Sodium in PDB 3dbo: Crystal Structure of A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis

The structure of Crystal Structure of A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis, PDB code: 3dbo was solved by L.Miallau, D.Cascio, D.Eisenberg, Integrated Center For Structure Andfunction Innovation (Isfi), Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.17 / 1.76
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.830, 64.830, 164.650, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 24.7

The binding sites of Sodium atom in the Crystal Structure of A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis (pdb code 3dbo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis, PDB code: 3dbo:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis


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 A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:19.8 occ:1.00 OG1 B:THR54 2.6 9.0 1.0 OG1 B:THR51 2.7 8.7 1.0 O B:LEU25 2.9 11.4 1.0 OG1 B:THR50 3.2 10.9 1.0 N B:THR51 3.3 10.0 1.0 CB B:THR54 3.5 7.1 1.0 CB B:THR51 3.5 9.4 1.0 CG2 B:THR51 3.5 9.0 1.0 CG1 B:ILE118 3.5 6.6 1.0 CD1 B:ILE118 3.6 11.1 1.0 CG2 B:ILE118 3.7 8.9 1.0 CA B:ASP26 3.7 14.2 1.0 CA B:THR51 3.9 10.0 1.0 C B:LEU25 3.9 12.8 1.0 N B:THR54 4.0 7.0 1.0 C B:THR50 4.2 10.0 1.0 O B:THR51 4.3 10.9 1.0 CB B:ILE118 4.3 8.1 1.0 C B:ASP26 4.3 14.5 1.0 N B:ASP26 4.3 12.8 1.0 CA B:THR54 4.3 8.6 1.0 C B:THR51 4.4 9.6 1.0 CB B:THR50 4.4 10.4 1.0 CA B:THR50 4.5 10.8 1.0 CG1 B:VAL24 4.6 10.2 1.0 N B:THR27 4.6 13.9 1.0 CG2 B:THR54 4.7 10.9 1.0 CB B:ASP26 4.7 14.6 1.0 O B:ASP26 4.9 15.7 1.0 CB B:VAL53 4.9 7.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis


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 A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:20.3 occ:1.00 O B:LEU127 2.7 12.9 1.0 O B:HOH328 2.7 13.6 1.0 O B:SER144 2.9 14.6 1.0 N B:GLU146 2.9 11.8 1.0 CA B:VAL145 3.4 12.1 1.0 C B:VAL145 3.6 12.0 1.0 O B:GLU146 3.6 12.0 1.0 C B:LEU127 3.7 14.4 1.0 CA B:ALA123 3.8 11.5 1.0 C B:SER144 3.8 14.8 1.0 N B:ALA123 3.8 10.6 1.0 CA B:PRO128 3.9 13.2 1.0 CA B:GLU146 4.0 12.7 1.0 N B:VAL145 4.1 12.9 1.0 CB B:ALA123 4.1 11.7 1.0 N B:PRO128 4.2 13.8 1.0 C B:GLU146 4.2 11.4 1.0 C B:ALA122 4.2 10.9 1.0 N B:VAL129 4.3 12.2 1.0 CB B:ALA122 4.3 11.3 1.0 CB B:GLU146 4.3 12.8 0.5 C B:PRO128 4.4 12.8 1.0 CB B:VAL145 4.5 12.2 1.0 CB B:GLU146 4.5 12.6 0.5 O B:ALA122 4.5 12.0 1.0 CG2 B:VAL129 4.6 11.8 1.0 CG1 B:VAL145 4.7 11.7 1.0 N B:LEU127 4.8 15.8 1.0 O B:VAL145 4.8 12.1 1.0 CG2 B:VAL145 4.8 11.2 1.0 CA B:LEU127 4.9 15.4 1.0 O B:ALA119 4.9 9.8 1.0 CA B:ALA122 4.9 11.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:36.6 occ:1.00 O B:ACT305 2.8 33.9 0.5 O B:LEU78 3.3 12.7 1.0 C B:ACT305 3.5 33.8 0.5 CD1 B:LEU78 3.9 13.8 1.0 CG B:LEU78 4.0 12.0 1.0 CD1 B:LEU55 4.0 13.9 1.0 CG2 B:VAL81 4.1 21.2 1.0 C B:LEU78 4.1 13.0 1.0 CA B:ALA82 4.1 26.2 1.0 OXT B:ACT305 4.2 34.0 0.5 CH3 B:ACT305 4.2 33.5 0.5 CB B:ALA82 4.3 26.4 1.0 N B:ALA82 4.3 24.5 1.0 NH2 A:ARG53 4.5 38.0 0.2 CA B:GLU79 4.6 14.5 1.0 C B:VAL81 4.7 23.1 1.0 N B:GLU79 4.8 13.3 1.0 CD2 B:LEU78 4.8 12.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of A Member of the Vapbc Family of Toxin-Antitoxin Systems, Vapbc-5, From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:20.7 occ:1.00 O B:ALA65 2.7 17.6 1.0 O B:VAL62 2.8 10.5 1.0 NE B:ARG71 2.8 15.9 1.0 O B:LEU63 3.3 14.1 1.0 N B:ALA65 3.3 15.4 1.0 C B:LEU63 3.5 12.8 1.0 NH2 B:ARG71 3.6 16.6 1.0 C B:ALA65 3.6 17.6 1.0 CZ B:ARG71 3.6 18.2 1.0 CB B:ALA65 3.7 15.9 1.0 CA B:ALA65 3.7 16.7 1.0 CD B:ARG71 3.7 14.7 1.0 C B:VAL62 3.9 11.0 1.0 CG B:ARG71 3.9 13.9 1.0 C B:ALA64 4.0 15.4 1.0 CA B:LEU63 4.0 11.5 1.0 N B:ALA64 4.1 13.2 1.0 N B:LEU63 4.4 10.4 1.0 CB B:ARG71 4.5 13.3 1.0 CA B:ALA64 4.5 14.6 1.0 O B:ALA64 4.7 16.1 1.0 N B:ALA66 4.9 19.0 1.0 NH1 B:ARG71 4.9 18.3 1.0

L.Miallau, M.Faller, J.Chiang, M.Arbing, F.Guo, D.Cascio, D.Eisenberg. Structure and Proposed Activity of A Member of the Vapbc Family of Toxin-Antitoxin Systems: Vapbc-5 From Mycobacterium Tuberculosis. J.Biol.Chem. V. 284 276 2009.
ISSN: ISSN 0021-9258
PubMed: 18952600
DOI: 10.1074/JBC.M805061200