.69, B:C.94, B:C.94, B:C.152, B:S.187, A:C.61, A:C.87, A:C.87, A:C.153 Salt bridges: A:E.152 CLF.8: 19 residues within 4Å: Chain C: C.61, Y.63, P.84, V.85, G.86, C.87, Y.90, E.152, C.153, G.184 Chain D: C.69, P.71, S.91, G.93, C.94, Y.97, T.151, C.152, S.187 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C, 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 Salt bridges: C:E.152

4 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 6 residues within 4Å: Chain E: S.16, D.39, D.43, D.125 Ligands: ALF.10, ADP.11 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.16, E:D.39 MG.12: 6 residues within 4Å: Chain F: S.16, D.39, D.43, D.125 Ligands: ALF.13, ADP.15 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:S.16, F:D.39 MG.16: 6 residues within 4Å: Chain G: S.16, D.39, D.43, D.125 Ligands: ALF.17, ADP.19 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:S.16, G:D.39 MG.20: 6 residues within 4Å: Chain H: S.16, D.39, D.43, D.125 Ligands: ALF.21, ADP.22 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:S.16, H:D.39

4 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.10: 13 residues within 4Å: Chain E: K.10, G.11, G.12, K.15, S.16, D.39, K.41, D.43, G.128 Chain F: K.10, D.129 Ligands: MG.9, ADP.11 No protein-ligand interaction detected (PLIP) ALF.13: 12 residues within 4Å: Chain E: K.10 Chain F: K.10, G.11, G.12, K.15, S.16, D.39, K.41, D.43, G.128 Ligands: MG.12, ADP.15 No protein-ligand interaction detected (PLIP) ALF.17: 13 residues within 4Å: Chain G: K.10, G.11, G.12, K.15, S.16, D.39, K.41, D.43, G.128 Chain H: K.10, D.129 Ligands: MG.16, ADP.19 No protein-ligand interaction detected (PLIP) ALF.21: 12 residues within 4Å: Chain G: K.10 Chain H: K.10, G.11, G.12, K.15, S.16, D.39, K.41, D.43, G.128 Ligands: MG.20, ADP.22 No protein-ligand interaction detected (PLIP)

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.11: 22 residues within 4Å: Chain E: K.10, G.11, G.12, I.13, G.14, K.15, S.16, T.17, N.185, V.211, P.212, R.213, D.214, V.217, Q.218, E.221, Q.236 Chain F: K.10, E.154, M.156 Ligands: MG.9, ALF.10 18 PLIP interactions: 15 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:G.14, E:K.15, E:S.16, E:S.16, E:T.17, E:T.17, E:D.43, E:N.185, E:N.185, E:D.214, E:Q.218, E:E.221, E:Q.236, F:M.155 Salt bridges: E:K.15, F:K.10, F:K.10 pi-Cation interactions: E:R.213 ADP.15: 22 residues within 4Å: Chain E: K.10, E.154, M.156 Chain F: K.10, G.11, G.12, I.13, G.14, K.15, S.16, T.17, N.185, V.211, P.212, R.213, D.214, V.217, Q.218, E.221, Q.236 Ligands: MG.12, ALF.13 19 PLIP interactions: 16 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:G.14, F:K.15, F:S.16, F:S.16, F:T.17, F:T.17, F:D.43, F:N.185, F:N.185, F:R.213, F:D.214, F:Q.218, F:E.221, F:Q.236, E:M.155 Salt bridges: F:K.15, E:K.10, E:K.10 pi-Cation interactions: F:R.213 ADP.19: 22 residues within 4Å: Chain G: K.10, G.11, G.12, I.13, G.14, K.15, S.16, T.17, N.185, V.211, P.212, R.213, D.214, V.217, Q.218, E.221, Q.236 Chain H: K.10, E.154, M.156 Ligands: MG.16, ALF.17 16 PLIP interactions: 14 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:G.14, G:K.15, G:S.16, G:S.16, G:T.17, G:T.17, G:N.185, G:N.185, G:D.214, G:Q.218, G:E.221, G:Q.236 Salt bridges: G:K.15, H:K.10, H:K.10 pi-Cation interactions: G:R.213 ADP.22: 22 residues within 4Å: Chain G: K.10, E.154, M.156 Chain H: K.10, G.11, G.12, I.13, G.14, K.15, S.16, T.17, N.185, V.211, P.212, R.213, D.214, V.217, Q.218, E.221, Q.236 Ligands: MG.20, ALF.21 18 PLIP interactions: 15 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:G.12, H:G.14, H:K.15, H:S.16, H:S.16, H:T.17, H:T.17, H:N.185, H:N.185, H:D.214, H:Q.218, H:E.221, H:Q.236, G:M.155 Salt bridges: H:K.15, G:K.10, G:K.10 pi-Cation interactions: H:R.213

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

SF4.14: 14 residues within 4Å: Chain A: L.157, I.158 Chain B: V.156, I.157 Chain E: C.97, A.98, G.99, V.131, C.132 Chain F: C.97, A.98, G.99, V.131, C.132 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F, Metal complexes: E:C.97, E:C.132, F:C.97, F:C.132 SF4.18: 14 residues within 4Å: Chain C: L.157, I.158 Chain D: V.156, I.157 Chain G: C.97, A.98, G.99, V.131, C.132 Chain H: C.97, A.98, G.99, V.131, C.132 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain H, Metal complexes: G:C.97, G:C.132, H:C.97, H:C.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schindelin, H. et al., Structure of ADP x AIF4(-)-stabilized nitrogenase complex and its implications for signal transduction. Nature (1997)

Release Date

1997-11-12

Peptides

NITROGENASE MOLYBDENUM-IRON PROTEIN: AC
NITROGENASE MOLYBDENUM-IRON PROTEIN: 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

NITROGENASE MOLYBDENUM-IRON PROTEIN

NITROGENASE IRON PROTEIN

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