Cobalt in PDB 5ypd: Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105N Mutant) in Complex with Methionine

All present enzymatic activity of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105N Mutant) in Complex with Methionine:
3.4.11.18;

The structure of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105N Mutant) in Complex with Methionine, PDB code: 5ypd was solved by C.B.Sandeep, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.57 / 1.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.226, 44.909, 57.295, 90.00, 94.17, 90.00
R / Rfree (%)	14.4 / 18.2

The structure of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105N Mutant) in Complex with Methionine also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Cobalt atom in the Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105N Mutant) in Complex with Methionine (pdb code 5ypd). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105N Mutant) in Complex with Methionine, PDB code: 5ypd:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105N Mutant) in Complex with Methionine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105N Mutant) in Complex with Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:20.6 occ:1.00 OXT A:MET305 1.9 26.0 1.0 OE1 A:GLU269 2.0 20.3 1.0 NE2 A:HIS205 2.1 20.1 1.0 OE2 A:GLU238 2.1 20.2 1.0 OD2 A:ASP142 2.2 19.8 1.0 C A:MET305 2.7 30.0 1.0 CD A:GLU269 2.9 18.2 1.0 O A:MET305 3.0 26.2 1.0 CG A:ASP142 3.1 18.4 1.0 CD2 A:HIS205 3.1 17.2 1.0 CE1 A:HIS205 3.1 18.0 1.0 CD A:GLU238 3.1 23.7 1.0 CO A:CO302 3.3 20.1 1.0 OE2 A:GLU269 3.4 17.7 1.0 OE1 A:GLU238 3.5 25.0 1.0 OD1 A:ASP142 3.5 19.6 1.0 OG1 A:THR236 3.7 18.8 1.0 CG2 A:THR236 3.8 18.9 1.0 CB A:THR236 4.1 18.8 1.0 CA A:MET305 4.1 22.9 1.0 ND1 A:HIS205 4.2 19.2 1.0 CG A:HIS205 4.2 18.4 1.0 CB A:ASP142 4.2 16.9 1.0 CG A:GLU269 4.2 19.3 1.0 N A:MET305 4.3 22.7 1.0 CG A:GLU238 4.3 21.2 1.0 O A:HOH438 4.6 29.6 1.0 NE2 A:HIS212 4.7 24.6 1.0 O A:HOH484 4.8 39.9 1.0 CB A:GLU238 4.8 20.3 1.0

Cobalt binding site 2 out of 2 in the Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105N Mutant) in Complex with Methionine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105N Mutant) in Complex with Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:20.1 occ:1.00 OD1 A:ASP142 2.0 19.6 1.0 OXT A:MET305 2.0 26.0 1.0 OE2 A:GLU269 2.1 17.7 1.0 OD1 A:ASP131 2.1 22.6 1.0 N A:MET305 2.2 22.7 1.0 OD2 A:ASP131 2.3 21.5 1.0 CG A:ASP131 2.6 21.7 1.0 C A:MET305 2.9 30.0 1.0 CG A:ASP142 2.9 18.4 1.0 CD A:GLU269 3.0 18.2 1.0 CA A:MET305 3.0 22.9 1.0 OD2 A:ASP142 3.2 19.8 1.0 OE1 A:GLU269 3.3 20.3 1.0 CO A:CO301 3.3 20.6 1.0 O A:MET305 4.1 26.2 1.0 OG1 A:THR133 4.1 23.5 1.0 CB A:ASP131 4.1 19.3 1.0 ND2 A:ASN144 4.2 18.9 1.0 O A:HOH409 4.3 28.2 1.0 CB A:ASP142 4.3 16.9 1.0 CG A:GLU269 4.3 19.3 1.0 O A:HOH405 4.4 28.1 1.0 CB A:MET305 4.5 25.5 1.0 N A:THR143 4.5 19.0 1.0 O A:HOH438 4.6 29.6 1.0 O A:THR143 4.6 19.3 1.0 C A:ASP142 4.7 16.5 1.0 OE1 A:GLU238 4.7 25.0 1.0 OE2 A:GLU238 4.8 20.2 1.0 CA A:ASP142 4.8 17.4 1.0 CB A:ASN144 4.8 18.8 1.0 C A:THR143 4.8 20.1 1.0 CA A:ASP131 4.8 17.4 1.0 CB A:GLU269 4.9 17.5 1.0 C A:ASP131 4.9 19.4 1.0 N A:VAL132 5.0 18.8 1.0

C.B.Sandeep, A.Addlagatta. Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105N Mutant) in Complex with Methionine To Be Published.