Sodium in PDB 6k26: Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase

All present enzymatic activity of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase:
3.4.11.18;

The structure of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase, PDB code: 6k26 was solved by V.Pillalamarri, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.66 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.529, 50.010, 131.086, 90.00, 97.25, 90.00
R / Rfree (%)	16.6 / 20.8

The binding sites of Sodium atom in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase (pdb code 6k26). 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 Vibrio Cholerae Methionine Aminopeptidase, PDB code: 6k26:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase


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 Vibrio Cholerae Methionine Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:17.4 occ:1.00 O A:HOH493 2.2 21.7 1.0 O A:SER248 2.2 15.8 1.0 O A:ILE76 2.3 14.7 1.0 O A:ASN74 2.3 15.0 1.0 C A:SER248 3.3 14.2 1.0 C A:ASN74 3.3 15.6 1.0 C A:ILE76 3.4 15.3 1.0 O A:HOH560 3.5 18.4 1.0 N A:ASN74 3.6 15.9 1.0 N A:SER248 3.7 14.0 1.0 CA A:SER248 3.8 14.3 1.0 CA A:ASN74 3.9 16.0 1.0 C A:ILE73 3.9 15.2 1.0 CB A:SER248 3.9 15.8 1.0 N A:ILE76 4.0 14.3 1.0 O A:SER72 4.2 13.6 1.0 O A:ILE73 4.2 15.2 1.0 CA A:ILE76 4.3 15.0 1.0 N A:HIS75 4.3 14.6 1.0 O A:HOH437 4.3 16.0 1.0 N A:VAL77 4.4 15.5 1.0 N A:ALA249 4.4 14.2 1.0 C A:HIS75 4.5 15.7 1.0 C A:SER72 4.5 15.0 1.0 CA A:VAL77 4.5 14.9 1.0 OG A:SER248 4.5 16.5 1.0 N A:ILE73 4.7 15.8 1.0 CA A:ILE73 4.8 15.4 1.0 CA A:HIS75 4.8 14.4 1.0 CB A:SER72 4.8 16.4 1.0 CG1 A:ILE103 4.8 17.2 1.0 CD1 A:ILE103 4.8 17.4 1.0 CA A:ALA249 4.8 14.5 1.0 C A:LYS247 4.9 13.8 1.0 O A:VAL77 4.9 15.0 1.0 CB A:ILE76 4.9 15.1 1.0 C A:VAL77 5.0 15.6 1.0 CE A:MET122 5.0 15.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase


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 Vibrio Cholerae Methionine Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:20.4 occ:1.00 O B:HOH462 2.2 21.0 1.0 O B:SER248 2.2 16.7 1.0 O B:ASN74 2.3 18.5 1.0 O B:ILE76 2.3 18.3 1.0 C B:ASN74 3.3 17.6 1.0 C B:SER248 3.3 16.6 1.0 C B:ILE76 3.5 18.1 1.0 O B:HOH528 3.6 24.1 1.0 N B:ASN74 3.6 19.8 1.0 N B:SER248 3.8 17.4 1.0 CA B:SER248 3.9 18.3 1.0 CA B:ASN74 3.9 18.6 1.0 CB B:SER248 3.9 17.6 1.0 C B:ILE73 3.9 18.8 1.0 N B:ILE76 4.0 17.9 1.0 O B:SER72 4.2 14.2 1.0 O B:ILE73 4.2 18.7 1.0 CA B:ILE76 4.3 19.3 1.0 N B:HIS75 4.3 18.0 1.0 N B:VAL77 4.4 17.5 1.0 N B:ALA249 4.4 17.8 1.0 O B:HOH445 4.4 17.6 1.0 C B:HIS75 4.5 18.5 1.0 C B:SER72 4.5 17.4 1.0 CA B:VAL77 4.6 18.1 1.0 OG B:SER248 4.6 19.1 1.0 N B:ILE73 4.7 15.2 1.0 CA B:ILE73 4.7 17.7 1.0 CG1 B:ILE103 4.7 16.6 1.0 CA B:HIS75 4.7 18.2 1.0 CD1 B:ILE103 4.7 17.3 1.0 CB B:SER72 4.8 16.1 1.0 CA B:ALA249 4.8 17.2 1.0 CB B:ILE76 4.9 18.8 1.0 O B:VAL77 4.9 18.6 1.0 CE B:MET122 4.9 16.7 1.0 C B:LYS247 5.0 18.0 1.0

V.Pillalamarri, A.Addlagatta. Discovery of New Variants of Methionine Aminopeptidases From Vibrio Species and Identification of Novel Inhibitors To Be Published.