Sodium in PDB 3hss: A Higher Resolution Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid

The structure of A Higher Resolution Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid, PDB code: 3hss 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)	40.32 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.454, 100.454, 135.162, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.9

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

Sodium binding site 1 out of 2 in the A Higher Resolution 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 A Higher Resolution Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na268 b:30.8 occ:1.00 O A:HOH538 2.3 32.4 1.0 O A:ALA223 2.3 19.6 1.0 O A:LEU226 2.4 19.7 1.0 O A:HOH537 2.4 36.9 1.0 O A:HOH544 2.4 43.9 1.0 O A:GLY229 2.7 20.6 1.0 C A:ALA223 3.5 19.4 1.0 C A:LEU226 3.6 19.6 1.0 C A:GLY229 3.6 20.7 1.0 O A:ASP224 3.7 20.5 1.0 N A:GLY229 3.8 20.6 1.0 CA A:ASP224 3.9 20.3 1.0 C A:ASP224 4.0 19.2 1.0 CA A:GLY229 4.0 20.1 1.0 N A:ASP224 4.2 19.3 1.0 O A:PRO227 4.3 22.7 1.0 C A:PRO227 4.3 22.1 1.0 N A:LEU226 4.4 17.7 1.0 CA A:LEU226 4.4 18.3 1.0 O A:HOH543 4.5 40.4 1.0 O A:HOH539 4.5 63.7 1.0 CA A:PRO227 4.5 21.8 1.0 N A:PRO227 4.5 21.1 1.0 CA A:ALA223 4.6 18.0 1.0 CB A:LEU226 4.7 17.6 1.0 N A:ARG230 4.8 20.5 1.0 N A:ASN228 4.8 21.5 1.0 N A:ALA225 4.8 16.5 0.7 C A:ASN228 4.9 21.4 1.0 C A:ALA225 5.0 16.5 0.7

Sodium binding site 2 out of 2 in the A Higher Resolution 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 A Higher Resolution Structure of RV0554 From Mycobacterium Tuberculosis Complexed with Malonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Na264 b:38.2 occ:1.00 O B:HOH466 2.1 44.7 1.0 O B:LEU226 2.3 28.9 1.0 O B:ALA223 2.4 31.0 1.0 O B:HOH465 2.4 42.1 1.0 O B:GLY229 3.0 30.4 1.0 O B:ASP224 3.2 34.6 1.0 C B:LEU226 3.5 28.4 1.0 C B:ALA223 3.5 30.8 1.0 C B:ASP224 3.7 32.7 1.0 C B:GLY229 3.8 29.2 1.0 CA B:ASP224 3.8 33.3 1.0 N B:GLY229 3.9 28.3 1.0 O B:HOH464 4.0 43.8 1.0 O B:PRO227 4.1 29.8 1.0 N B:ASP224 4.1 32.1 1.0 N B:LEU226 4.1 29.2 1.0 CA B:GLY229 4.1 28.7 1.0 C B:PRO227 4.3 29.8 1.0 CA B:LEU226 4.3 29.0 1.0 N B:PRO227 4.4 28.9 1.0 CA B:PRO227 4.5 29.1 1.0 N B:ALA225 4.6 31.1 0.7 CA B:ALA223 4.6 29.9 1.0 C B:ALA225 4.6 29.3 0.7 CB B:LEU226 4.7 28.9 1.0 N B:ASN228 4.8 29.0 1.0 N B:ARG230 4.9 28.9 1.0 C B:ASN228 5.0 28.8 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