Sodium in PDB 4k8h: OYE1-W116V Complexed with (R)-Carvone

All present enzymatic activity of OYE1-W116V Complexed with (R)-Carvone:
1.6.99.1;

The structure of OYE1-W116V Complexed with (R)-Carvone, PDB code: 4k8h was solved by B.Sullivan, 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)	35.48 / 1.55
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	141.443, 141.443, 42.851, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 16.2

The structure of OYE1-W116V Complexed with (R)-Carvone also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the OYE1-W116V Complexed with (R)-Carvone (pdb code 4k8h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the OYE1-W116V Complexed with (R)-Carvone, PDB code: 4k8h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the OYE1-W116V Complexed with (R)-Carvone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of OYE1-W116V Complexed with (R)-Carvone within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:32.7 occ:1.00 C12 A:1PE408 2.4 21.5 0.7 OH4 A:1PE408 2.8 21.5 0.7 OH6 A:1PE408 2.9 21.5 0.7 HD2 A:TYR375 3.0 13.6 0.9 O A:HOH824 3.0 37.0 1.0 OH5 A:1PE408 3.1 21.5 0.7 OH2 A:1PE408 3.2 21.5 0.7 HE2 A:TYR375 3.3 14.7 0.8 C22 A:1PE408 3.4 21.5 0.7 OH3 A:1PE408 3.4 21.5 0.7 C14 A:1PE408 3.6 21.5 0.7 C16 A:1PE408 3.6 21.5 0.7 CD2 A:TYR375 3.7 11.4 0.9 C23 A:1PE408 3.7 21.5 0.7 C25 A:1PE408 3.7 21.5 0.7 C13 A:1PE408 3.7 21.5 0.7 C26 A:1PE408 3.7 21.5 0.7 C15 A:1PE408 3.8 21.5 0.7 C24 A:1PE408 3.8 21.5 0.7 OH7 A:1PE408 3.8 21.5 0.7 CE2 A:TYR375 3.8 12.3 0.8 HZ A:PHE123 4.7 27.0 1.0 CG A:TYR375 4.9 11.6 0.9 HB2 A:TYR375 5.0 14.1 0.9

Sodium binding site 2 out of 2 in the OYE1-W116V Complexed with (R)-Carvone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of OYE1-W116V Complexed with (R)-Carvone within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:32.7 occ:0.91 HE1 A:TRP52 2.1 18.7 1.0 O2 A:PGE407 2.7 22.7 0.6 O4 A:PGE407 2.8 22.7 0.6 NE1 A:TRP52 3.0 15.6 1.0 O1 A:PGE407 3.0 22.7 0.6 O3 A:PGE407 3.0 22.7 0.6 C1 A:PGE407 3.4 22.7 0.6 C4 A:PGE407 3.5 22.7 0.6 C2 A:PGE407 3.7 22.7 0.6 C3 A:PGE407 3.7 22.7 0.6 C5 A:PGE407 3.7 22.7 0.6 HB3 A:ASP51 3.8 18.6 1.0 HD1 A:TRP52 3.8 18.5 1.0 CD1 A:TRP52 3.8 15.4 1.0 C6 A:PGE407 3.9 22.7 0.6 HZ2 A:TRP52 4.0 20.8 1.0 CE2 A:TRP52 4.0 16.0 1.0 CZ2 A:TRP52 4.4 17.3 1.0 HB2 A:ALA379 4.5 17.4 1.0 CB A:ASP51 4.7 15.5 1.0 HB2 A:ASP51 4.9 18.6 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