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Sodium in PDB 5yxf: Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105L Mutant) in Complex with Methionine

Enzymatic activity of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105L Mutant) in Complex with Methionine

All present enzymatic activity of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105L Mutant) in Complex with Methionine:
3.4.11.18;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105L Mutant) in Complex with Methionine, PDB code: 5yxf 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) 35.37 / 1.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.302, 48.326, 56.225, 90.00, 95.19, 90.00
R / Rfree (%) 16.9 / 20.7

Other elements in 5yxf:

The structure of Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105L 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 (C105L Mutant) in Complex with Methionine (pdb code 5yxf). 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 (C105L Mutant) in Complex with Methionine, PDB code: 5yxf:

Sodium binding site 1 out of 1 in 5yxf

Go back to Sodium Binding Sites List in 5yxf
Sodium binding site 1 out of 1 in the Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105L 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 (C105L Mutant) in Complex with Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:29.7
occ:1.00
 O A:HOH531 2.2 28.8 1.0
O A:VAL111 2.3 34.6 1.0
O A:ASN109 2.3 27.9 1.0
O A:THR265 2.4 29.2 1.0
OG1 A:THR265 2.7 24.1 0.4
C A:THR265 3.3 28.5 1.0
C A:VAL111 3.3 30.1 1.0
C A:ASN109 3.4 26.4 1.0
CG2 A:THR265 3.4 32.6 0.6
O A:HOH637 3.4 27.3 1.0
N A:ASN109 3.7 29.3 1.0
N A:THR265 3.8 27.8 1.0
CB A:THR265 3.8 26.2 0.4
CA A:THR265 3.9 26.4 0.4
CA A:THR265 3.9 28.2 0.6
N A:VAL111 3.9 28.4 1.0
C A:LEU108 3.9 26.2 1.0
CA A:ASN109 4.0 28.2 1.0
O A:LEU108 4.0 28.4 1.0
CB A:THR265 4.1 31.5 0.6
O A:SER107 4.1 26.5 1.0
O A:HOH549 4.2 26.9 1.0
CA A:VAL111 4.2 29.0 1.0
N A:ILE112 4.2 28.6 1.0
N A:GLU110 4.3 26.5 1.0
C A:GLU110 4.3 25.5 1.0
N A:ALA266 4.4 25.3 1.0
CA A:ILE112 4.5 29.9 1.0
OG1 A:THR265 4.5 31.1 0.6
C A:SER107 4.5 29.0 1.0
CG2 A:THR265 4.6 22.9 0.4
O A:ILE112 4.6 27.9 1.0
CA A:GLU110 4.6 27.0 1.0
CA A:ALA266 4.8 24.4 1.0
CB A:VAL111 4.8 30.6 1.0
C A:ILE112 4.8 29.0 1.0
CD1 A:ILE127 4.8 28.7 1.0
CA A:LEU108 4.8 29.8 0.7
CA A:LEU108 4.8 27.5 0.3
N A:LEU108 4.9 29.4 1.0
CB A:SER107 4.9 26.9 1.0
C A:TRP264 5.0 33.3 1.0
CG1 A:ILE127 5.0 28.3 1.0

Reference:

C.B.Sandeep, A.Addlagatta. Mycobacterium Tuberculosis Methionine Aminopeptidase Type 1C (C105L Mutant) in Complex with Methionine To Be Published.
Page generated: Tue Dec 15 11:51:36 2020

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