Sodium in PDB 5m09: Crystal Structure of Mycobacterium Tuberculosis Pkni Kinase Domain, C20A_R136N Double Mutant

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Pkni Kinase Domain, C20A_R136N Double Mutant:
2.7.11.1;

The structure of Crystal Structure of Mycobacterium Tuberculosis Pkni Kinase Domain, C20A_R136N Double Mutant, PDB code: 5m09 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)	47.94 / 2.98
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	110.870, 110.870, 181.760, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.1

The binding sites of Sodium atom in the Crystal Structure of Mycobacterium Tuberculosis Pkni Kinase Domain, C20A_R136N Double Mutant (pdb code 5m09). 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_R136N Double Mutant, PDB code: 5m09:
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_R136N Double 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_R136N Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:74.1 occ:1.00 O A:ALA65 2.9 54.4 1.0 O A:VAL75 3.2 58.6 1.0 O A:LEU67 3.6 48.0 1.0 CG A:GLU74 3.8 66.2 1.0 OE2 A:GLU74 3.8 0.6 1.0 C A:ALA65 4.1 53.7 1.0 C A:VAL75 4.1 55.3 1.0 CD A:GLU74 4.2 0.5 1.0 CD2 A:HIS76 4.3 58.3 1.0 N A:VAL75 4.5 49.9 1.0 CB A:GLU74 4.5 51.9 1.0 C A:LEU67 4.7 45.1 1.0 CA A:HIS76 4.7 51.0 1.0 O A:ARG66 4.7 49.4 1.0 N A:HIS76 4.8 49.9 1.0 C A:ARG66 4.8 50.0 1.0 CA A:GLU74 4.9 50.0 1.0 CA A:ALA65 5.0 47.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Tuberculosis Pkni Kinase Domain, C20A_R136N Double 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_R136N Double Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:49.5 occ:1.00 O B:VAL75 2.3 53.2 1.0 O B:HOH406 2.5 54.5 1.0 O B:ALA65 2.7 54.1 1.0 C B:VAL75 3.3 50.6 1.0 N B:VAL75 3.5 46.2 1.0 CG B:GLU74 3.7 66.8 1.0 OE1 B:GLU74 3.7 0.9 1.0 C B:ALA65 3.8 54.1 1.0 CB B:GLU74 4.0 47.8 1.0 CD B:GLU74 4.0 0.1 1.0 CA B:VAL75 4.1 45.7 1.0 O B:LEU67 4.1 48.3 1.0 C B:GLU74 4.1 49.0 1.0 CD2 B:HIS76 4.2 50.6 1.0 N B:HIS76 4.2 44.9 1.0 CA B:GLU74 4.2 45.7 1.0 CA B:ALA65 4.3 49.9 1.0 CA B:HIS76 4.4 44.9 1.0 NE2 B:HIS76 4.9 51.0 1.0 N B:ARG66 4.9 49.4 1.0 O B:ALA64 5.0 52.6 1.0 O B:GLU74 5.0 49.0 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