SMTL ID : 8oie.1

Iron Nitrogenase Complex from Rhodobacter capsulatus

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-4-mer

Ligands

2 x S5Q: FeFe cofactor(Non-covalent)

S5Q.1: 15 residues within 4Å: Chain A: V.57, K.83, Q.176, H.180, Y.211, C.257, S.260, P.335, G.336, G.337, S.338, K.339, F.362, H.423 Ligands: HCA.2 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.257, A:H.423 S5Q.11: 16 residues within 4Å: Chain F: V.57, K.83, Q.176, H.180, Y.211, C.257, R.259, S.260, P.335, G.336, G.337, S.338, K.339, F.362, H.423 Ligands: HCA.12 2 PLIP interactions: 2 interactions with chain F, Metal complexes: F:C.257, F:H.423

2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)

HCA.2: 8 residues within 4Å: Chain A: C.52, K.83, Q.176, K.361, G.405, K.406, H.423 Ligands: S5Q.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:H.423 Hydrogen bonds: A:Q.176, A:K.361, A:K.406, A:H.423 Water bridges: A:K.83, A:K.83, A:N.421 Salt bridges: A:H.56, A:K.83, A:K.361, A:K.361, A:H.423, A:H.423 HCA.12: 9 residues within 4Å: Chain F: C.52, H.56, K.83, Q.176, K.361, G.405, K.406, H.423 Ligands: S5Q.11 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:H.423 Hydrogen bonds: F:Q.176, F:K.361, F:K.406, F:H.423 Water bridges: F:K.83, F:K.83 Salt bridges: F:K.83, F:K.361, F:K.361, F:H.423, F:H.423

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

CLF.3: 17 residues within 4Å: Chain A: C.49, Y.51, P.72, G.74, C.75, D.78, C.138, G.170 Chain C: C.20, P.22, G.42, G.44, C.45, F.48, T.103, C.104, S.143 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A, Metal complexes: C:C.20, C:C.45, C:C.45, C:C.104, A:C.49, A:C.75, A:C.75, A:C.138 Salt bridges: A:D.78 CLF.13: 17 residues within 4Å: Chain F: C.49, Y.51, P.72, G.74, C.75, D.78, C.138, G.170 Chain H: C.20, P.22, G.42, G.44, C.45, F.48, T.103, C.104, S.143 9 PLIP interactions: 5 interactions with chain F, 4 interactions with chain H, Salt bridges: F:D.78 Metal complexes: F:C.49, F:C.75, F:C.75, F:C.138, H:C.20, H:C.45, H:C.45, H:C.104

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

ADP.4: 20 residues within 4Å: Chain D: 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, Y.240 Chain E: K.10, E.154, M.156 Ligands: MG.5, AF3.6 17 PLIP interactions: 3 interactions with chain E, 14 interactions with chain D Hydrogen bonds: E:M.156, D:K.10, D:G.12, D:I.13, D:G.14, D:K.15, D:S.16, D:T.17, D:T.17, D:N.185, D:P.212, D:D.214, D:Q.218, D:E.221 Salt bridges: E:K.10, E:K.10, D:K.15 ADP.8: 18 residues within 4Å: Chain D: K.10, E.154, M.155, M.156 Chain E: G.12, I.13, G.14, K.15, S.16, T.17, N.185, P.212, R.213, D.214, Q.218, E.221 Ligands: MG.9, AF3.10 17 PLIP interactions: 4 interactions with chain D, 13 interactions with chain E Hydrogen bonds: D:M.155, D:M.156, 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 Salt bridges: D:K.10, D:K.10, E:K.15 ADP.14: 20 residues within 4Å: Chain I: 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, Y.240 Chain J: K.10, E.154, M.155, M.156 Ligands: MG.15, AF3.16 18 PLIP interactions: 14 interactions with chain I, 4 interactions with chain J Hydrogen bonds: I:K.10, I:G.12, I:I.13, I:G.14, I:K.15, I:S.16, I:T.17, I:T.17, I:N.185, I:P.212, I:D.214, I:Q.218, I:E.221, J:M.155, J:M.156 Salt bridges: I:K.15, J:K.10, J:K.10 ADP.18: 18 residues within 4Å: Chain I: K.10, E.154, M.155, M.156 Chain J: G.12, I.13, G.14, K.15, S.16, T.17, N.185, P.212, R.213, D.214, Q.218, E.221 Ligands: MG.19, AF3.20 17 PLIP interactions: 4 interactions with chain I, 13 interactions with chain J Hydrogen bonds: I:M.155, I:M.156, J:G.12, J:I.13, J:G.14, J:K.15, J:S.16, J:T.17, J:T.17, J:N.185, J:P.212, J:D.214, J:Q.218, J:E.221 Salt bridges: I:K.10, I:K.10, J:K.15

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain D: S.16, D.125 Ligands: ADP.4, AF3.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.16 MG.9: 5 residues within 4Å: Chain E: S.16, D.40, D.125 Ligands: ADP.8, AF3.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.16 MG.15: 4 residues within 4Å: Chain I: S.16, D.125 Ligands: ADP.14, AF3.16 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.16 MG.19: 5 residues within 4Å: Chain J: S.16, D.40, D.125 Ligands: ADP.18, AF3.20 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.16

4 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.6: 12 residues within 4Å: Chain D: G.11, G.12, K.15, D.40, K.42, V.126, L.127, G.128 Chain E: K.10, D.129 Ligands: ADP.4, MG.5 No protein-ligand interaction detected (PLIP) AF3.10: 10 residues within 4Å: Chain D: K.10 Chain E: G.11, G.12, K.15, D.40, K.42, L.127, G.128 Ligands: ADP.8, MG.9 No protein-ligand interaction detected (PLIP) AF3.16: 11 residues within 4Å: Chain I: K.10, G.11, G.12, K.15, D.40, K.42, L.127, G.128 Chain J: K.10 Ligands: ADP.14, MG.15 No protein-ligand interaction detected (PLIP) AF3.20: 10 residues within 4Å: Chain I: K.10 Chain J: G.11, G.12, K.15, D.40, K.42, L.127, G.128 Ligands: ADP.18, MG.19 No protein-ligand interaction detected (PLIP)

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

SF4.7: 12 residues within 4Å: Chain A: L.142, I.143 Chain C: I.108 Chain D: C.97, A.98, G.99, V.131, C.132 Chain E: C.97, A.98, G.99, C.132 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E, Metal complexes: D:C.97, D:C.132, E:C.97, E:C.132 SF4.17: 13 residues within 4Å: Chain F: L.142, I.143 Chain H: I.108 Chain I: C.97, A.98, G.99, V.131, C.132 Chain J: C.97, A.98, G.99, V.131, C.132 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain I, Metal complexes: J:C.97, J:C.132, I:C.97, I:C.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, F.V. et al., Structural insights into the iron nitrogenase complex. Nat.Struct.Mol.Biol. (2024)

Release Date

2023-10-04

Peptides

Nitrogenase protein alpha chain: AF
Nitrogenase iron-iron protein delta chain: BG
Nitrogenase iron-iron protein, beta subunit: CH
Nitrogenase iron protein: DEIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
F

B
B

G
G

C
C

H
H

D
D

E
E

I
I

J
J

Nitrogenase protein alpha chain

Nitrogenase iron-iron protein delta chain

Nitrogenase iron-iron protein, beta subunit

Nitrogenase iron protein

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