SMTL ID : 1qgu.1

NITROGENASE MO-FE PROTEIN FROM KLEBSIELLA PNEUMONIAE, DITHIONITE-REDUCED STATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-oligomer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain D: P.369, A.394, N.395, W.398 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain B: P.369, A.394, N.395, W.398 Ligand excluded by PLIP

7 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain B: D.349, D.353 Chain D: K.106, E.107 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.349, B:D.353, D:K.106, D:E.107, H2O.1388, H2O.2760 MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain B: D.407 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.407, H2O.1395, H2O.1396, H2O.1397, H2O.1398, H2O.1399 MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: K.106, E.107 Chain D: D.349, D.353 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:K.106, B:E.107, D:D.349, D:D.353, H2O.1400, H2O.2763 MG.9: 1 residues within 4Å: Chain D: Q.434 No protein-ligand interaction detected (PLIP)

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

HCA.10: 8 residues within 4Å: Chain A: A.64, R.95, Q.190, G.422, I.423, K.424, H.440 Ligands: CFM.11 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.440 Hydrogen bonds: A:Q.190, A:I.423 Water bridges: A:K.424, A:K.424, A:K.424, A:Q.438, A:Q.438, B:R.103 Salt bridges: A:K.424, A:H.440, A:H.440 HCA.13: 8 residues within 4Å: Chain C: A.64, R.95, Q.190, G.422, I.423, K.424, H.440 Ligands: CFM.14 13 PLIP interactions: 1 interactions with chain D, 12 interactions with chain C Water bridges: D:R.103, C:R.96, C:K.424, C:K.424, C:K.424, C:Q.438, C:Q.438 Hydrophobic interactions: C:H.440 Hydrogen bonds: C:Q.190, C:I.423 Salt bridges: C:K.424, C:H.440, C:H.440

2 x CFM: FE-MO-S CLUSTER(Non-covalent)

CFM.11: 14 residues within 4Å: Chain A: V.69, R.95, H.194, Y.227, I.229, C.273, S.276, G.354, G.355, L.356, R.357, F.379, H.440 Ligands: HCA.10 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.378 Metal complexes: A:C.273 CFM.14: 14 residues within 4Å: Chain C: V.69, R.95, H.194, Y.227, I.229, C.273, S.276, G.354, G.355, L.356, R.357, F.379, H.440 Ligands: HCA.13 2 PLIP interactions: 2 interactions with chain C, Salt bridges: C:E.378 Metal complexes: C:C.273

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

CLF.12: 19 residues within 4Å: Chain A: C.61, Y.63, P.84, G.86, C.87, Y.90, E.152, C.153, G.184 Chain B: C.68, P.70, S.90, G.92, C.93, Y.96, F.97, T.150, C.151, S.186 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A, Metal complexes: B:C.68, B:C.93, B:C.93, B:C.151, A:C.61, A:C.87, A:C.87, A:C.153 Salt bridges: A:E.152 CLF.15: 18 residues within 4Å: Chain C: C.61, Y.63, P.84, G.86, C.87, Y.90, E.152, C.153, G.184 Chain D: C.68, P.70, S.90, G.92, C.93, Y.96, T.150, C.151, S.186 9 PLIP interactions: 5 interactions with chain C, 4 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.68, D:C.93, D:C.93, D:C.151

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.16: 7 residues within 4Å: Chain A: D.443, Y.444, S.445, R.459, M.463 Chain D: T.356, W.357 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: K.75, T.100, D.254 Chain B: F.23, K.26, R.27, E.30 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: A.93, R.95, R.96, N.97, Y.98, Y.99, T.110 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: P.176, N.208, R.209, E.261 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: K.267, L.268, Q.313, F.314 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: T.356, W.357 Chain C: D.443, Y.444, M.463 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain C: P.176, N.208, R.209, E.261 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: N.48, L.192, H.195, Y.279, H.381 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: K.237, S.248, L.249, D.252, T.272, E.276 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: E.51, F.55, F.418, R.433 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: N.54, F.55, R.57, C.421, H.425 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: H.474, R.477, Q.478 Chain D: M.350, M.487, T.491 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain D: K.237, S.248, L.249, D.252, T.272, E.276 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain A: Y.444 Chain B: C.10, Y.11 Chain D: W.357, L.501, S.514, R.519 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain D: N.54, F.55, R.57, C.421, H.425 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain D: R.27, Q.28, E.30, E.31, A.32 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mayer, S.M. et al., New insights into structure-function relationships in nitrogenase: A 1.6 A resolution X-ray crystallographic study of Klebsiella pneumoniae MoFe-protein. J.Mol.Biol. (1999)

Release Date

1999-11-01

Peptides

PROTEIN (NITROGENASE MOLYBDENUM IRON PROTEIN): AC
PROTEIN (NITROGENASE MOLYBDENUM IRON PROTEIN): BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

PROTEIN (NITROGENASE MOLYBDENUM IRON PROTEIN)

PROTEIN (NITROGENASE MOLYBDENUM IRON PROTEIN)

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