SMTL ID : 6n4l.1

Dithionite-reduced ADP-bound form of the nitrogenase Fe-protein from A. vinelandii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 21 residues within 4Å: Chain A: 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, Y.240 Chain B: M.156, M.274 Ligands: MG.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:K.10, A:G.12, A:I.13, A:G.14, A:K.15, A:S.16, A:T.17, A:T.17, A:N.185, A:P.212, A:D.214, A:Q.218, A:E.221, A:Q.236, A:Y.240 Water bridges: A:S.16, A:S.16, A:R.213, A:R.213, A:R.213, A:R.213, A:R.213 Salt bridges: A:K.15 pi-Cation interactions: A:R.213 ADP.4: 21 residues within 4Å: Chain A: M.156, M.274 Chain B: 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, Y.240 Ligands: MG.5 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:K.10, B:G.12, B:I.13, B:G.14, B:K.15, B:S.16, B:T.17, B:T.17, B:N.185, B:P.212, B:D.214, B:Q.218, B:E.221, B:Q.236 Water bridges: B:S.16, B:S.16, B:R.213, B:R.213, B:R.213, B:R.213, B:R.213, B:E.221, B:E.221 Salt bridges: B:K.15 pi-Cation interactions: B:R.213

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.16, D.39, D.43 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.16, H2O.2, H2O.2, H2O.3, H2O.4 MG.5: 4 residues within 4Å: Chain B: S.16, D.39, D.43 Ligands: ADP.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.16, H2O.12, H2O.12, H2O.14, H2O.14

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

SF4.3: 9 residues within 4Å: Chain A: C.97, A.98, C.132, G.133, F.135 Chain B: G.96, C.97, C.132 Ligands: SF4.6 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.97, A:C.132 SF4.6: 9 residues within 4Å: Chain A: G.96, C.97, C.132 Chain B: C.97, A.98, C.132, G.133, F.135 Ligands: SF4.3 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.97, B:C.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wenke, B.B. et al., Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S]2+/1+/0States of the Nitrogenase Fe-Protein. Angew. Chem. Int. Ed. Engl. (2019)

Release Date

2019-02-13

Peptides

Nitrogenase iron protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Nitrogenase iron protein 1

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