Sodium in PDB 4ge8: OYE1-W116I Complexed with (S)-Carvone

All present enzymatic activity of OYE1-W116I Complexed with (S)-Carvone:
1.6.99.1;

The structure of OYE1-W116I Complexed with (S)-Carvone, PDB code: 4ge8 was solved by Y.A.Pompeu, J.D.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.17 / 1.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	140.928, 140.928, 42.484, 90.00, 90.00, 90.00
R / Rfree (%)	13.7 / 17

The structure of OYE1-W116I Complexed with (S)-Carvone also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the OYE1-W116I Complexed with (S)-Carvone (pdb code 4ge8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the OYE1-W116I Complexed with (S)-Carvone, PDB code: 4ge8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the OYE1-W116I Complexed with (S)-Carvone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of OYE1-W116I Complexed with (S)-Carvone within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:47.8 occ:1.00 O A:HOH838 2.6 52.3 1.0 OH5 A:1PE409 2.9 41.6 1.0 OH4 A:1PE409 3.1 43.4 1.0 OH3 A:1PE409 3.2 49.3 1.0 C13 A:1PE409 3.5 41.8 1.0 C22 A:1PE409 3.5 44.7 1.0 C24 A:1PE409 3.5 36.0 1.0 C12 A:1PE409 3.6 55.2 1.0 C15 A:1PE409 3.7 42.4 1.0 CD2 A:TYR375 3.7 21.4 1.0 C14 A:1PE409 3.7 36.1 1.0 C23 A:1PE409 3.7 41.3 1.0 C25 A:1PE409 3.8 37.8 1.0 CE2 A:TYR375 3.8 20.8 1.0 OH6 A:1PE409 4.2 58.8 1.0 CG A:TYR375 4.9 18.8 1.0

Sodium binding site 2 out of 4 in the OYE1-W116I Complexed with (S)-Carvone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of OYE1-W116I Complexed with (S)-Carvone within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:71.7 occ:1.00 C23 A:1PE410 2.5 38.1 0.6 OH4 A:1PE410 2.8 32.1 0.6 C13 A:1PE410 3.0 28.0 0.6 N A:ALA10 3.1 21.7 1.0 OH3 A:1PE410 3.2 33.5 0.6 C22 A:1PE410 3.3 32.4 0.6 OH5 A:1PE410 3.3 52.7 0.6 C15 A:1PE410 3.6 32.5 0.6 CB A:ALA10 3.7 21.4 1.0 C24 A:1PE410 3.8 30.5 0.6 CA A:GLN9 3.8 24.6 1.0 C25 A:1PE410 3.9 37.9 0.6 C A:GLN9 3.9 22.1 1.0 CA A:ALA10 4.0 20.9 1.0 C14 A:1PE410 4.0 42.7 0.6 CG A:GLN9 4.2 32.7 1.0 CB A:GLN9 4.5 29.4 1.0 O A:ALA10 4.5 24.2 1.0 O A:PRO8 4.6 27.2 1.0 C A:ALA10 4.8 21.2 1.0 N A:GLN9 4.9 24.5 1.0

Sodium binding site 3 out of 4 in the OYE1-W116I Complexed with (S)-Carvone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of OYE1-W116I Complexed with (S)-Carvone within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:75.0 occ:1.00 O A:HOH826 3.0 48.1 1.0 OH5 A:1PE408 3.1 50.4 0.8 C23 A:1PE408 3.2 43.5 0.8 OH4 A:1PE408 3.2 43.1 0.8 C25 A:1PE408 3.3 41.0 0.8 OH6 A:1PE408 3.5 57.8 0.8 NE1 A:TRP52 3.6 19.0 1.0 OH3 A:1PE408 3.7 50.2 0.8 C13 A:1PE408 3.7 39.0 0.8 C14 A:1PE408 3.8 43.5 0.8 C22 A:1PE408 3.8 50.8 0.8 C15 A:1PE408 3.8 50.7 0.8 C24 A:1PE408 3.9 42.5 0.8 CD1 A:TRP52 4.3 18.2 1.0 CB A:ASP51 4.6 20.5 1.0 CE2 A:TRP52 4.7 19.2 1.0 O A:HOH759 4.9 40.4 1.0 CG A:ASP51 5.0 22.9 1.0

Sodium binding site 4 out of 4 in the OYE1-W116I Complexed with (S)-Carvone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of OYE1-W116I Complexed with (S)-Carvone within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:67.9 occ:1.00 OH4 A:1PE413 2.9 60.5 1.0 OH2 A:1PE413 3.1 44.9 1.0 OH3 A:1PE413 3.2 32.5 1.0 O A:HOH785 3.5 32.6 1.0 C24 A:1PE413 3.5 59.8 1.0 C13 A:1PE413 3.8 34.4 1.0 C12 A:1PE413 3.9 31.4 1.0 C23 A:1PE413 4.0 35.6 1.0 C22 A:1PE413 4.1 24.8 1.0 CE1 A:HIS380 4.2 21.7 1.0 O A:HOH951 4.7 45.2 1.0 CZ2 A:TRP396 4.8 29.9 1.0 NE2 A:HIS380 4.9 23.1 1.0

Y.A.Pompeu, B.Sullivan, J.D.Stewart. X‑Ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in An Alkene Reductase Acs Catalysis V. 3 2376 2013.
ISSN: ESSN 2155-5435
DOI: 10.1021/CS400622E