SMTL ID : 7tqk.1

Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (1 mM KSeCN)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: C.98, A.99, G.100, C.133, G.134, F.136 Chain B: C.98, C.133 Ligands: SFS.2, SF4.5, SFS.6 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.98, A:C.133 SF4.5: 11 residues within 4Å: Chain A: C.98, C.133 Chain B: C.98, A.99, G.100, C.133, G.134, F.136 Ligands: SF4.1, SFS.2, SFS.6 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.98, B:C.133

2 x SFS: Fe4-Se4 cluster(Non-covalent)

SFS.2: 11 residues within 4Å: Chain A: C.98, A.99, G.100, C.133, G.134, F.136 Chain B: C.98, C.133 Ligands: SF4.1, SF4.5, SFS.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.98, A:C.133 SFS.6: 11 residues within 4Å: Chain A: C.98, C.133 Chain B: C.98, A.99, G.100, C.133, G.134, F.136 Ligands: SF4.1, SFS.2, SF4.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.98, B:C.133

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

ADP.3: 19 residues within 4Å: Chain A: K.11, G.13, I.14, G.15, K.16, S.17, T.18, N.186, V.212, P.213, R.214, D.215, V.218, Q.219, E.222, Q.237, Y.241 Chain B: M.157 Ligands: MG.4 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:K.11, A:G.13, A:I.14, A:G.15, A:K.16, A:S.17, A:T.18, A:T.18, A:N.186, A:P.213, A:D.215, A:Q.219, A:E.222, A:Q.237 Water bridges: A:K.16, A:S.17, A:D.40, A:K.42, A:D.126, A:R.214, A:R.214, A:R.214 Salt bridges: A:K.16 pi-Cation interactions: A:R.214 ADP.7: 19 residues within 4Å: Chain A: M.157 Chain B: K.11, G.13, I.14, G.15, K.16, S.17, T.18, N.186, V.212, P.213, R.214, D.215, V.218, Q.219, E.222, Q.237, Y.241 Ligands: MG.8 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:K.11, B:G.13, B:I.14, B:G.15, B:K.16, B:S.17, B:T.18, B:T.18, B:N.186, B:P.213, B:D.215, B:Q.219, B:E.222, B:Q.237, B:Y.241 Water bridges: B:K.16, B:S.17, B:D.40, B:K.42, B:D.126, B:R.214, B:R.214, B:R.214 Salt bridges: B:K.16 pi-Cation interactions: B:R.214

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: S.17, D.40, D.44 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.17, H2O.3, H2O.3, H2O.4, H2O.4 MG.8: 4 residues within 4Å: Chain B: S.17, D.40, D.44 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.17, H2O.11, H2O.11, H2O.12, H2O.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buscagan, T.M. et al., Selenocyanate derived Se-incorporation into the Nitrogenase Fe protein cluster. Elife (2022)

Release Date

2022-09-14

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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