Sodium in PDB 4k7v: OYE1-W116A Complexed with (R)-Carvone

All present enzymatic activity of OYE1-W116A Complexed with (R)-Carvone:
1.6.99.1;

The structure of OYE1-W116A Complexed with (R)-Carvone, PDB code: 4k7v 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)	35.42 / 1.52
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	140.853, 140.853, 42.841, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 18.3

The structure of OYE1-W116A Complexed with (R)-Carvone also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the OYE1-W116A Complexed with (R)-Carvone (pdb code 4k7v). 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-W116A Complexed with (R)-Carvone, PDB code: 4k7v:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the OYE1-W116A 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-W116A Complexed with (R)-Carvone within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:29.3 occ:0.80 OH3 A:1PE406 2.4 18.7 0.4 C12 A:1PE406 2.5 18.7 0.4 OH4 A:1PE406 2.8 18.7 0.4 OH6 A:1PE406 2.8 18.7 0.4 HD2 A:TYR375 2.9 20.0 0.8 OH2 A:1PE406 3.0 18.7 0.4 C22 A:1PE406 3.0 18.7 0.4 OH5 A:1PE406 3.2 18.7 0.4 HE2 A:TYR375 3.4 20.1 0.7 C23 A:1PE406 3.5 18.7 0.4 C14 A:1PE406 3.6 18.7 0.4 CD2 A:TYR375 3.6 16.7 0.8 C26 A:1PE406 3.6 18.7 0.4 C13 A:1PE406 3.7 18.7 0.4 C24 A:1PE406 3.8 18.7 0.4 C25 A:1PE406 3.8 18.7 0.4 CE2 A:TYR375 3.9 16.7 0.7 C15 A:1PE406 3.9 18.7 0.4 OH7 A:1PE406 4.0 18.7 0.4 C16 A:1PE406 4.2 18.7 0.4 HZ A:PHE123 4.6 32.5 1.0 CG A:TYR375 4.8 15.1 0.9 HB2 A:TYR375 4.9 16.0 0.8

Sodium binding site 2 out of 2 in the OYE1-W116A 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-W116A Complexed with (R)-Carvone within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:28.7 occ:1.00 O A:TYR375 2.2 17.0 0.8 OE1 A:GLN376 2.3 25.6 1.0 O A:HOH703 2.4 37.3 1.0 O A:ASP372 2.4 20.2 1.0 HB2 A:GLN376 3.2 23.2 1.0 CD A:GLN376 3.2 23.4 1.0 C A:TYR375 3.4 14.4 0.8 O A:HOH589 3.5 25.8 1.0 HA A:THR373 3.6 20.4 1.0 C A:ASP372 3.6 17.4 1.0 O A:HOH673 3.7 33.3 1.0 HA A:GLN376 3.8 23.2 1.0 HE22 A:GLN376 3.9 28.6 1.0 CB A:GLN376 3.9 19.4 1.0 O A:HOH807 3.9 41.4 1.0 NE2 A:GLN376 3.9 23.8 1.0 H A:TYR375 3.9 17.0 0.8 HB2 A:TYR375 4.0 16.0 0.8 CA A:GLN376 4.1 19.3 1.0 CG A:GLN376 4.1 20.4 1.0 N A:GLN376 4.2 17.5 1.0 HA A:ASP372 4.3 22.3 1.0 CA A:THR373 4.4 17.0 1.0 N A:THR373 4.4 16.9 1.0 CA A:TYR375 4.4 14.3 0.8 N A:TYR375 4.5 14.2 0.8 CA A:ASP372 4.6 18.6 1.0 CB A:TYR375 4.6 13.3 0.9 HB3 A:ASP372 4.6 24.8 1.0 HG3 A:GLN376 4.7 24.5 1.0 HE21 A:GLN376 4.7 28.6 1.0 HB3 A:TYR375 4.7 16.0 0.8 HB3 A:GLN376 4.7 23.2 1.0 HG2 A:GLN376 4.8 24.5 1.0 OH2 A:1PE406 4.8 18.7 0.4 C A:THR373 4.9 16.2 1.0 HG22 A:THR373 5.0 23.3 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