SMTL ID : 1qh1.1

NITROGENASE MOFE PROTEIN FROM KLEBSIELLA PNEUMONIAE, PHENOSAFRANIN OXIDIZED STATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-2-2-mer

Ligands

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

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 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.51, H2O.101 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 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.51, H2O.51, H2O.51, H2O.51, H2O.51 MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.22: 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.51, H2O.101 MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

HCA.2: 8 residues within 4Å: Chain A: A.64, R.95, Q.190, G.422, I.423, K.424, H.440 Ligands: CFM.3 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A Water bridges: B:R.103, A:K.424, A:K.424, A:K.424, A:Q.438, A:Q.438, A:S.441 Hydrophobic interactions: A:H.440 Hydrogen bonds: A:Q.190, A:I.423 Salt bridges: A:K.424, A:H.440, A:H.440 HCA.17: 8 residues within 4Å: Chain C: A.64, R.95, Q.190, G.422, I.423, K.424, H.440 Ligands: CFM.18 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:H.440 Hydrogen bonds: C:Q.190, C:I.423 Water bridges: C:R.96, C:K.424, C:K.424, C:K.424, C:Q.438, C:Q.438, C:S.441, D:R.103 Salt bridges: C:K.424, C:H.440, C:H.440

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

CFM.3: 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.2 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.378 Metal complexes: A:C.273 CFM.18: 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.17 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.4: 18 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, T.150, C.151, S.186 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Salt bridges: A:E.152 Metal complexes: A:C.61, A:C.87, A:C.87, A:C.153, B:C.68, B:C.93, B:C.93, B:C.151, B:S.186 CLF.19: 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 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C, Metal complexes: D:C.68, D:C.93, D:C.93, D:C.151, D:S.186, C:C.61, C:C.87, C:C.87, C:C.153 Salt bridges: C:E.152

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

EDO.5: 7 residues within 4Å: Chain A: K.75, T.100, D.254 Chain B: F.23, K.26, R.27, E.30 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.75, A:T.100 Water bridges: A:T.100, A:T.100, A:T.100 EDO.6: 7 residues within 4Å: Chain A: A.93, R.95, R.96, N.97, Y.98, Y.99, T.110 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:A.93, A:N.97 Water bridges: A:A.93, D:L.517 EDO.7: 4 residues within 4Å: Chain A: P.176, N.208, R.209, E.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.208, A:R.209, A:R.209 EDO.8: 4 residues within 4Å: Chain A: K.267, P.291, Q.313, F.314 No protein-ligand interaction detected (PLIP) EDO.13: 6 residues within 4Å: Chain B: K.237, S.248, L.249, D.252, T.272, E.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.249, B:L.249 Water bridges: B:D.252 EDO.14: 8 residues within 4Å: Chain B: L.501, S.514, R.519 Chain C: Y.98, Y.444, S.445 Chain D: S.9, C.10 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:R.519, B:R.519, C:Y.98, D:S.9, D:S.9 EDO.15: 4 residues within 4Å: Chain B: T.356, W.357 Chain C: D.443, Y.444 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:T.356, C:D.443 Water bridges: B:T.356, B:K.361, C:S.445, C:S.445, C:R.459 EDO.20: 4 residues within 4Å: Chain C: P.176, N.208, R.209, E.261 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.208, C:R.209, C:R.209 Water bridges: C:N.208 EDO.24: 6 residues within 4Å: Chain A: D.443, Y.444, R.459, M.463 Chain D: T.356, W.357 9 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D, 4 interactions with chain A Water bridges: B:S.9, B:S.9, D:T.356, D:K.361, A:S.445, A:S.445, A:R.459 Hydrogen bonds: D:T.356, A:D.443 EDO.25: 6 residues within 4Å: Chain B: Q.448, R.464, R.472 Chain D: D.502, S.503, F.515 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:R.464, B:R.464, B:R.472, D:D.502 Water bridges: B:Q.448, D:S.503, D:S.503 EDO.26: 6 residues within 4Å: Chain D: K.237, S.248, L.249, D.252, T.272, E.276 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:L.249, D:L.249 Water bridges: D:K.237, D:D.252, D:D.252, D:D.252 EDO.27: 8 residues within 4Å: Chain A: Y.444, S.445 Chain B: S.9, C.10 Chain D: L.501, S.514, D.516, R.519 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:S.514, D:R.519, D:R.519 Water bridges: B:S.9, B:S.9 EDO.28: 5 residues within 4Å: Chain D: N.54, F.55, R.57, C.421, H.425 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.57

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

CL.9: 4 residues within 4Å: Chain B: P.369, A.394, N.395, W.398 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain D: P.369, A.394, N.395, W.398 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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