Sodium in PDB 6oze: Crystal Structure of the Catalytic Domain of Human Endonuclease V (C140S/C225S/C226A/C228S)

The structure of Crystal Structure of the Catalytic Domain of Human Endonuclease V (C140S/C225S/C226A/C228S), PDB code: 6oze was solved by N.L.Samara, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.73 / 1.50
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	50.949, 50.949, 102.978, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 19.1

The binding sites of Sodium atom in the Crystal Structure of the Catalytic Domain of Human Endonuclease V (C140S/C225S/C226A/C228S) (pdb code 6oze). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Catalytic Domain of Human Endonuclease V (C140S/C225S/C226A/C228S), PDB code: 6oze:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human Endonuclease V (C140S/C225S/C226A/C228S)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Catalytic Domain of Human Endonuclease V (C140S/C225S/C226A/C228S) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:36.1 occ:1.00 O A:HOH462 2.3 37.9 1.0 O A:LEU176 2.3 37.1 1.0 O A:ARG174 2.3 32.2 1.0 O A:HOH521 2.5 57.6 1.0 O A:HOH470 2.5 58.3 1.0 OE1 A:GLN177 2.8 70.6 1.0 C A:ARG174 3.4 33.7 1.0 C A:LEU176 3.5 29.4 1.0 NH2 A:ARG198 3.5 33.9 0.2 NH1 A:ARG198 3.9 33.3 0.8 CD A:GLN177 4.0 65.3 1.0 N A:LEU176 4.2 26.6 1.0 O A:ILE173 4.2 26.7 1.0 CA A:ARG174 4.3 29.8 1.0 C A:LEU175 4.3 27.9 1.0 CA A:GLN177 4.3 31.5 1.0 N A:GLN177 4.3 29.6 1.0 N A:LEU175 4.3 26.4 1.0 O A:HOH444 4.4 60.5 1.0 O A:HOH419 4.4 41.1 1.0 CA A:LEU176 4.5 28.2 1.0 CA A:LEU175 4.5 31.4 1.0 CG A:GLN177 4.7 43.6 1.0 O A:LEU175 4.7 30.6 1.0 CZ A:ARG198 4.8 31.6 0.2 CG A:ARG174 5.0 31.9 1.0 NE2 A:GLN177 5.0 70.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human Endonuclease V (C140S/C225S/C226A/C228S)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Catalytic Domain of Human Endonuclease V (C140S/C225S/C226A/C228S) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:41.0 occ:1.00 O A:LEU45 2.3 27.3 1.0 OE1 A:GLN46 2.4 51.1 1.0 O A:HOH487 2.5 35.1 1.0 O A:HOH507 2.6 57.3 1.0 O A:PHE72 2.7 27.5 1.0 O A:HOH449 2.8 45.4 1.0 C A:LEU45 3.4 26.9 1.0 CD A:GLN46 3.6 53.3 1.0 C A:PHE72 3.7 24.5 1.0 CD A:PRO73 3.7 29.0 1.0 O A:HOH417 3.7 41.8 1.0 CA A:GLN46 4.0 29.1 1.0 N A:PRO73 4.1 24.1 1.0 N A:GLN46 4.1 28.5 1.0 CD1 A:PHE72 4.2 25.3 1.0 O A:HOH529 4.3 48.0 1.0 CG A:GLN46 4.3 43.8 1.0 N A:LEU45 4.4 26.6 1.0 CA A:LEU45 4.5 25.3 1.0 NE2 A:GLN46 4.6 69.1 1.0 CB A:GLN46 4.7 32.1 1.0 CB A:PHE72 4.8 25.5 1.0 O A:PHE42 4.8 31.2 1.0 CA A:PHE72 4.8 23.4 1.0 N A:GLY44 4.9 32.0 1.0 C A:GLY44 4.9 34.8 1.0

J.Wu, N.L.Samara, I.Kuraoka, W.Yang. Evolution of Inosine-Specific Endonuclease V From Bacterial Dnase to Eukaryotic Rnase. Mol.Cell V. 76 44 2019.
ISSN: ISSN 1097-2765
PubMed: 31444105
DOI: 10.1016/J.MOLCEL.2019.06.046