Sodium in PDB 4gxm: OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation

All present enzymatic activity of OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation:
1.6.99.1;

The structure of OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation, PDB code: 4gxm 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)	34.23 / 1.36
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	141.120, 141.120, 42.920, 90.00, 90.00, 90.00
R / Rfree (%)	10.8 / 13.7

The structure of OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation (pdb code 4gxm). 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-W116L in Complex with Aromatic Product of R-Carvone Dismutation, PDB code: 4gxm:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:39.3 occ:1.00 N A:ALA10 2.8 12.8 1.0 C24 A:1PE406 3.1 31.8 0.8 OH6 A:1PE406 3.1 34.2 0.8 OH5 A:1PE406 3.3 30.4 0.8 C13 A:1PE406 3.3 32.0 0.8 OH4 A:1PE406 3.5 31.9 0.8 CB A:ALA10 3.5 12.5 1.0 CA A:GLN9 3.6 16.4 1.0 C14 A:1PE406 3.6 30.9 0.8 C26 A:1PE406 3.7 32.9 0.8 C16 A:1PE406 3.7 31.9 0.8 C A:GLN9 3.7 14.5 1.0 CA A:ALA10 3.7 12.6 1.0 C15 A:1PE406 4.1 34.1 0.8 C25 A:1PE406 4.1 32.3 0.8 CG A:GLN9 4.2 25.4 1.0 O A:ALA10 4.5 15.6 1.0 CB A:GLN9 4.5 21.6 1.0 O A:PRO8 4.5 17.1 1.0 C A:ALA10 4.6 12.5 1.0 N A:GLN9 4.7 15.3 1.0 O A:GLN9 4.9 14.7 1.0 C A:PRO8 5.0 15.3 1.0

Sodium binding site 2 out of 4 in the OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:37.5 occ:1.00 NE1 A:TRP52 2.9 10.6 1.0 OH5 A:1PE403 2.9 36.0 0.9 C26 A:1PE403 3.2 39.0 0.9 OH4 A:1PE403 3.2 37.4 0.9 OH6 A:1PE403 3.3 38.8 0.9 C24 A:1PE403 3.4 36.6 0.9 C14 A:1PE403 3.6 35.9 0.9 C13 A:1PE403 3.7 37.9 0.9 C16 A:1PE403 3.7 40.6 0.9 CD1 A:TRP52 3.7 10.3 1.0 C25 A:1PE403 4.0 37.0 0.9 CE2 A:TRP52 4.0 10.8 1.0 OH7 A:1PE403 4.1 42.5 0.9 C15 A:1PE403 4.2 37.9 0.9 O A:HOH1018 4.4 36.5 1.0 CZ2 A:TRP52 4.5 11.2 1.0 CB A:ASP51 4.6 10.5 1.0

Sodium binding site 3 out of 4 in the OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:40.9 occ:1.00 OH3 A:1PE410 2.4 35.8 0.8 O A:HOH990 2.6 40.3 1.0 OH6 A:1PE410 2.7 32.5 0.8 C22 A:1PE410 2.9 34.5 0.8 OH4 A:1PE410 2.9 34.0 0.8 O A:HOH607 3.2 15.7 1.0 OH5 A:1PE410 3.2 30.6 0.8 C23 A:1PE410 3.4 34.9 0.8 C14 A:1PE410 3.5 31.8 0.8 C25 A:1PE410 3.5 30.4 0.8 C15 A:1PE410 3.6 31.2 0.8 C26 A:1PE410 3.6 32.0 0.8 C13 A:1PE410 3.7 34.6 0.8 C24 A:1PE410 3.7 33.0 0.8 C12 A:1PE410 4.4 34.8 0.8 O A:HOH771 4.4 27.7 1.0 CB A:TYR313 4.5 8.1 1.0 O A:ASP310 4.6 8.7 1.0 OG A:SER314 4.6 8.8 1.0

Sodium binding site 4 out of 4 in the OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of OYE1-W116L in Complex with Aromatic Product of R-Carvone Dismutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:38.1 occ:1.00 OH4 A:1PE409 3.1 38.3 1.0 OH5 A:1PE409 3.1 31.3 1.0 C26 A:1PE409 3.6 37.4 1.0 CE1 A:HIS380 3.7 14.3 1.0 OH6 A:1PE409 3.8 36.8 1.0 C24 A:1PE409 3.8 35.3 1.0 C15 A:1PE409 3.9 34.0 1.0 C14 A:1PE409 3.9 32.0 1.0 C25 A:1PE409 3.9 30.8 1.0 O A:HOH779 4.1 25.4 1.0 NE2 A:HIS380 4.5 14.9 1.0 O A:HOH939 4.7 32.8 1.0 ND1 A:HIS380 4.7 11.9 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