SMTL ID : 1m34.1 (1 other biounit)

Nitrogenase Complex From Azotobacter Vinelandii Stabilized By ADP-Tetrafluoroaluminate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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.64, G.94, R.95, Q.190, G.423, I.424, K.425, H.441 Ligands: CFM.2 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.190, A:I.424 Water bridges: A:G.94, A:K.425, A:H.441, B:Y.97 Salt bridges: A:K.425, A:H.441 HCA.5: 9 residues within 4Å: Chain C: A.64, V.69, R.95, Q.190, G.423, I.424, K.425, H.441 Ligands: CFM.6 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:H.441 Hydrogen bonds: C:G.94, C:Q.190, C:I.424, C:H.441 Water bridges: C:K.425, C:K.425, C:E.439, D:Y.97, D:R.104, D:R.104 Salt bridges: C:K.425, 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: 14 residues within 4Å: Chain C: V.69, R.95, H.194, Y.228, I.230, C.274, S.277, 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: 4 residues within 4Å: Chain B: D.352, D.356 Chain D: R.107, E.108 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:R.107, D:E.108, B:D.352, B:D.356, H2O.12 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.25

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

CLF.4: 17 residues within 4Å: Chain A: C.61, Y.63, P.84, V.85, C.87, Y.90, 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: 17 residues within 4Å: Chain C: C.61, Y.63, P.84, V.85, C.87, Y.90, E.152, C.153, G.184 Chain D: C.69, P.71, S.91, G.93, C.94, Y.97, C.152, S.187 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D, Salt bridges: C:E.152 Metal complexes: C:C.61, C:C.87, C:C.87, C:C.153, D:C.69, D:C.94, D:C.94, D:C.152, D:S.187

4 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain E: S.16 Ligands: ALF.10, ADP.12 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.16, H2O.26, H2O.26, H2O.26 MG.13: 3 residues within 4Å: Chain F: S.16 Ligands: ALF.14, ADP.15 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.16, H2O.28, H2O.28, H2O.28 MG.16: 4 residues within 4Å: Chain G: S.16, D.39 Ligands: ALF.17, ADP.19 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:S.16, H2O.30, H2O.30, H2O.30 MG.20: 5 residues within 4Å: Chain H: S.16, D.39, D.43 Ligands: ALF.21, ADP.22 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:S.16, H2O.31, H2O.31, H2O.31

4 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.10: 12 residues within 4Å: Chain E: G.11, G.12, K.15, D.39, K.41, L.127, G.128 Chain F: K.10, G.11, D.129 Ligands: MG.9, ADP.12 No protein-ligand interaction detected (PLIP) ALF.14: 12 residues within 4Å: Chain E: K.10, G.11, D.129 Chain F: G.11, G.12, K.15, D.39, K.41, L.127, G.128 Ligands: MG.13, ADP.15 No protein-ligand interaction detected (PLIP) ALF.17: 12 residues within 4Å: Chain G: G.11, G.12, K.15, D.39, K.41, L.127, G.128 Chain H: K.10, G.11, D.129 Ligands: MG.16, ADP.19 No protein-ligand interaction detected (PLIP) ALF.21: 12 residues within 4Å: Chain G: K.10, G.11, D.129 Chain H: G.11, G.12, K.15, D.39, K.41, L.127, G.128 Ligands: MG.20, ADP.22 No protein-ligand interaction detected (PLIP)

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

SF4.11: 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 F, 2 interactions with chain E, Metal complexes: F:C.97, F:C.132, E:C.97, E: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

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

ADP.12: 22 residues within 4Å: Chain E: K.10, G.12, I.13, G.14, K.15, S.16, T.17, N.185, P.212, R.213, D.214, V.217, Q.218, E.221, Q.236, Y.240 Chain F: K.10, E.154, M.155, M.156 Ligands: MG.9, ALF.10 23 PLIP interactions: 19 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:K.10, E:G.12, E:I.13, E:G.14, E:K.15, E:S.16, E:T.17, E:T.17, E:N.185, E:P.212, E:D.214, E:Q.218, E:E.221, E:Q.236, F:M.156 Water bridges: E:K.15, E:K.15, E:S.16, F:K.10 Salt bridges: E:K.15, F:K.10, F:K.10 pi-Cation interactions: E:R.213 ADP.15: 23 residues within 4Å: Chain E: K.10, E.154, M.155, M.156 Chain F: K.10, 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, Y.240 Ligands: MG.13, ALF.14 22 PLIP interactions: 18 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:K.10, F:G.12, F:I.13, F:G.14, F:K.15, F:S.16, F:T.17, F:T.17, F:N.185, F:P.212, F:D.214, F:Q.218, F:E.221, F:Q.236, E:M.156 Water bridges: F:S.16, F:K.41, F:R.213, E:K.10 Salt bridges: F:K.15, E:K.10, E:K.10 ADP.19: 23 residues within 4Å: Chain G: K.10, 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, Y.240 Chain H: K.10, E.154, M.155, M.156 Ligands: MG.16, ALF.17 26 PLIP interactions: 20 interactions with chain G, 6 interactions with chain H Hydrogen bonds: G:K.10, G:G.12, G:I.13, G:G.14, G:K.15, G:S.16, G:T.17, G:T.17, G:N.185, G:P.212, G:D.214, G:Q.218, G:E.221, G:Q.236, G:Y.240, H:M.155, H:M.156 Water bridges: G:K.15, G:D.125, G:R.213, G:R.213, H:K.10, H:K.10 Salt bridges: G:K.15, H:K.10, H:K.10 ADP.22: 23 residues within 4Å: Chain G: K.10, E.154, M.155, M.156 Chain H: K.10, G.11, G.12, I.13, G.14, K.15, S.16, T.17, N.185, P.212, R.213, D.214, V.217, Q.218, E.221, Q.236, Y.240 Ligands: MG.20, ALF.21 25 PLIP interactions: 4 interactions with chain G, 21 interactions with chain H Hydrogen bonds: G:M.156, H:G.12, H:I.13, H:G.14, H:K.15, H:S.16, H:T.17, H:T.17, H:N.185, H:P.212, H:R.213, H:R.213, H:D.214, H:Q.218, H:E.221, H:Q.236, H:Y.240 Water bridges: G:K.10, H:S.16, H:S.16, H:D.125 Salt bridges: G:K.10, G:K.10, H:K.15 pi-Cation interactions: H:R.213

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
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 1

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