Sodium in PDB 3hys: Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid

The structure of Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid, PDB code: 3hys was solved by J.M.Johnston, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.435, 100.435, 135.064, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 22.3

The binding sites of Sodium atom in the Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid (pdb code 3hys). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid, PDB code: 3hys:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na267 b:39.1 occ:1.00 O A:HOH309 2.2 30.0 1.0 O A:LEU226 2.4 25.8 1.0 O A:ALA223 2.4 25.7 1.0 O A:HOH308 2.7 37.5 1.0 O A:GLY229 2.8 25.6 1.0 C A:ALA223 3.6 24.1 1.0 C A:LEU226 3.6 24.9 1.0 C A:GLY229 3.7 25.8 1.0 O A:ASP224 3.8 22.0 1.0 N A:GLY229 3.8 23.5 1.0 CA A:ASP224 3.9 24.6 1.0 C A:ASP224 4.0 22.9 1.0 CA A:GLY229 4.0 23.9 1.0 N A:ASP224 4.2 23.8 1.0 O A:PRO227 4.3 26.8 1.0 C A:PRO227 4.3 26.2 1.0 N A:LEU226 4.4 22.8 1.0 CA A:PRO227 4.5 25.3 1.0 CA A:LEU226 4.5 22.8 1.0 N A:PRO227 4.6 25.6 1.0 CA A:ALA223 4.7 22.7 1.0 N A:ARG230 4.8 26.3 1.0 CB A:LEU226 4.8 21.6 1.0 N A:ASN228 4.8 24.8 1.0 C A:ASN228 4.9 24.9 1.0 N A:ALA225 4.9 19.5 0.7

Sodium binding site 2 out of 2 in the Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na267 b:40.9 occ:1.00 O B:LEU226 2.3 30.9 1.0 O B:HOH282 2.4 44.3 1.0 O B:ALA223 2.4 36.7 1.0 O B:GLY229 3.0 34.3 1.0 O B:ASP224 3.2 39.3 1.0 C B:ALA223 3.5 35.4 1.0 C B:LEU226 3.5 32.5 1.0 C B:ASP224 3.7 37.4 1.0 CA B:ASP224 3.8 38.1 1.0 N B:GLY229 3.8 32.7 1.0 C B:GLY229 3.9 32.1 1.0 O B:PRO227 3.9 35.4 1.0 N B:ASP224 4.1 36.3 1.0 CA B:GLY229 4.1 31.4 1.0 C B:PRO227 4.2 34.9 1.0 N B:LEU226 4.2 32.8 1.0 CA B:LEU226 4.4 32.9 1.0 O B:HOH283 4.4 44.7 1.0 CA B:PRO227 4.4 34.6 1.0 N B:PRO227 4.5 33.2 1.0 C B:ALA225 4.7 32.9 0.7 CA B:ALA223 4.7 32.9 1.0 N B:ALA225 4.7 34.9 0.7 N B:ASN228 4.8 34.0 1.0 CB B:LEU226 4.8 32.2 1.0 C B:ASN228 5.0 33.2 1.0

J.M.Johnston, M.Jiang, Z.Guo, E.N.Baker. Structural and Functional Analysis of RV0554 From Mycobacterium Tuberculosis: Testing A Putative Role in Menaquinone Biosynthesis. Acta Crystallogr.,Sect.D V. 66 909 2010.
ISSN: ISSN 0907-4449
PubMed: 20693690
DOI: 10.1107/S0907444910025771