Zinc in PDB 2xs4: Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium

The structure of Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium, PDB code: 2xs4 was solved by N.Cerda-Costa, T.Guevara, A.Y.Karim, M.Ksiazek, K.-A.Nguyen, J.L.Arolas, J.Potempa, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.70
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	85.790, 85.790, 53.480, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.6

The structure of Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium (pdb code 2xs4). 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 Karilysin Catalytic Mmp Domain in Complex with Magnesium, PDB code: 2xs4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn998 b:14.5 occ:1.00 NE2 A:HIS117 2.0 14.9 1.0 NE2 A:HIS102 2.0 14.3 1.0 OD1 A:ASP104 2.0 16.1 1.0 ND1 A:HIS133 2.1 13.8 1.0 CG A:ASP104 2.9 19.4 1.0 CD2 A:HIS102 2.9 15.2 1.0 CE1 A:HIS117 3.0 16.3 1.0 CE1 A:HIS133 3.0 15.3 1.0 CD2 A:HIS117 3.0 14.6 1.0 CE1 A:HIS102 3.0 14.7 1.0 CG A:HIS133 3.1 14.1 1.0 OD2 A:ASP104 3.2 18.7 1.0 CB A:HIS133 3.5 13.5 1.0 O A:TYR106 4.0 23.3 1.0 ND1 A:HIS117 4.1 15.8 1.0 CG A:HIS102 4.1 16.8 1.0 ND1 A:HIS102 4.1 14.2 1.0 CG A:HIS117 4.1 15.1 1.0 NE2 A:HIS133 4.1 14.6 1.0 CD2 A:HIS133 4.2 14.5 1.0 CB A:ASP104 4.3 20.3 1.0 CE2 A:PHE119 4.5 16.0 1.0 CB A:TYR106 4.6 24.3 1.0 CZ A:PHE119 4.8 17.7 1.0 C A:TYR106 4.9 24.0 1.0 CE1 A:PHE108 4.9 19.4 1.0 O A:HOH2108 4.9 8.4 1.0 CZ A:PHE108 5.0 19.1 1.0 CA A:HIS133 5.0 13.3 1.0

Zinc binding site 2 out of 2 in the Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Karilysin Catalytic Mmp Domain in Complex with Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:13.3 occ:1.00 NE2 A:HIS155 2.0 12.3 1.0 NE2 A:HIS165 2.1 13.8 1.0 N B:ALA301 2.1 14.5 1.0 NE2 A:HIS159 2.2 12.7 1.0 O B:ALA301 2.2 15.2 1.0 C B:ALA301 2.9 16.4 1.0 CD2 A:HIS165 3.0 13.9 1.0 CE1 A:HIS155 3.0 13.4 1.0 CA B:ALA301 3.0 15.7 1.0 CD2 A:HIS155 3.0 12.7 1.0 CE1 A:HIS165 3.1 14.5 1.0 CD2 A:HIS159 3.1 12.8 1.0 CE1 A:HIS159 3.1 13.9 1.0 CB B:ALA301 3.8 16.0 1.0 OE2 A:GLU156 4.1 14.6 1.0 ND1 A:HIS155 4.1 12.4 1.0 CG A:HIS165 4.1 13.3 1.0 CG A:HIS155 4.2 12.6 1.0 ND1 A:HIS165 4.2 14.2 1.0 N B:PHE302 4.2 17.8 1.0 ND1 A:HIS159 4.3 13.8 1.0 O A:HOH2191 4.3 12.0 1.0 CG A:HIS159 4.3 13.1 1.0 OE1 A:GLU156 4.7 15.8 1.0 CD A:GLU156 4.7 13.3 1.0 O A:HOH2115 4.8 30.1 1.0 CB A:PRO175 4.9 15.7 1.0 CE A:MET173 4.9 12.6 1.0 CA B:PHE302 5.0 19.1 1.0

N.Cerda-Costa, T.Guevara, A.Y.Karim, M.Ksiazek, K.A.Nguyen, J.L.Arolas, J.Potempa, F.X.Gomis-Ruth. The Structure of the Catalytic Domain of Tannerella Forsythia Karilysin Reveals It Is A Bacterial Xenologue of Animal Matrix Metalloproteinases. Mol.Microbiol. V. 79 119 2011.
ISSN: ISSN 0950-382X
PubMed: 21166898
DOI: 10.1111/J.1365-2958.2010.07434.X