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Sodium in PDB 4gbu: OYE1-W116A in Complex with Aromatic Product of S-Carvone Dismutation

Enzymatic activity of OYE1-W116A in Complex with Aromatic Product of S-Carvone Dismutation

All present enzymatic activity of OYE1-W116A in Complex with Aromatic Product of S-Carvone Dismutation:
1.6.99.1;

Protein crystallography data

The structure of OYE1-W116A in Complex with Aromatic Product of S-Carvone Dismutation, PDB code: 4gbu 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) 21.04 / 1.18
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.121, 141.121, 42.813, 90.00, 90.00, 90.00
R / Rfree (%) 10 / 12.1

Other elements in 4gbu:

The structure of OYE1-W116A in Complex with Aromatic Product of S-Carvone Dismutation also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the OYE1-W116A in Complex with Aromatic Product of S-Carvone Dismutation (pdb code 4gbu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the OYE1-W116A in Complex with Aromatic Product of S-Carvone Dismutation, PDB code: 4gbu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4gbu

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Sodium binding site 1 out of 5 in the OYE1-W116A in Complex with Aromatic Product of S-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-W116A in Complex with Aromatic Product of S-Carvone Dismutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:26.6
occ:1.00
 OH3 A:1PE410 2.8 26.8 0.9
OH5 A:1PE410 2.8 23.7 0.9
O A:HOH1130 3.1 39.8 1.0
OH4 A:1PE410 3.1 24.9 0.9
O A:HOH915 3.2 28.6 1.0
C24 A:1PE410 3.3 23.9 0.9
C12 A:1PE410 3.5 29.4 0.9
C15 A:1PE410 3.5 25.4 0.9
C22 A:1PE410 3.6 27.6 0.9
C13 A:1PE410 3.6 26.0 0.9
CD2 A:TYR375 3.6 9.3 1.0
C14 A:1PE410 3.6 21.6 0.9
C25 A:1PE410 3.6 23.5 0.9
C23 A:1PE410 3.6 27.2 0.9
OH6 A:1PE410 3.7 29.8 0.9
CE2 A:TYR375 3.8 10.1 1.0
CG A:TYR375 4.8 8.9 1.0

Sodium binding site 2 out of 5 in 4gbu

Go back to Sodium Binding Sites List in 4gbu
Sodium binding site 2 out of 5 in the OYE1-W116A in Complex with Aromatic Product of S-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-W116A in Complex with Aromatic Product of S-Carvone Dismutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:33.2
occ:1.00
 N A:ALA10 2.8 11.4 1.0
C23 A:1PE411 3.0 26.8 0.8
C22 A:1PE411 3.2 27.3 0.8
OH4 A:1PE411 3.3 28.7 0.8
OH3 A:1PE411 3.4 27.2 0.8
C13 A:1PE411 3.4 25.4 0.8
C24 A:1PE411 3.5 32.1 0.8
OH5 A:1PE411 3.6 31.0 0.8
C15 A:1PE411 3.6 30.2 0.8
CA A:GLN9 3.6 14.1 1.0
C14 A:1PE411 3.6 31.3 0.8
CB A:ALA10 3.6 13.1 1.0
C A:GLN9 3.7 13.0 1.0
CA A:ALA10 3.8 11.4 1.0
C25 A:1PE411 3.8 29.8 0.8
CG A:GLN9 4.2 27.9 1.0
O A:PRO8 4.4 15.9 1.0
CB A:GLN9 4.4 20.7 1.0
O A:ALA10 4.5 14.3 1.0
N A:GLN9 4.6 14.1 1.0
C A:ALA10 4.7 11.4 1.0
O A:GLN9 4.9 14.4 1.0
C A:PRO8 4.9 13.5 1.0

Sodium binding site 3 out of 5 in 4gbu

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Sodium binding site 3 out of 5 in the OYE1-W116A in Complex with Aromatic Product of S-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-W116A in Complex with Aromatic Product of S-Carvone Dismutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:34.2
occ:1.00
 OH4 A:1PE405 2.9 21.4 0.7
NE1 A:TRP52 2.9 10.6 1.0
OH5 A:1PE405 3.1 19.9 0.7
OH6 A:1PE405 3.1 31.8 0.7
OH3 A:1PE405 3.1 26.4 0.7
O A:HOH890 3.4 43.2 1.0
C12 A:1PE405 3.4 30.8 0.7
C23 A:1PE405 3.5 23.8 0.7
C25 A:1PE405 3.7 21.1 0.7
C14 A:1PE405 3.7 20.2 0.7
C13 A:1PE405 3.7 22.2 0.7
CD1 A:TRP52 3.8 10.0 1.0
C22 A:1PE405 3.8 27.7 0.7
C24 A:1PE405 3.8 20.8 0.7
C15 A:1PE405 3.9 26.9 0.7
CE2 A:TRP52 4.0 10.1 1.0
O A:HOH1125 4.4 35.3 1.0
CZ2 A:TRP52 4.4 11.1 1.0
CB A:ASP51 4.6 9.5 1.0

Sodium binding site 4 out of 5 in 4gbu

Go back to Sodium Binding Sites List in 4gbu
Sodium binding site 4 out of 5 in the OYE1-W116A in Complex with Aromatic Product of S-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-W116A in Complex with Aromatic Product of S-Carvone Dismutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na414

b:43.9
occ:1.00
 OH3 A:1PE415 2.9 24.7 1.0
OH4 A:1PE415 3.0 35.8 1.0
C12 A:1PE415 3.6 25.6 1.0
CE1 A:HIS380 3.8 13.3 1.0
C22 A:1PE415 3.8 24.1 1.0
C23 A:1PE415 3.8 25.6 1.0
OH2 A:1PE415 3.9 27.9 1.0
C13 A:1PE415 3.9 29.9 1.0
C24 A:1PE415 3.9 34.6 1.0
O A:HOH820 4.0 25.2 1.0
NE2 A:HIS380 4.6 13.9 1.0
ND1 A:HIS380 4.7 11.1 1.0
O A:HOH882 4.7 34.6 1.0

Sodium binding site 5 out of 5 in 4gbu

Go back to Sodium Binding Sites List in 4gbu
Sodium binding site 5 out of 5 in the OYE1-W116A in Complex with Aromatic Product of S-Carvone Dismutation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of OYE1-W116A in Complex with Aromatic Product of S-Carvone Dismutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na416

b:30.0
occ:1.00
 C22 A:1PE406 2.6 37.4 0.8
OH3 A:1PE406 2.9 36.7 0.8
OH4 A:1PE406 2.9 30.0 0.8
O A:HOH611 3.0 18.2 1.0
OH6 A:1PE406 3.0 29.7 0.8
OH5 A:1PE406 3.1 25.3 0.8
C14 A:1PE406 3.4 28.8 0.8
C23 A:1PE406 3.4 33.3 0.8
C25 A:1PE406 3.5 25.7 0.8
C13 A:1PE406 3.6 31.6 0.8
C24 A:1PE406 3.6 30.5 0.8
C12 A:1PE406 3.8 39.4 0.8
C15 A:1PE406 3.8 27.8 0.8
C26 A:1PE406 3.9 30.0 0.8
O A:HOH976 4.1 36.1 1.0
O A:HOH810 4.3 24.4 1.0
CB A:TYR313 4.4 7.5 1.0
O A:ASP310 4.5 8.6 1.0
OH2 A:1PE406 4.6 42.0 0.8
OG A:SER314 4.6 8.0 1.0

Reference:

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
Page generated: Mon Oct 7 15:32:28 2024

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