Sodium in PDB 4ook: Third Metal Bound M.Tuberculosis Methionine Aminopeptidase

All present enzymatic activity of Third Metal Bound M.Tuberculosis Methionine Aminopeptidase:
3.4.11.18;

The structure of Third Metal Bound M.Tuberculosis Methionine Aminopeptidase, PDB code: 4ook was solved by R.Reddi, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.81 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.221, 48.136, 56.284, 90.00, 95.25, 90.00
R / Rfree (%)	17.5 / 23.1

The structure of Third Metal Bound M.Tuberculosis Methionine Aminopeptidase also contains other interesting chemical elements:

Cobalt

(Co)

3 atoms

The binding sites of Sodium atom in the Third Metal Bound M.Tuberculosis Methionine Aminopeptidase (pdb code 4ook). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Third Metal Bound M.Tuberculosis Methionine Aminopeptidase, PDB code: 4ook:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Third Metal Bound M.Tuberculosis Methionine Aminopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Third Metal Bound M.Tuberculosis Methionine Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:35.2 occ:1.00 OG1 A:THR265 2.7 24.7 1.0 O A:ILE112 2.8 22.1 1.0 O A:HOH483 2.9 23.6 1.0 O A:ALA266 3.4 23.0 1.0 CG A:MET240 3.4 24.5 1.0 C A:ALA266 3.4 20.5 1.0 N A:ALA266 3.5 22.9 1.0 CB A:MET240 3.5 20.2 1.0 C A:ILE112 3.6 26.3 1.0 CB A:THR265 3.7 23.4 1.0 C A:THR265 3.7 23.8 1.0 CA A:ALA266 3.7 22.4 1.0 CG2 A:THR265 3.7 25.7 1.0 CA A:ILE112 3.7 24.5 1.0 CB A:GLN267 3.9 21.5 1.0 CA A:MET240 3.9 19.2 1.0 O A:HOH455 3.9 21.5 1.0 N A:GLN267 4.0 21.1 1.0 O A:THR265 4.1 24.4 1.0 O A:VAL111 4.2 26.6 1.0 CG2 A:ILE112 4.2 24.7 1.0 CA A:THR265 4.3 24.9 1.0 N A:ILE241 4.4 20.5 1.0 CA A:GLN267 4.5 21.0 1.0 O A:HOH476 4.5 29.7 1.0 C A:MET240 4.6 17.8 1.0 CB A:ILE112 4.6 23.5 1.0 N A:ILE112 4.7 21.3 1.0 OE1 A:GLN267 4.8 20.7 1.0 SD A:MET240 4.8 26.8 1.0 C A:VAL111 4.9 26.2 1.0 N A:CYS113 4.9 25.9 1.0 CG A:GLN267 4.9 20.3 1.0 O A:ILE241 4.9 21.5 1.0 OD1 A:ASN242 5.0 29.8 1.0

Sodium binding site 2 out of 2 in the Third Metal Bound M.Tuberculosis Methionine Aminopeptidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Third Metal Bound M.Tuberculosis Methionine Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:36.4 occ:1.00 O A:MET50 2.8 19.1 1.0 O A:HIS140 3.1 19.3 1.0 CA A:GLY141 3.3 20.3 1.0 C A:MET50 3.6 20.5 1.0 CB A:MET50 3.6 19.6 1.0 CG2 A:THR271 3.7 15.5 1.0 CE A:MET50 3.7 19.9 1.0 CA A:MET50 3.8 20.2 1.0 N A:GLY54 3.8 19.9 1.0 CA A:GLY54 3.9 22.8 1.0 C A:HIS140 3.9 19.6 1.0 N A:GLY141 4.0 20.2 1.0 CD1 A:LEU282 4.0 21.8 1.0 CG A:MET50 4.0 21.2 1.0 CB A:LEU282 4.1 22.1 1.0 CB A:THR271 4.2 16.5 1.0 OG1 A:THR271 4.5 17.5 1.0 CB A:ALA53 4.5 18.4 1.0 C A:GLY141 4.6 20.9 1.0 C A:ALA53 4.6 19.7 1.0 N A:ARG51 4.7 21.9 1.0 CG A:LEU282 4.7 20.5 1.0 SD A:MET50 4.8 21.9 1.0 N A:ASP142 4.8 18.6 1.0 CG2 A:THR283 4.9 22.1 1.0

R.Reddi, T.Arya, C.Kishor, R.Gumpena, R.J.Ganji, S.Bhukya, A.Addlagatta. Selective Targeting of the Conserved Active Site Cysteine of Mycobacterium Tuberculosis Methionine Aminopeptidase with Electrophilic Reagents Febs J. V. 281 4240 2014.
ISSN: ISSN 1742-464X
PubMed: 24841365
DOI: 10.1111/FEBS.12847