Sodium in PDB 5m07: Crystal Structure of Mycobacterium Tuberculosis Pkni Kinase Domain, C20A Mutant

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Pkni Kinase Domain, C20A Mutant:
2.7.11.1;

The structure of Crystal Structure of Mycobacterium Tuberculosis Pkni Kinase Domain, C20A Mutant, PDB code: 5m07 was solved by M.N.Lisa, T.Wagner, M.Alexandre, N.Barilone, B.Raynal, P.M.Alzari, M.Bellinzoni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.14 / 2.50
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.304, 108.304, 185.471, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 23.5

The binding sites of Sodium atom in the Crystal Structure of Mycobacterium Tuberculosis Pkni Kinase Domain, C20A Mutant (pdb code 5m07). 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 Mycobacterium Tuberculosis Pkni Kinase Domain, C20A Mutant, PDB code: 5m07:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Pkni Kinase Domain, C20A Mutant


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 Mycobacterium Tuberculosis Pkni Kinase Domain, C20A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:96.7 occ:1.00 O A:ALA65 2.6 73.7 1.0 O A:VAL75 2.6 68.8 1.0 C A:VAL75 3.6 67.7 1.0 C A:ALA65 3.7 72.8 1.0 OE2 A:GLU74 3.9 0.9 1.0 CA A:HIS76 3.9 70.5 1.0 CG A:GLU74 4.1 80.8 1.0 ND1 A:HIS76 4.1 78.9 1.0 N A:HIS76 4.2 67.6 1.0 O A:HOH404 4.3 74.9 1.0 CA A:ALA65 4.4 67.5 1.0 CD A:GLU74 4.5 0.7 1.0 O A:HIS76 4.6 74.8 1.0 O A:LEU67 4.7 70.8 1.0 O A:HOH468 4.7 80.1 1.0 N A:VAL75 4.7 62.2 1.0 C A:HIS76 4.7 73.8 1.0 N A:ARG66 4.8 69.9 1.0 CA A:VAL75 4.8 60.6 1.0 CB A:ALA65 4.9 69.5 1.0 CB A:HIS76 5.0 72.7 1.0 CG A:HIS76 5.0 76.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Pkni Kinase Domain, C20A Mutant


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 Mycobacterium Tuberculosis Pkni Kinase Domain, C20A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:66.1 occ:1.00 O B:ALA65 2.3 72.2 1.0 O B:VAL75 2.3 69.1 1.0 O B:HOH420 2.3 64.8 1.0 O B:HOH417 2.5 78.4 1.0 O B:HOH405 2.7 65.4 1.0 C B:ALA65 3.3 71.2 1.0 C B:VAL75 3.4 69.5 1.0 N B:VAL75 3.7 65.7 1.0 CA B:ALA65 3.9 65.1 1.0 O B:LEU67 4.0 69.7 1.0 CA B:VAL75 4.1 64.5 1.0 NH2 A:ARG16 4.2 85.7 1.0 N B:HIS76 4.3 68.0 1.0 CB B:GLU74 4.3 68.9 1.0 N B:ARG66 4.3 67.7 1.0 CG B:GLU74 4.4 81.8 1.0 CA B:HIS76 4.5 69.5 1.0 C B:GLU74 4.5 69.0 1.0 CA B:GLU74 4.6 66.5 1.0 O B:ALA64 4.6 67.0 1.0 CB B:ALA65 4.7 66.8 1.0 C B:ARG66 4.7 69.5 1.0 CD B:GLU74 4.7 0.9 1.0 CA B:ARG66 4.7 68.2 1.0 ND1 B:HIS76 4.8 75.5 1.0 CB B:VAL75 4.9 67.3 1.0 OE2 B:GLU74 4.9 0.5 1.0 N B:LEU67 4.9 64.3 1.0 O B:ARG66 5.0 71.6 1.0

M.N.Lisa, T.Wagner, M.Alexandre, N.Barilone, B.Raynal, P.M.Alzari, M.Bellinzoni. The Crystal Structure of Pkni From Mycobacterium Tuberculosis Shows An Inactive, Pseudokinase-Like Conformation. Febs J. V. 284 602 2017.
ISSN: ISSN 1742-4658
PubMed: 28054744
DOI: 10.1111/FEBS.14003