Sodium in PDB 8i61: Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with Barbituric Acid and Citric Acid, Form I

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with Barbituric Acid and Citric Acid, Form I:
3.2.2.27;

The structure of Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with Barbituric Acid and Citric Acid, Form I, PDB code: 8i61 was solved by P.Raj, A.Paul, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.85 / 1.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.05, 63.65, 45.31, 90, 112.82, 90
R / Rfree (%)	12.1 / 16.3

The binding sites of Sodium atom in the Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with Barbituric Acid and Citric Acid, Form I (pdb code 8i61). 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 Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with Barbituric Acid and Citric Acid, Form I, PDB code: 8i61:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with Barbituric Acid and Citric Acid, Form I


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 Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with Barbituric Acid and Citric Acid, Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:13.2 occ:1.00 OE1 A:GLN67 2.4 10.2 1.0 O4 A:CIT302 2.4 15.9 1.0 O A:HOH637 2.4 17.3 1.0 O7 A:CIT302 2.4 15.4 1.0 O6 A:CIT302 2.4 18.0 1.0 O A:HOH566 2.5 15.7 1.0 C6 A:CIT302 3.1 17.4 1.0 CD A:GLN67 3.2 8.7 1.0 C3 A:CIT302 3.2 13.4 1.0 C5 A:CIT302 3.4 12.8 1.0 NE2 A:GLN67 3.5 10.1 1.0 O A:HOH512 3.7 28.0 1.0 C4 A:CIT302 3.8 13.6 1.0 NA A:NA307 3.9 14.3 1.0 O A:HOH516 4.1 25.9 1.0 O5 A:CIT302 4.2 15.0 1.0 O2 A:CIT302 4.3 19.7 1.0 O3 A:CIT302 4.4 12.5 1.0 O A:HOH423 4.4 22.8 1.0 O A:HOH677 4.4 30.1 1.0 CG A:GLN67 4.6 8.6 1.0 C2 A:CIT302 4.6 14.9 1.0 O A:HOH710 4.6 29.6 1.0 O A:HOH522 4.7 19.1 1.0 NH2 A:ARG141 4.8 13.5 1.0 CB A:GLN67 4.9 7.3 1.0 C1 A:CIT302 4.9 17.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with Barbituric Acid and Citric Acid, Form I


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 Mycobacterium Tuberculosis Uracil-Dna Glycosylase in Complex with Barbituric Acid and Citric Acid, Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:14.3 occ:1.00 O4 A:CIT302 2.7 15.9 1.0 OE1 A:GLN67 2.8 10.2 1.0 O A:HOH506 2.8 8.5 1.0 N A:ASP171 3.0 9.4 1.0 N A:ARG170 3.3 9.5 1.0 C5 A:CIT302 3.4 12.8 1.0 O3 A:CIT302 3.4 12.5 1.0 CG A:ASP171 3.5 9.6 1.0 CB A:ASP171 3.5 9.3 1.0 CD A:GLN67 3.6 8.7 1.0 CB A:GLN67 3.7 7.3 1.0 OD2 A:ASP171 3.7 11.4 1.0 OD1 A:ASP171 3.7 11.0 1.0 CG A:GLN67 3.7 8.6 1.0 CA A:ASP171 3.9 9.2 1.0 NA A:NA306 3.9 13.2 1.0 C A:ARG170 4.0 10.3 1.0 CA A:ARG170 4.0 11.0 1.0 C A:GLY169 4.0 9.9 1.0 CB A:ARG170 4.2 13.3 1.0 CA A:GLY169 4.3 9.6 1.0 CA A:GLN67 4.5 6.0 1.0 N A:ALA172 4.7 9.9 1.0 O A:HOH637 4.7 17.3 1.0 O A:GLY169 4.8 10.0 1.0 NH2 A:ARG141 4.8 13.5 1.0 C A:ASP171 4.8 10.8 1.0 CD2 A:HIS191 4.8 7.6 1.0 NE2 A:GLN67 4.9 10.1 1.0 C4 A:CIT302 4.9 13.6 1.0 O6 A:CIT302 4.9 18.0 1.0 O A:TRP168 4.9 9.2 1.0

S.Kesharwani, P.Raj, A.Paul, K.Roy, A.Bhanot, A.Mehta, A.Gopal, U.Varshney, B.Gopal, S.Sundriyal. Crystal Structures of Non-Uracil Ring Fragments in Complex with Mycobacterium Tuberculosis Uracil Dna Glycosylase (Mtung) As A Starting Point For Novel Inhibitor Design: A Case Study with the Barbituric Acid Fragment Eur.J.Med.Chem. V. 258 15604 2023.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2023.115604