SMTL ID : 4xpi.1

Fe protein independent substrate reduction by nitrogenase variants altered in intramolecular electron transfer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

hetero-2-2-mer

Ligands

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

HCA.1: 7 residues within 4Å: Chain A: A.63, R.94, Q.189, G.422, I.423, H.440 Ligands: ICS.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:H.440 Hydrogen bonds: A:Q.189, A:I.423 Water bridges: A:K.424, A:K.424, A:K.424, A:K.424, A:K.424, A:E.438, B:R.104, B:R.104 Salt bridges: A:H.440, A:H.440 HCA.14: 7 residues within 4Å: Chain C: A.63, R.94, Q.189, G.422, I.423, H.440 Ligands: ICS.15 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:H.440 Hydrogen bonds: C:Q.189, C:I.423 Water bridges: C:G.93, C:R.95, C:K.424, C:K.424, C:K.424, C:K.424, C:E.438, C:E.438, D:H.97, D:R.104 Salt bridges: C:H.440, C:H.440

2 x ICS: iron-sulfur-molybdenum cluster with interstitial carbon(Non-covalent)

ICS.2: 15 residues within 4Å: Chain A: V.68, R.94, H.193, Y.227, I.229, C.273, S.276, I.353, G.354, G.355, L.356, R.357, F.379, H.440 Ligands: HCA.1 2 PLIP interactions: 2 interactions with chain A, Salt bridges: A:E.378 Metal complexes: A:C.273 ICS.15: 14 residues within 4Å: Chain C: V.68, R.94, H.193, Y.227, C.273, S.276, I.353, G.354, G.355, L.356, R.357, F.379, H.440 Ligands: HCA.14 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Salt bridges: C:E.378 Metal complexes: C:C.273, H2O.25

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: K.41, S.46, N.47, H.381, N.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.47, A:N.382 Water bridges: A:H.381 GOL.6: 3 residues within 4Å: Chain B: N.398, K.399, R.400 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.399, B:R.400, B:R.400 GOL.7: 7 residues within 4Å: Chain A: I.99 Chain B: F.14, L.15, K.20, L.23 Chain D: Q.512, A.513 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.14, B:K.20, B:K.20 GOL.9: 8 residues within 4Å: Chain B: Y.232, S.481, T.482, T.483, G.488, Q.491, I.492, T.495 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.481, B:S.481, B:G.488 GOL.10: 7 residues within 4Å: Chain B: F.229, E.230, T.231, Y.232, G.469, F.470 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.230, B:T.231, B:G.469 Water bridges: B:T.231 GOL.11: 10 residues within 4Å: Chain B: E.230, Y.232, N.235, Q.293, I.317, M.319, F.374, T.483, L.484 Ligands: GOL.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.230, B:N.235, B:T.483, B:T.483 GOL.12: 9 residues within 4Å: Chain A: R.91, T.102, T.109, M.110 Chain B: N.64, F.449, I.450, R.452, D.453 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.64, B:R.452, B:R.452, B:D.453, A:R.91, A:T.109, A:T.109 Water bridges: A:T.102 GOL.16: 3 residues within 4Å: Chain C: H.194, D.198, R.201 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.201 Water bridges: C:R.201, C:R.201 GOL.17: 1 residues within 4Å: Chain C: R.341 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.341 GOL.18: 10 residues within 4Å: Chain C: K.66, S.90, R.91, A.92, R.94, N.96, V.108, T.109, M.110 Ligands: GOL.19 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.66, C:A.92, C:N.96, C:M.110 GOL.19: 10 residues within 4Å: Chain B: Y.516, H.518, D.519 Chain C: A.92, R.94, R.95, N.96, Y.97, T.109 Ligands: GOL.18 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:A.92, C:R.94, B:D.519, B:D.519 Water bridges: C:Y.98, C:Y.98 GOL.20: 5 residues within 4Å: Chain C: K.131, E.135, T.138 Chain D: L.54, Q.57 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.131, C:K.131, C:T.138 GOL.21: 8 residues within 4Å: Chain C: R.26, S.50, Q.51, L.54, M.55, T.56, D.401, T.403 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.51, C:Q.51, C:Q.51, C:L.54, C:T.56 Water bridges: C:R.26, C:L.54 GOL.23: 2 residues within 4Å: Chain B: P.12 Chain D: E.507 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.507 GOL.25: 6 residues within 4Å: Chain D: F.229, E.230, T.231, Y.232, F.374, F.470 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:E.230, D:T.231, D:T.231, D:Y.232, D:Q.293 Water bridges: D:N.235, D:Q.293

2 x 1CL: FE(8)-S(7) CLUSTER, OXIDIZED(Covalent)

1CL.4: 15 residues within 4Å: Chain A: C.60, Y.62, P.83, G.85, C.86, Y.89, C.152, G.183 Chain B: C.69, S.91, G.93, C.94, H.97, C.152, S.187 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Salt bridges: A:E.151 Metal complexes: A:C.60, A:C.86, A:C.86, A:C.152, B:C.69, B:C.94, B:C.94, B:C.152, B:S.187 1CL.22: 15 residues within 4Å: Chain C: C.60, Y.62, P.83, G.85, C.86, Y.89, C.152, G.183 Chain D: C.69, S.91, G.93, C.94, H.97, C.152, S.187 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D, Salt bridges: C:E.151 Metal complexes: C:C.60, C:C.86, C:C.86, C:C.152, D:C.69, D:C.94, D:C.94, D:C.152, D:S.187

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain B: D.352, D.356 Chain D: R.107, E.108 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:D.352, B:D.356, D:R.107, H2O.10, H2O.27 CA.13: 4 residues within 4Å: Chain B: R.107, E.108 Chain D: D.352, D.356 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:D.352, D:D.356, B:R.107, H2O.12, H2O.27

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 3 residues within 4Å: Chain B: T.48, K.49, E.50 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.49, B:E.50 TRS.24: 3 residues within 4Å: Chain D: T.48, K.49, E.50 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Danyal, K. et al., Fe protein-independent substrate reduction by nitrogenase MoFe protein variants. Biochemistry (2015)

Release Date

2015-10-14

Peptides

Nitrogenase molybdenum-iron protein alpha chain: AC
Nitrogenase molybdenum-iron protein beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Nitrogenase molybdenum-iron protein alpha chain

Nitrogenase molybdenum-iron protein beta chain