SMTL ID : 4wza.1

Asymmetric Nucleotide Binding in the Nitrogenase Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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.62, R.93, Q.188, G.421, I.422, H.439 Ligands: ICS.2 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A Water bridges: B:R.104, A:G.92, A:K.423, A:K.423, A:K.423, A:K.423, A:K.423 Hydrophobic interactions: A:H.439 Hydrogen bonds: A:Q.188, A:I.422 Salt bridges: A:K.423, A:H.439, A:H.439 HCA.5: 8 residues within 4Å: Chain C: A.62, R.93, Q.188, G.421, I.422, K.423, H.439 Ligands: ICS.6 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:H.439 Hydrogen bonds: C:Q.188, C:I.422 Water bridges: C:G.92, C:E.377, C:E.377, C:K.423, C:K.423, C:K.423, D:R.104 Salt bridges: C:K.423, C:H.439, C:H.439

2 x ICS: iron-sulfur-molybdenum cluster with interstitial carbon(Non-covalent)

ICS.2: 15 residues within 4Å: Chain A: V.67, R.93, H.192, Y.226, I.228, C.272, S.275, I.352, G.353, G.354, L.355, R.356, F.378, H.439 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.377 Metal complexes: A:C.272 ICS.6: 15 residues within 4Å: Chain C: V.67, R.93, H.192, Y.226, I.228, C.272, S.275, I.352, G.353, G.354, L.355, R.356, F.378, H.439 Ligands: HCA.5 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.377 Metal complexes: C:C.272

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

CLF.3: 19 residues within 4Å: Chain A: C.59, Y.61, P.82, G.84, C.85, Y.88, E.150, C.151, G.182 Chain B: C.69, P.71, S.91, G.93, C.94, Y.97, F.98, T.151, C.152, S.187 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B, Salt bridges: A:E.150 Metal complexes: A:C.59, A:C.85, A:C.85, A:C.151, B:C.69, B:C.94, B:C.94, B:C.152 CLF.7: 19 residues within 4Å: Chain C: C.59, Y.61, P.82, G.84, C.85, Y.88, E.150, C.151, G.182 Chain D: C.69, P.71, S.91, G.93, C.94, Y.97, F.98, T.151, C.152, S.187 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain D, Salt bridges: C:E.150 Metal complexes: C:C.59, C:C.85, C:C.85, C:C.151, D:C.69, D:C.94, D:C.94, D:C.152

2 x FE: FE (III) ION(Non-covalent)

FE.4: 4 residues within 4Å: Chain B: R.107, E.108 Chain D: D.352, D.356 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:R.107, B:E.108, D:D.352, D:D.356, H2O.17, H2O.66 FE.8: 4 residues within 4Å: Chain B: D.352, D.356 Chain D: R.107, E.108 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.352, B:D.356, D:R.107, D:E.108, H2O.16, H2O.65

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

SF4.9: 11 residues within 4Å: Chain A: L.155 Chain B: V.156 Chain E: C.97, A.98, G.99, V.131, C.132 Chain F: C.97, A.98, G.99, 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 SF4.14: 13 residues within 4Å: Chain C: L.155 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 H, 2 interactions with chain G, Metal complexes: H:C.97, H:C.132, G:C.97, G:C.132

4 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain E: S.16, D.39, D.43, D.125 Ligands: ADP.11 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:S.16, H2O.69, H2O.69, H2O.69, H2O.69 MG.12: 4 residues within 4Å: Chain F: S.16, D.43, D.125 Ligands: ACP.13 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.16, H2O.71, H2O.71, H2O.72 MG.15: 4 residues within 4Å: Chain G: S.16, D.39, D.43 Ligands: ADP.16 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:S.16, H2O.75, H2O.75, H2O.75, H2O.76 MG.17: 2 residues within 4Å: Chain H: S.16 Ligands: ACP.18 4 PLIP interactions: 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:S.16, H2O.80, H2O.80, H2O.80

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

ADP.11: 20 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, E.221, Q.236, Y.240 Chain F: K.10, M.156 Ligands: MG.10 22 PLIP interactions: 21 interactions with chain E, 1 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:R.213, E:D.214, E:E.221, E:Q.236, E:Y.240 Water bridges: E:K.15, E:K.15, E:S.16, E:D.39 Salt bridges: E:K.15, F:K.10 pi-Cation interactions: E:R.213 ADP.16: 21 residues within 4Å: Chain G: K.10, G.11, G.12, I.13, G.14, K.15, S.16, T.17, K.41, N.185, V.211, P.212, R.213, D.214, V.217, Q.218, E.221, Q.236, Y.240 Chain H: M.156 Ligands: MG.15 27 PLIP interactions: 26 interactions with chain G, 1 interactions with chain H Hydrogen bonds: 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:R.213, G:D.214, G:Q.218, G:E.221, G:Q.236, G:Y.240 Water bridges: G:S.16, G:D.39, G:K.41, G:K.41, G:K.41, G:K.41, G:R.46, G:D.125, H:K.10 Salt bridges: G:K.15, G:K.41 pi-Cation interactions: G:R.213

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.13: 24 residues within 4Å: Chain E: K.10, M.156 Chain F: K.10, G.11, G.12, I.13, G.14, K.15, S.16, T.17, D.39, K.41, L.127, G.128, N.185, V.211, P.212, R.213, D.214, V.217, Q.218, E.221, Q.236 Ligands: MG.12 24 PLIP interactions: 23 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.12, F:I.13, F:G.14, F:K.15, F:K.15, F:K.15, F:S.16, F:T.17, F:T.17, F:D.39, F:D.39, F:K.41, F:G.128, F:N.185, F:P.212, F:D.214, F:Q.218, F:E.221, F:Q.236, E:K.10 Water bridges: F:S.16, F:S.16, F:S.16 pi-Cation interactions: F:R.213 ACP.18: 24 residues within 4Å: Chain G: K.10, M.156 Chain H: K.10, G.11, G.12, I.13, G.14, K.15, S.16, T.17, D.39, K.41, L.127, G.128, N.185, V.211, P.212, R.213, D.214, V.217, Q.218, E.221, Q.236 Ligands: MG.17 27 PLIP interactions: 24 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:G.12, H:I.13, H:G.14, H:K.15, H:K.15, H:K.15, H:S.16, H:T.17, H:T.17, H:D.39, H:D.39, H:K.41, H:G.128, H:N.185, H:P.212, H:R.213, H:D.214, H:Q.218, H:E.221, H:Q.236, G:K.10 Water bridges: H:S.16, H:S.16, H:S.16, G:K.10, G:M.156 pi-Cation interactions: H:R.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tezcan, F.A. et al., Structural evidence for asymmetrical nucleotide interactions in nitrogenase. J.Am.Chem.Soc. (2015)

Release Date

2014-12-31

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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