Zinc in PDB 3d2z: Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys

All present enzymatic activity of Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys:
3.5.1.28;

The structure of Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys, PDB code: 3d2z was solved by F.Kerff, S.Petrella, R.Herman, E.Sauvage, F.Mercier, A.Luxen, J.M.Frere, B.Joris, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.90 / 2.80
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.160, 89.160, 183.640, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 26.5

The structure of Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys (pdb code 3d2z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys, PDB code: 3d2z:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn262 b:19.6 occ:1.00 OD1 A:ASP161 1.9 9.6 1.0 ND1 A:HIS151 1.9 10.9 1.0 O A:HOH322 2.0 2.2 1.0 ND1 A:HIS35 2.3 13.2 1.0 CG A:ASP161 2.8 9.2 1.0 CG A:HIS151 2.9 10.1 1.0 CE1 A:HIS151 3.0 11.2 1.0 OD2 A:ASP161 3.0 9.8 1.0 CE1 A:HIS35 3.1 12.8 1.0 CB A:HIS151 3.2 9.1 1.0 CG A:HIS35 3.3 12.9 1.0 CB A:HIS35 3.7 12.2 1.0 N B:ALA1 3.9 32.9 1.0 CD2 A:HIS151 4.0 10.8 1.0 NE2 A:HIS151 4.0 10.9 1.0 CB B:ALA1 4.1 32.4 1.0 CB A:ASP161 4.2 8.4 1.0 CA A:HIS35 4.3 11.8 1.0 NE2 A:HIS35 4.3 13.3 1.0 CD2 A:HIS35 4.4 13.0 1.0 CA B:ALA1 4.6 32.2 1.0 CD A:LYS159 4.7 8.8 1.0 CA A:HIS151 4.8 8.4 1.0 CG A:LYS159 4.8 9.0 1.0 O A:TYR36 4.9 11.1 1.0 OE2 A:GLU104 4.9 15.5 1.0 N A:TYR36 4.9 11.9 1.0 NZ A:LYS159 5.0 9.2 1.0 O A:HIS84 5.0 14.3 1.0

Zinc binding site 2 out of 2 in the Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of the N-Acetylmuramyl-L-Alanine Amidase Amid From E.Coli with the Product L-Ala-D-Gamma-Glu-L-Lys within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn263 b:52.6 occ:1.00 O A:HOH337 3.0 2.0 1.0 NE1 A:TRP73 4.0 16.1 1.0 CZ2 A:TRP73 4.5 15.6 1.0 CE2 A:TRP73 4.6 16.1 1.0

F.Kerff, S.Petrella, F.Mercier, E.Sauvage, R.Herman, A.Pennartz, A.Zervosen, A.Luxen, J.M.Frere, B.Joris, P.Charlier. Specific Structural Features of the N-Acetylmuramoyl-L-Alanine Amidase Amid From Escherichia Coli and Mechanistic Implications For Enzymes of This Family. J.Mol.Biol. V. 397 249 2010.
ISSN: ISSN 0022-2836
PubMed: 20036252
DOI: 10.1016/J.JMB.2009.12.038