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Sodium in PDB 8pbg: Mutant K1556T of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate

Enzymatic activity of Mutant K1556T of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate

All present enzymatic activity of Mutant K1556T of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate:
2.1.3.2; 3.5.2.3; 6.3.5.5;

Protein crystallography data

The structure of Mutant K1556T of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate, PDB code: 8pbg was solved by F.Del Cano-Ochoa, S.Ramon-Maiques, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.53 / 1.46
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.06, 159.031, 61.933, 90, 90, 90
R / Rfree (%) 12.3 / 15

Other elements in 8pbg:

The structure of Mutant K1556T of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Fluorine (F) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Mutant K1556T of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate (pdb code 8pbg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Mutant K1556T of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate, PDB code: 8pbg:

Sodium binding site 1 out of 1 in 8pbg

Go back to Sodium Binding Sites List in 8pbg
Sodium binding site 1 out of 1 in the Mutant K1556T of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mutant K1556T of the Dihydroorotase Domain of Human Cad Protein Bound to the Inhibitor Fluoroorotate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1909

b:29.7
occ:1.00
 O A:GLY1806 2.3 20.5 1.0
O A:HOH2251 2.4 30.5 1.0
O A:GLY1804 2.4 23.6 1.0
O A:GLU1524 2.6 23.7 1.0
O A:HOH2253 2.8 32.6 1.0
HA A:GLU1524 3.2 24.7 1.0
O A:HOH2002 3.3 33.6 1.0
C A:GLY1804 3.4 22.6 1.0
HA2 A:GLY1804 3.4 26.9 1.0
C A:GLY1806 3.5 19.6 1.0
C A:GLU1524 3.5 22.4 1.0
HB3 A:GLU1524 3.6 25.2 1.0
HA A:GLN1807 3.7 22.9 1.0
HG2 A:GLN1807 3.8 25.7 1.0
CA A:GLU1524 3.8 20.6 1.0
CA A:GLY1804 3.9 22.4 1.0
CB A:GLU1524 4.1 21.0 1.0
O A:HOH2315 4.1 52.2 1.0
HG2 A:GLU1524 4.2 25.9 1.0
N A:GLY1806 4.2 19.3 1.0
C A:TYR1805 4.2 20.3 1.0
HA3 A:GLY1804 4.3 26.9 1.0
O A:TYR1805 4.3 22.2 1.0
H A:GLY1806 4.4 23.2 1.0
N A:TYR1805 4.4 22.1 1.0
N A:GLN1807 4.4 18.9 1.0
HG3 A:GLN1807 4.4 25.7 1.0
CA A:GLY1806 4.4 19.4 1.0
CA A:GLN1807 4.5 19.1 1.0
CG A:GLN1807 4.5 21.4 1.0
O A:HOH2318 4.6 49.3 1.0
HA A:TYR1805 4.6 25.4 1.0
CA A:TYR1805 4.7 21.2 1.0
HE2 A:PHE1531 4.7 23.0 1.0
CG A:GLU1524 4.7 21.6 1.0
N A:ALA1525 4.8 21.7 1.0
HA A:ALA1525 4.9 26.2 1.0
O A:HOH2052 4.9 22.9 1.0
O A:HOH2293 4.9 45.4 1.0
HA3 A:GLY1806 5.0 23.2 1.0
HB2 A:GLU1524 5.0 25.2 1.0
O A:ALA1523 5.0 19.4 1.0

Reference:

F.Del Cano-Ochoa, B.G.Ng, A.Rubio-Del-Campo, S.Mahajan, M.P.Wilson, M.Vilar, D.Rymen, P.Sanchez-Pintos, J.Kenny, M.Ley Martos, T.Campos, S.B.Wortmann, H.H.Freeze, S.Ramon-Maiques. Beyond Genetics: Deciphering the Impact of Missense Variants in Cad Deficiency. J Inherit Metab Dis 2023.
ISSN: ISSN 1573-2665
PubMed: 37540500
DOI: 10.1002/JIMD.12667
Page generated: Mon Aug 18 15:00:29 2025

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