Zinc in PDB 1vs0: Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A

The structure of Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A, PDB code: 1vs0 was solved by D.Akey, A.Martins, J.Aniukwu, M.S.Glickman, S.Shuman, J.M.Berger, Tbstructural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.40
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.102, 57.102, 368.957, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 24.8

The structure of Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A (pdb code 1vs0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A, PDB code: 1vs0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9002 b:21.9 occ:1.00 O1P A:APK481 2.0 22.0 1.0 OD1 A:ASP483 2.1 25.9 1.0 OE1 A:GLU613 2.3 29.4 1.0 OE2 A:GLU613 2.4 27.9 1.0 OD2 A:ASP483 2.5 26.8 1.0 CG A:ASP483 2.6 25.8 1.0 CD A:GLU613 2.7 26.4 1.0 P A:APK481 3.1 25.9 1.0 NZ A:APK481 3.4 20.6 1.0 O A:HOH9015 3.9 15.2 1.0 CB A:ASP483 4.2 23.3 1.0 O2P A:APK481 4.2 22.4 1.0 CG A:GLU613 4.2 25.5 1.0 O5' A:APK481 4.2 23.2 1.0 C5' A:APK481 4.3 27.3 1.0 O A:HOH9110 4.4 31.2 1.0 O A:HOH9012 4.8 12.7 1.0 O A:HOH9204 4.8 57.8 1.0 CE A:LYS637 4.8 21.0 1.0 CE A:APK481 4.8 17.8 1.0 CA A:ASP483 4.9 21.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn9004 b:21.3 occ:1.00 OE1 A:GLU727 1.9 30.8 1.0 CL A:CL9007 2.2 24.8 1.0 CD A:GLU727 2.7 28.6 1.0 OE2 A:GLU727 2.8 29.1 1.0 O A:HOH9023 4.0 20.0 1.0 NH2 A:ARG748 4.0 33.3 1.0 CG A:GLU727 4.1 28.2 1.0 NH2 A:ARG745 4.2 21.3 0.5 NE A:ARG748 4.5 34.7 1.0 O A:HOH9232 4.7 64.0 1.0 CZ A:ARG748 4.7 33.6 1.0 CB A:GLU727 5.0 27.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn9001 b:34.6 occ:1.00 OE2 B:GLU613 1.7 48.5 1.0 O1P B:APK481 1.9 28.6 1.0 OD2 B:ASP483 2.2 43.1 1.0 CD B:GLU613 2.6 47.6 1.0 OD1 B:ASP483 2.8 41.8 1.0 CG B:ASP483 2.8 41.9 1.0 OE1 B:GLU613 2.9 48.4 1.0 P B:APK481 3.2 31.2 1.0 NZ B:APK481 3.6 31.7 1.0 CG B:GLU613 3.9 45.5 1.0 O B:HOH9012 4.1 16.8 1.0 O B:HOH9123 4.2 39.0 1.0 CB B:ASP483 4.3 38.7 1.0 O5' B:APK481 4.3 31.4 1.0 O2P B:APK481 4.3 31.1 1.0 O B:HOH9187 4.5 49.3 1.0 O B:HOH9186 4.5 48.0 1.0 C5' B:APK481 4.5 32.7 1.0 CE B:LYS637 4.6 33.5 1.0 O B:HOH9014 4.8 15.0 1.0 CB B:GLU613 4.9 41.1 1.0 CA B:ASP483 4.9 34.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Ligase Domain From M. Tuberculosis Ligd at 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn9003 b:23.3 occ:1.00 CL B:CL9008 1.9 26.8 1.0 OE1 B:GLU727 2.1 31.5 1.0 OE2 B:GLU727 2.6 29.6 1.0 CD B:GLU727 2.7 30.6 1.0 OE2 B:GLU643 4.2 12.8 0.5 CG B:GLU727 4.2 28.2 1.0 NH2 B:ARG745 4.4 42.0 1.0 NH2 B:ARG748 4.5 31.3 1.0 NE B:ARG748 4.5 32.7 1.0 NH1 B:ARG745 4.7 43.7 1.0 CG2 B:THR641 4.9 28.5 1.0 CB B:GLU727 5.0 29.1 1.0

D.Akey, A.Martins, J.Aniukwu, M.S.Glickman, S.Shuman, J.M.Berger. Crystal Structure and Nonhomologous End-Joining Function of the Ligase Component of Mycobacterium Dna Ligase D. J.Biol.Chem. V. 281 13412 2006.
ISSN: ISSN 0021-9258
PubMed: 16476729
DOI: 10.1074/JBC.M513550200