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Sodium in PDB 8pbh: Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate

Enzymatic activity of Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate

All present enzymatic activity of Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate:
2.1.3.2; 3.5.2.3; 6.3.5.5;

Protein crystallography data

The structure of Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate, PDB code: 8pbh 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) 48.76 / 1.87
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 82.413, 159.722, 61.575, 90, 90, 90
R / Rfree (%) 15.3 / 19.2

Other elements in 8pbh:

The structure of Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate (pdb code 8pbh). 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 R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate, PDB code: 8pbh:

Sodium binding site 1 out of 1 in 8pbh

Go back to Sodium Binding Sites List in 8pbh
Sodium binding site 1 out of 1 in the Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mutant R1617Q of the Dihydroorotase Domain of Human Cad Protein Bound to the Substrate Carbamoyl Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1906

b:32.8
occ:1.00
 O A:HOH2189 2.3 34.2 1.0
O A:GLY1804 2.3 27.6 1.0
O A:HOH2163 2.4 37.5 1.0
O A:GLY1806 2.4 23.6 1.0
O A:GLU1524 2.6 25.5 1.0
O A:HOH2174 2.8 39.9 1.0
C A:GLY1804 3.3 25.5 1.0
HA A:GLU1524 3.3 31.1 1.0
HA2 A:GLY1804 3.4 31.4 1.0
C A:GLY1806 3.5 24.3 1.0
C A:GLU1524 3.6 26.2 1.0
HB3 A:GLU1524 3.6 32.4 1.0
HA A:GLN1807 3.8 27.7 1.0
CA A:GLU1524 3.8 26.0 1.0
CA A:GLY1804 3.9 26.1 1.0
HG2 A:GLN1807 3.9 29.4 1.0
HG2 A:GLU1524 4.0 31.8 1.0
N A:GLY1806 4.1 24.4 1.0
C A:TYR1805 4.1 24.5 1.0
CB A:GLU1524 4.2 27.0 1.0
HA3 A:GLY1804 4.2 31.4 1.0
H A:GLY1806 4.3 29.3 1.0
O A:HOH2220 4.3 54.3 1.0
O A:TYR1805 4.3 24.6 1.0
N A:TYR1805 4.3 25.6 1.0
HG3 A:GLN1807 4.3 29.4 1.0
CA A:GLY1806 4.4 24.3 1.0
N A:GLN1807 4.5 23.8 1.0
HA A:TYR1805 4.5 30.4 1.0
CG A:GLN1807 4.5 24.5 1.0
CA A:GLN1807 4.5 23.1 1.0
CA A:TYR1805 4.6 25.4 1.0
CG A:GLU1524 4.6 26.5 1.0
N A:ALA1525 4.8 26.4 1.0
HE2 A:PHE1531 4.8 25.7 1.0
HA A:ALA1525 4.8 32.5 1.0
HA3 A:GLY1806 5.0 29.1 1.0
O A:HOH2076 5.0 25.9 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: Wed Oct 9 12:55:13 2024

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