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Sodium in PDB 5yoh: Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105M Mutant) in Complex with Methionine

Enzymatic activity of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105M Mutant) in Complex with Methionine

All present enzymatic activity of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105M Mutant) in Complex with Methionine:
3.4.11.18;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105M Mutant) in Complex with Methionine, PDB code: 5yoh 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) 28.59 / 1.63
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.332, 48.690, 56.151, 90.00, 95.30, 90.00
R / Rfree (%) 16.6 / 21.8

Other elements in 5yoh:

The structure of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105M Mutant) in Complex with Methionine also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105M Mutant) in Complex with Methionine (pdb code 5yoh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105M Mutant) in Complex with Methionine, PDB code: 5yoh:

Sodium binding site 1 out of 1 in 5yoh

Go back to Sodium Binding Sites List in 5yoh
Sodium binding site 1 out of 1 in the Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105M Mutant) in Complex with Methionine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105M Mutant) in Complex with Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:21.4
occ:1.00
 O A:HOH475 2.2 22.0 1.0
O A:ASN109 2.3 19.8 1.0
O A:VAL111 2.3 24.1 1.0
O A:THR265 2.4 20.8 1.0
OG1 A:THR265 2.7 16.4 0.5
C A:THR265 3.3 20.4 1.0
C A:ASN109 3.3 20.2 1.0
C A:VAL111 3.4 20.3 1.0
O A:HOH579 3.5 19.8 1.0
CG2 A:THR265 3.5 23.7 0.5
N A:THR265 3.7 19.9 1.0
N A:ASN109 3.8 20.6 1.0
CB A:THR265 3.8 18.6 0.5
CA A:THR265 3.8 18.5 0.5
CA A:THR265 3.9 20.2 0.5
N A:VAL111 3.9 21.9 1.0
CA A:ASN109 4.0 21.0 1.0
C A:LEU108 4.0 19.3 0.6
C A:LEU108 4.0 17.7 0.4
O A:LEU108 4.0 21.6 0.6
O A:LEU108 4.0 19.0 0.4
O A:HOH424 4.1 18.1 1.0
CB A:THR265 4.1 21.9 0.5
O A:SER107 4.2 18.8 1.0
CA A:VAL111 4.2 20.7 1.0
N A:ILE112 4.3 19.0 1.0
C A:GLU110 4.3 19.4 1.0
N A:GLU110 4.3 19.5 1.0
N A:ALA266 4.3 16.8 1.0
OG1 A:THR265 4.4 22.8 0.5
CA A:ILE112 4.5 20.6 1.0
CG2 A:THR265 4.5 17.6 0.5
CA A:GLU110 4.6 20.3 1.0
C A:SER107 4.6 20.4 1.0
O A:ILE112 4.7 18.8 1.0
CA A:ALA266 4.8 17.3 1.0
C A:ILE112 4.8 20.7 1.0
CB A:VAL111 4.8 21.4 1.0
CA A:LEU108 4.8 16.7 0.4
CA A:LEU108 4.9 21.5 0.6
CD1 A:ILE127 4.9 20.1 1.0
N A:LEU108 4.9 22.5 0.6
C A:TRP264 4.9 24.1 1.0
O A:GLU110 4.9 22.3 1.0
CB A:SER107 5.0 18.4 1.0

Reference:

C.B.Sandeep, A.Addlagatta. Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105M Mutant) in Complex with Methionine To Be Published.
Page generated: Tue Dec 15 11:51:03 2020

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