Sodium in PDB 4b6c: Structure of the M. Smegmatis Gyrb Atpase Domain in Complex with An Aminopyrazinamide

All present enzymatic activity of Structure of the M. Smegmatis Gyrb Atpase Domain in Complex with An Aminopyrazinamide:
5.99.1.3;

The structure of Structure of the M. Smegmatis Gyrb Atpase Domain in Complex with An Aminopyrazinamide, PDB code: 4b6c was solved by J.A.Tucker, P.S.Shirude, P.Madhavapeddi, S.Hussein, R.Basu, S.Ghorpade, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.06 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	43.455, 82.251, 191.941, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25.4

The binding sites of Sodium atom in the Structure of the M. Smegmatis Gyrb Atpase Domain in Complex with An Aminopyrazinamide (pdb code 4b6c). 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 the M. Smegmatis Gyrb Atpase Domain in Complex with An Aminopyrazinamide, PDB code: 4b6c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the M. Smegmatis Gyrb Atpase Domain in Complex with An Aminopyrazinamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the M. Smegmatis Gyrb Atpase Domain in Complex with An Aminopyrazinamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1257 b:47.3 occ:1.00 OG1 A:THR167 2.3 36.6 1.0 O A:ASP80 2.4 34.5 1.0 O A:HOH2042 2.4 38.8 1.0 O A:GLY81 2.5 27.6 1.0 O A:HOH2041 3.0 45.6 1.0 C A:ASP80 3.3 33.3 1.0 O A:THR167 3.3 35.7 1.0 C A:GLY81 3.4 29.8 1.0 CB A:THR167 3.5 37.8 1.0 C A:THR167 3.8 36.5 1.0 CA A:GLY81 4.0 27.3 1.0 CA A:THR167 4.0 33.5 1.0 N A:GLY81 4.0 28.4 1.0 O A:PHE61 4.1 36.7 1.0 N A:THR167 4.3 35.2 1.0 CA A:ASP80 4.4 28.5 1.0 O A:HOH2043 4.4 40.3 1.0 N A:ARG82 4.4 27.7 1.0 CB A:ASP80 4.6 30.4 1.0 N A:GLY168 4.7 32.9 1.0 CG2 A:THR167 4.7 35.8 1.0 CA A:ARG82 4.8 28.7 1.0 CG A:ASP80 5.0 34.8 1.0

Sodium binding site 2 out of 2 in the Structure of the M. Smegmatis Gyrb Atpase Domain in Complex with An Aminopyrazinamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the M. Smegmatis Gyrb Atpase Domain in Complex with An Aminopyrazinamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1257 b:40.8 occ:1.00 OG1 B:THR167 2.3 30.7 1.0 O B:HOH2010 2.4 42.1 1.0 O B:HOH2044 2.4 60.3 1.0 O B:HOH2011 2.5 47.0 1.0 O B:ASP80 2.6 30.6 1.0 O B:HOH2043 2.6 35.8 1.0 O B:GLY81 2.9 27.4 1.0 O B:THR167 3.0 30.1 1.0 C B:ASP80 3.5 29.1 1.0 CB B:THR167 3.5 32.0 1.0 C B:THR167 3.7 30.7 1.0 C B:GLY81 3.8 27.4 1.0 CA B:THR167 3.9 29.3 1.0 N B:THR167 4.0 31.7 1.0 N B:GLY81 4.2 23.5 1.0 CA B:GLY81 4.3 23.0 1.0 O B:PHE61 4.3 36.9 1.0 CA B:ASP80 4.4 24.0 1.0 CB B:ASP80 4.5 25.8 1.0 CG2 B:THR167 4.6 27.8 1.0 N B:GLY168 4.7 26.1 1.0 N B:ARG82 4.7 24.9 1.0

P.S.Shirude, P.Madhavapeddi, J.A.Tucker, K.Murugan, V.Patil, H.Basavarajappa, A.V.Raichurkar, V.Humnabadkar, S.Hussein, S.Sharma, V.K.Ramya, C.B.Narayan, T.S.Balganesh, V.K.Sambandamurthy. Aminopyrazinamides: Novel and Specific Gyrb Inhibitors That Kill Replicating and Nonreplicating Mycobacterium Tuberculosis. Acs Chem. Biol. V. 8 519 2013.
ISSN: ESSN 1554-8937
PubMed: 23268609
DOI: 10.1021/CB300510W