Zinc in PDB 3rdr: Structure of the Catalytic Domain of Xlya

All present enzymatic activity of Structure of the Catalytic Domain of Xlya:
3.5.1.28;

The structure of Structure of the Catalytic Domain of Xlya, PDB code: 3rdr was solved by L.Y.Low, R.C.Liddington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.35 / 2.20
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	96.700, 96.700, 114.300, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 23.5

The structure of Structure of the Catalytic Domain of Xlya also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Structure of the Catalytic Domain of Xlya (pdb code 3rdr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of the Catalytic Domain of Xlya, PDB code: 3rdr:

Zinc binding site 1 out of 1 in the Structure of the Catalytic Domain of Xlya


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 Catalytic Domain of Xlya within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn190 b:33.7 occ:1.00 ND1 A:HIS32 2.2 18.0 1.0 ND1 A:HIS133 2.2 16.1 1.0 CL A:CL158 2.3 24.1 1.0 SG A:CYS141 2.4 21.5 1.0 CG A:HIS133 3.1 17.5 1.0 CE1 A:HIS32 3.1 16.7 1.0 CG A:HIS32 3.2 20.5 1.0 CE1 A:HIS133 3.3 15.6 1.0 CB A:CYS141 3.3 23.5 1.0 CB A:HIS133 3.3 16.5 1.0 CB A:HIS32 3.6 19.4 1.0 O A:HOH159 3.9 24.5 1.0 CA A:HIS32 4.2 19.4 1.0 NE2 A:HIS32 4.3 18.3 1.0 CD2 A:HIS133 4.3 18.1 1.0 NE2 A:HIS133 4.3 17.8 1.0 CD2 A:HIS32 4.4 19.6 1.0 OE2 A:GLU96 4.7 18.8 1.0 CA A:CYS141 4.7 25.5 1.0 O A:HIS80 4.8 24.6 1.0 CA A:HIS133 4.9 21.5 1.0 N A:ASN33 5.0 19.7 1.0 C A:CYS141 5.0 24.3 1.0

L.Y.Low, C.Yang, M.Perego, A.Osterman, R.Liddington. Role of Net Charge on Catalytic Domain and Influence of Cell Wall Binding Domain on Bactericidal Activity, Specificity, and Host Range of Phage Lysins. J.Biol.Chem. V. 286 34391 2011.
ISSN: ISSN 0021-9258
PubMed: 21816821
DOI: 10.1074/JBC.M111.244160