SMTL ID : 4fgc.1

Crystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF, Bound to Substrate PreQ0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-10-mer

Ligands

8 x PQ0: 2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDINE-5-CARBONITRILE(Non-covalent)

PQ0.1: 11 residues within 4Å: Chain A: F.34, F.47, V.78, E.79, S.80 Chain B: A.56, P.57, F.96, H.97, E.98, I.131 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:V.78, A:E.79, A:S.80, B:H.97 Water bridges: B:E.98 Salt bridges: B:E.98 pi-Stacking: B:F.96, B:F.96 PQ0.5: 10 residues within 4Å: Chain B: F.34, V.78, E.79, S.80 Chain C: A.56, P.57, F.96, H.97, E.98, I.131 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:F.96, C:F.96 Hydrogen bonds: C:H.97, B:V.78, B:E.79, B:S.80 Water bridges: C:E.98 Salt bridges: C:E.98 pi-Cation interactions: C:F.96 PQ0.8: 10 residues within 4Å: Chain C: F.34, V.78, E.79, S.80 Chain D: A.56, P.57, F.96, H.97, E.98, I.131 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:V.78, C:E.79, C:S.80, D:H.97 Water bridges: D:E.98 Salt bridges: D:E.98 pi-Stacking: D:F.96 PQ0.11: 11 residues within 4Å: Chain D: F.34, F.47, V.78, E.79, S.80 Chain E: A.56, K.58, F.96, H.97, E.98, I.131 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:H.97, D:V.78, D:S.80 Salt bridges: E:E.98 pi-Stacking: E:F.96, E:F.96 PQ0.14: 11 residues within 4Å: Chain F: F.34, F.47, V.78, E.79, S.80 Chain G: A.56, P.57, F.96, H.97, E.98, I.131 8 PLIP interactions: 4 interactions with chain G, 4 interactions with chain F Hydrogen bonds: G:H.97, F:V.78, F:E.79, F:E.79, F:S.80 Salt bridges: G:E.98 pi-Stacking: G:F.96, G:F.96 PQ0.18: 10 residues within 4Å: Chain G: F.34, V.78, E.79, S.80 Chain H: A.56, P.57, F.96, H.97, E.98, I.131 9 PLIP interactions: 5 interactions with chain H, 4 interactions with chain G Hydrophobic interactions: H:F.96, H:F.96 Hydrogen bonds: H:H.97, G:V.78, G:E.79, G:E.79, G:S.80 Salt bridges: H:E.98 pi-Cation interactions: H:F.96 PQ0.21: 10 residues within 4Å: Chain H: F.34, V.78, E.79, S.80 Chain I: A.56, P.57, F.96, H.97, E.98, I.131 7 PLIP interactions: 3 interactions with chain I, 4 interactions with chain H Hydrogen bonds: I:H.97, H:V.78, H:E.79, H:E.79, H:S.80 Salt bridges: I:E.98 pi-Stacking: I:F.96 PQ0.24: 11 residues within 4Å: Chain I: F.34, F.47, V.78, E.79, S.80 Chain J: A.56, K.58, F.96, H.97, E.98, I.131 7 PLIP interactions: 4 interactions with chain J, 3 interactions with chain I Hydrogen bonds: J:H.97, I:V.78, I:E.79, I:S.80 Salt bridges: J:E.98 pi-Stacking: J:F.96, J:F.96

16 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain B: D.163, R.165 Chain J: R.165 Ligands: CA.25 5 PLIP interactions: 1 interactions with chain J, 4 Ligand-Water interactions Metal complexes: J:R.165, H2O.2, H2O.2, H2O.4, H2O.4 CA.4: 5 residues within 4Å: Chain B: S.54, L.55, D.63, D.95, H.97 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:S.54, B:L.55, B:D.63, B:D.95, B:D.95 CA.6: 4 residues within 4Å: Chain C: D.163, R.165 Chain I: R.165 Ligands: CA.22 4 PLIP interactions: 1 interactions with chain I, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: I:R.165, C:D.163, H2O.4, H2O.4 CA.7: 5 residues within 4Å: Chain C: S.54, L.55, D.63, D.95, H.97 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.54, C:L.55, C:D.95, C:D.95, H2O.5 CA.9: 4 residues within 4Å: Chain D: D.163, R.165 Chain H: R.165 Ligands: CA.19 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: D:D.163, H:R.165, H2O.5, H2O.5, H2O.12 CA.10: 4 residues within 4Å: Chain D: S.54, L.55, D.63, D.95 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:S.54, D:L.55, D:D.63, D:D.95, D:D.95 CA.12: 4 residues within 4Å: Chain E: D.163, R.165 Chain G: R.165 Ligands: CA.15 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.163, H2O.7, H2O.7, H2O.8, H2O.10 CA.13: 5 residues within 4Å: Chain E: S.54, L.55, D.63, H.93, D.95 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:S.54, E:L.55, E:D.63, E:D.95, E:D.95 CA.15: 4 residues within 4Å: Chain E: R.165 Chain G: D.163, R.165 Ligands: CA.12 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:R.165, H2O.10, H2O.10, H2O.11, H2O.12 CA.17: 5 residues within 4Å: Chain G: S.54, L.55, D.63, D.95, H.97 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:S.54, G:L.55, G:D.63, G:D.95, G:D.95 CA.19: 4 residues within 4Å: Chain D: R.165 Chain H: D.163, R.165 Ligands: CA.9 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: D:R.165, H:D.163, H2O.12, H2O.12 CA.20: 5 residues within 4Å: Chain H: S.54, L.55, D.63, D.95, H.97 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:S.54, H:L.55, H:D.95, H:D.95, H2O.13 CA.22: 4 residues within 4Å: Chain C: R.165 Chain I: D.163, R.165 Ligands: CA.6 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: C:R.165, I:D.163, H2O.4, H2O.13, H2O.13 CA.23: 4 residues within 4Å: Chain I: S.54, L.55, D.63, D.95 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:S.54, I:L.55, I:D.63, I:D.95, I:D.95 CA.25: 4 residues within 4Å: Chain B: R.165 Chain J: D.163, R.165 Ligands: CA.2 5 PLIP interactions: 1 interactions with chain J, 4 Ligand-Water interactions Metal complexes: J:D.163, H2O.2, H2O.15, H2O.15, H2O.16 CA.26: 5 residues within 4Å: Chain J: S.54, L.55, D.63, H.93, D.95 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:S.54, J:L.55, J:D.63, J:D.95, J:D.95

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.3: 9 residues within 4Å: Chain B: Y.150, Y.158 Chain C: Y.150, N.154 Chain D: Y.150, N.154 Chain E: Y.150, N.154, Y.158 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.150, C:Y.150 PE4.16: 9 residues within 4Å: Chain G: Y.150, Y.158 Chain H: Y.150, N.154 Chain I: Y.150, N.154 Chain J: Y.150, N.154, Y.158 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:Y.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chikwana, V.M. et al., Structural basis of biological nitrile reduction. J.Biol.Chem. (2012)

Release Date

2012-07-11

Peptides

NADPH-dependent 7-cyano-7-deazaguanine reductase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

NADPH-dependent 7-cyano-7-deazaguanine reductase