Zinc in PDB 4m6g: Structure of the Mycobacterium Tuberculosis Peptidoglycan Amidase RV3717 in Complex with L-Alanine-Iso-D-Glutamine Reaction Product

The structure of Structure of the Mycobacterium Tuberculosis Peptidoglycan Amidase RV3717 in Complex with L-Alanine-Iso-D-Glutamine Reaction Product, PDB code: 4m6g was solved by D.M.Prigozhin, D.Mavrici, J.P.Huizar, H.J.Vansell, T.Alber, Tb Structuralgenomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.06 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.982, 75.958, 49.454, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.5

The binding sites of Zinc atom in the Structure of the Mycobacterium Tuberculosis Peptidoglycan Amidase RV3717 in Complex with L-Alanine-Iso-D-Glutamine Reaction Product (pdb code 4m6g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Mycobacterium Tuberculosis Peptidoglycan Amidase RV3717 in Complex with L-Alanine-Iso-D-Glutamine Reaction Product, PDB code: 4m6g:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Mycobacterium Tuberculosis Peptidoglycan Amidase RV3717 in Complex with L-Alanine-Iso-D-Glutamine Reaction Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Mycobacterium Tuberculosis Peptidoglycan Amidase RV3717 in Complex with L-Alanine-Iso-D-Glutamine Reaction Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:26.4 occ:0.89 OE1 A:GLU70 2.0 26.3 1.0 NE2 A:HIS35 2.0 30.5 1.0 ND1 A:HIS125 2.1 15.2 1.0 OE2 A:GLU70 2.2 30.8 1.0 N B:ALA1 2.3 28.1 1.0 CD A:GLU70 2.4 21.6 1.0 CD2 A:HIS35 2.8 26.4 1.0 CA B:ALA1 2.9 28.9 1.0 CE1 A:HIS125 2.9 24.1 1.0 CE1 A:HIS35 3.1 32.5 1.0 CG A:HIS125 3.2 27.5 1.0 O A:HOH509 3.5 30.6 1.0 C B:ALA1 3.5 32.3 1.0 CB A:HIS125 3.7 27.4 1.0 O B:ALA1 3.9 34.7 1.0 CG A:GLU70 3.9 28.2 1.0 CG A:HIS35 4.1 24.6 1.0 NE2 A:HIS125 4.1 24.7 1.0 ND1 A:HIS35 4.2 25.8 1.0 CB B:ALA1 4.2 26.3 1.0 CD2 A:HIS125 4.2 18.1 1.0 O A:ALA126 4.3 29.9 1.0 N B:ZGL2 4.3 32.8 1.0 CA A:HIS125 4.4 26.2 1.0 N A:ALA126 4.5 25.3 1.0 O B:ZGL2 4.5 29.8 1.0 CA A:GLY61 4.8 33.1 1.0 OE1 A:GLU200 4.9 35.4 1.0 CB A:GLU70 4.9 29.7 1.0 C A:HIS125 5.0 22.0 1.0

Zinc binding site 2 out of 2 in the Structure of the Mycobacterium Tuberculosis Peptidoglycan Amidase RV3717 in Complex with L-Alanine-Iso-D-Glutamine Reaction Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Mycobacterium Tuberculosis Peptidoglycan Amidase RV3717 in Complex with L-Alanine-Iso-D-Glutamine Reaction Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:42.2 occ:0.83 NE2 A:HIS71 2.0 26.5 1.0 CE1 A:HIS71 3.0 29.8 1.0 CD2 A:HIS71 3.0 25.8 1.0 O A:HOH551 3.1 37.5 1.0 ND1 A:HIS71 4.1 32.5 1.0 CB A:PRO69 4.1 28.8 1.0 CG A:HIS71 4.2 27.2 1.0 CG A:PRO69 4.2 33.0 1.0 O A:GLY37 4.4 30.6 1.0

D.M.Prigozhin, D.Mavrici, J.P.Huizar, H.J.Vansell, T.Alber. Structural and Biochemical Analyses of Mycobacterium Tuberculosis N-Acetylmuramyl-L-Alanine Amidase RV3717 Point to A Role in Peptidoglycan Fragment Recycling. J.Biol.Chem. V. 288 31549 2013.
ISSN: ISSN 0021-9258
PubMed: 24019530
DOI: 10.1074/JBC.M113.510792