Atomistry » Sodium » PDB 4gxj-4hfc » 4h4i
Atomistry »
  Sodium »
    PDB 4gxj-4hfc »
      4h4i »

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

Go back to Sodium Binding Sites List in 4h4i
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: Mon Oct 7 15:44:07 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy