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Sodium in PDB 4h4i: OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone

Enzymatic activity of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone

All present enzymatic activity of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone:
1.6.99.1;

Protein crystallography data

The structure of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone, PDB code: 4h4i 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) 23.55 / 1.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.004, 141.004, 42.818, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 14.6

Other elements in 4h4i:

The structure of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone (pdb code 4h4i). 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-W116V Complexed with the Dismutation Product of (S)-Carvone, PDB code: 4h4i:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4h4i

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Sodium binding site 1 out of 5 in the OYE1-W116V Complexed with the Dismutation Product of (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-W116V Complexed with the Dismutation Product of (S)-Carvone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:29.0
occ:1.00
OH5 A:1PE409 2.8 23.1 0.7
O A:HOH916 3.0 30.5 1.0
OH4 A:1PE409 3.1 25.3 0.7
OH3 A:1PE409 3.3 31.2 0.7
O A:HOH1130 3.3 40.7 1.0
C24 A:1PE409 3.5 24.0 0.7
C12 A:1PE409 3.5 33.3 0.7
C13 A:1PE409 3.5 28.2 0.7
C22 A:1PE409 3.6 31.5 0.7
C15 A:1PE409 3.6 24.8 0.7
C14 A:1PE409 3.7 21.2 0.7
C25 A:1PE409 3.7 22.7 0.7
CD2 A:TYR375 3.7 11.9 1.0
C23 A:1PE409 3.7 30.1 0.7
OH6 A:1PE409 3.7 29.5 0.7
CE2 A:TYR375 3.9 11.5 1.0
CG A:TYR375 5.0 9.7 1.0

Sodium binding site 2 out of 5 in 4h4i

Go back to Sodium Binding Sites List in 4h4i
Sodium binding site 2 out of 5 in the OYE1-W116V Complexed with the Dismutation Product of (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-W116V Complexed with the Dismutation Product of (S)-Carvone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:34.9
occ:1.00
C23 A:1PE410 2.8 26.8 0.8
N A:ALA10 2.9 10.9 1.0
OH4 A:1PE410 3.1 28.8 0.8
C22 A:1PE410 3.1 27.3 0.8
C13 A:1PE410 3.3 24.6 0.8
OH3 A:1PE410 3.3 27.0 0.8
C15 A:1PE410 3.4 31.1 0.8
C24 A:1PE410 3.5 33.2 0.8
OH5 A:1PE410 3.5 30.0 0.8
CB A:ALA10 3.6 11.8 1.0
CA A:GLN9 3.6 13.3 1.0
C14 A:1PE410 3.7 31.5 0.8
C A:GLN9 3.7 12.1 1.0
C25 A:1PE410 3.7 28.8 0.8
CA A:ALA10 3.8 11.2 1.0
CG A:GLN9 4.3 24.8 1.0
O A:PRO8 4.5 15.7 1.0
CB A:GLN9 4.5 19.6 1.0
O A:ALA10 4.5 14.5 1.0
C A:ALA10 4.7 10.9 1.0
N A:GLN9 4.7 13.2 1.0
O A:GLN9 4.9 13.4 1.0
C A:PRO8 5.0 14.3 1.0

Sodium binding site 3 out of 5 in 4h4i

Go back to Sodium Binding Sites List in 4h4i
Sodium binding site 3 out of 5 in the OYE1-W116V Complexed with the Dismutation Product of (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-W116V Complexed with the Dismutation Product of (S)-Carvone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:34.0
occ:1.00
OH4 A:1PE404 2.9 21.9 0.6
NE1 A:TRP52 3.0 10.4 1.0
OH3 A:1PE404 3.0 27.9 0.6
OH5 A:1PE404 3.1 20.4 0.6
O A:HOH889 3.3 45.4 1.0
C23 A:1PE404 3.4 24.3 0.6
C22 A:1PE404 3.5 28.8 0.6
C12 A:1PE404 3.6 33.0 0.6
C25 A:1PE404 3.6 21.8 0.6
C13 A:1PE404 3.6 22.7 0.6
OH6 A:1PE404 3.7 34.6 0.6
CD1 A:TRP52 3.7 9.5 1.0
C14 A:1PE404 3.8 20.6 0.6
C24 A:1PE404 3.8 21.1 0.6
C15 A:1PE404 4.0 28.2 0.6
CE2 A:TRP52 4.1 9.8 1.0
O A:HOH1126 4.4 38.5 1.0
CZ2 A:TRP52 4.5 10.5 1.0
CB A:ASP51 4.7 10.2 1.0

Sodium binding site 4 out of 5 in 4h4i

Go back to Sodium Binding Sites List in 4h4i
Sodium binding site 4 out of 5 in the OYE1-W116V Complexed with the Dismutation Product of (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-W116V Complexed with the Dismutation Product of (S)-Carvone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na414

b:44.9
occ:1.00
OH3 A:1PE415 3.0 24.7 1.0
OH4 A:1PE415 3.1 34.3 1.0
C12 A:1PE415 3.6 28.2 1.0
OH2 A:1PE415 3.6 33.5 1.0
C22 A:1PE415 3.8 24.3 1.0
O A:HOH820 3.9 25.9 1.0
C24 A:1PE415 3.9 34.4 1.0
C23 A:1PE415 3.9 25.5 1.0
CE1 A:HIS380 3.9 13.4 1.0
C13 A:1PE415 4.0 27.7 1.0
O A:HOH881 4.2 39.5 1.0
NE2 A:HIS380 4.7 13.2 1.0
ND1 A:HIS380 4.9 11.7 1.0

Sodium binding site 5 out of 5 in 4h4i

Go back to Sodium Binding Sites List in 4h4i
Sodium binding site 5 out of 5 in the OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of OYE1-W116V Complexed with the Dismutation Product of (S)-Carvone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na417

b:30.0
occ:1.00
OH6 A:1PE405 2.7 29.0 0.7
OH4 A:1PE405 2.9 30.3 0.7
C22 A:1PE405 2.9 37.5 0.7
OH3 A:1PE405 3.0 37.3 0.7
OH5 A:1PE405 3.1 24.3 0.7
O A:HOH611 3.1 17.6 1.0
C23 A:1PE405 3.3 31.0 0.7
C14 A:1PE405 3.4 28.2 0.7
C26 A:1PE405 3.4 29.9 0.7
C25 A:1PE405 3.5 24.5 0.7
C13 A:1PE405 3.6 30.1 0.7
C15 A:1PE405 3.7 27.4 0.7
C24 A:1PE405 3.7 30.5 0.7
O A:HOH974 4.3 38.4 1.0
C12 A:1PE405 4.3 39.9 0.7
CB A:TYR313 4.4 8.1 1.0
O A:HOH810 4.4 26.6 1.0
O A:ASP310 4.6 8.0 1.0
OG A:SER314 4.6 7.6 1.0
OH2 A:1PE405 4.9 44.2 0.7

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: Tue Dec 15 06:42:41 2020

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