Sodium in PDB 9fs3: Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate

Enzymatic activity of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate

All present enzymatic activity of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate:
2.1.3.2; 3.5.1.2; 3.5.2.3; 6.3.4.16; 6.3.5.5;

Protein crystallography data

The structure of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate, PDB code: 9fs3 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)*	48.75 / 1.18
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	82.099, 158.499, 61.842, 90, 90, 90
*R / R_free (%)*	15.5 / 17.9

Other elements in 9fs3:

The structure of Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate (pdb code 9fs3). 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 S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate, PDB code: 9fs3:

Sodium binding site 1 out of 1 in 9fs3

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Sodium Binding Sites List in 9fs3

Sodium binding site 1 out of 1 in the Mutant S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to 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 S1538L of the Dihydroorotase Domain of Human Cad Protein Bound to Carbamoyl Aspartate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na1915 b:25.8 occ:1.00	O	A:HOH2268	2.2	23.8	1.0
	O	A:GLY1806	2.4	13.3	1.0
	O	A:HOH2328	2.4	21.0	1.0
	O	A:GLY1804	2.4	14.7	1.0
	O	A:GLU1524	2.5	16.0	1.0
	O	A:HOH2275	2.7	25.4	1.0
	HA	A:GLU1524	3.2	16.9	1.0
	O	A:HOH2007	3.3	22.7	1.0
	C	A:GLY1804	3.4	13.4	1.0
	HA2	A:GLY1804	3.4	16.8	1.0
	C	A:GLU1524	3.5	14.4	1.0
	HB3	A:GLU1524	3.5	17.4	1.0
	C	A:GLY1806	3.5	12.9	1.0
	CA	A:GLU1524	3.7	14.0	1.0
	HA	A:GLN1807	3.7	14.5	1.0
	HG2	A:GLN1807	3.8	16.1	1.0
	CA	A:GLY1804	3.9	14.0	1.0
	CB	A:GLU1524	4.1	14.5	1.0
	HG2	A:GLU1524	4.1	18.7	1.0
	O	A:HOH2337	4.2	37.4	1.0
	N	A:GLY1806	4.2	12.8	1.0
	C	A:TYR1805	4.2	13.2	1.0
	HA3	A:GLY1804	4.2	16.8	1.0
	H	A:GLY1806	4.4	15.4	1.0
	O	A:TYR1805	4.4	14.3	1.0
	N	A:TYR1805	4.4	13.1	1.0
	HG3	A:GLN1807	4.4	16.1	1.0
	N	A:GLN1807	4.5	12.7	1.0
	CA	A:GLY1806	4.5	12.6	1.0
	CA	A:GLN1807	4.5	12.1	1.0
	CG	A:GLN1807	4.5	13.4	1.0
	O	A:HOH2323	4.6	31.5	1.0
	HA	A:TYR1805	4.7	15.6	1.0
	CG	A:GLU1524	4.7	15.6	1.0
	HE2	A:PHE1531	4.7	13.5	1.0
	CA	A:TYR1805	4.7	13.0	1.0
	N	A:ALA1525	4.7	13.7	1.0
	O	A:HOH2321	4.8	33.3	1.0
	HA	A:ALA1525	4.8	17.1	1.0
	O	A:HOH2058	4.9	16.2	1.0
	HB2	A:GLU1524	4.9	17.4	1.0

Reference:

F.Del Cano-Ochoa, L.Ramadane-Morchadi, L.Eixeres, M.Moreno-Morcillo, R.Fernandez-Leiro, S.Ramon-Maiques. Disruption of Cad Oligomerization By Pathogenic Variants. J.Mol.Biol. V. 436 68832 2024.
ISSN: ESSN 1089-8638
PubMed: 39447673
DOI: 10.1016/J.JMB.2024.168832

Page generated: Mon Aug 18 17:06:16 2025

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