Sodium in PDB 5ltn: Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba

All present enzymatic activity of Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba:
2.7.7.48;

The structure of Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba, PDB code: 5ltn was solved by M.Saez-Ayala, E.L.Yekwa, B.Canard, K.Alvarez, F.Ferron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.59 / 1.88
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	107.185, 107.185, 53.807, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 21.6

The structure of Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba (pdb code 5ltn). 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 Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba, PDB code: 5ltn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba


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 Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:89.3 occ:1.00 OD1 A:ASP94 2.2 72.5 0.4 O1 A:PEG208 2.9 95.2 1.0 CG A:ASP94 2.9 68.0 0.4 OD2 A:ASP94 3.1 69.8 0.4 C1 A:PEG208 4.2 90.9 1.0 CB A:ASP94 4.3 59.3 0.6 CB A:ASP94 4.3 59.8 0.4 OD1 A:ASN95 4.5 93.7 1.0 CG A:ASP94 4.7 65.7 0.6 CA A:ASP94 4.7 55.8 0.4 CA A:ASP94 4.7 55.5 0.6 N A:ASN95 4.7 55.4 1.0 C A:ASP94 4.9 55.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba


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 Lymphocytic Choriomeningitis Mammarenavirus Endonuclease Complexed with Dpba within 5.0Å range: probe atom residue distance (Å) B Occ A:Na210 b:81.2 occ:1.00 OD1 A:ASP128 2.8 81.6 1.0 CD A:PRO83 3.8 65.4 1.0 CG A:ASP128 3.8 74.2 1.0 OD2 A:ASP128 4.0 79.0 1.0 CG A:PRO83 4.1 65.4 1.0 O A:CYS124 4.4 61.0 1.0 O A:HOH346 4.6 52.4 1.0 O A:GLY81 4.7 72.9 1.0

M.Saez-Ayala, E.L.Yekwa, M.Carcelli, B.Canard, K.Alvarez, F.Ferron. Crystal Structures of Lymphocytic Choriomeningitis Virusendonuclease Domain Complexed with Diketo-Acid Ligands. Iucrj V. 5 223 2018.
ISSN: ESSN 2052-2525
PubMed: 29765612
DOI: 10.1107/S2052252518001021