Zinc in PDB 2xs3: Structure of Karilysin Catalytic Mmp Domain

The structure of Structure of Karilysin Catalytic Mmp Domain, PDB code: 2xs3 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 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	121.370, 53.110, 86.300, 90.00, 134.55, 90.00
R / Rfree (%)	18.9 / 25.9

The binding sites of Zinc atom in the Structure of Karilysin Catalytic Mmp Domain (pdb code 2xs3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Karilysin Catalytic Mmp Domain, PDB code: 2xs3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Karilysin Catalytic Mmp Domain


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn998 b:53.3 occ:1.00 OD2 A:ASP104 1.8 39.6 1.0 NE2 A:HIS117 1.9 31.5 1.0 NE2 A:HIS102 2.0 35.7 1.0 ND1 A:HIS133 2.2 35.5 1.0 CE1 A:HIS117 2.8 33.7 1.0 CD2 A:HIS102 2.8 37.4 1.0 CG A:ASP104 2.8 42.3 1.0 CD2 A:HIS117 3.0 30.6 1.0 CE1 A:HIS102 3.0 36.9 1.0 CE1 A:HIS133 3.1 35.9 1.0 CG A:HIS133 3.2 33.8 1.0 OD1 A:ASP104 3.2 44.3 1.0 CB A:HIS133 3.5 31.4 1.0 O A:TYR106 3.9 49.7 1.0 ND1 A:HIS117 3.9 32.4 1.0 CG A:HIS102 4.0 42.0 1.0 ND1 A:HIS102 4.1 40.4 1.0 CG A:HIS117 4.1 31.4 1.0 CB A:ASP104 4.1 44.0 1.0 NE2 A:HIS133 4.3 35.0 1.0 CD2 A:HIS133 4.3 34.5 1.0 CE2 A:PHE119 4.6 28.1 1.0 C A:TYR106 4.9 51.6 1.0 CZ A:PHE119 4.9 29.1 1.0 CB A:TYR106 5.0 47.6 1.0 CZ A:PHE108 5.0 47.1 1.0

Zinc binding site 2 out of 4 in the Structure of Karilysin Catalytic Mmp Domain


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:27.8 occ:1.00 NE2 A:HIS155 1.9 19.0 1.0 N C:ALA201 2.0 39.8 1.0 NE2 A:HIS165 2.0 25.6 1.0 NE2 A:HIS159 2.2 22.1 1.0 O C:ALA201 2.3 41.3 1.0 CE1 A:HIS155 2.8 22.8 1.0 CD2 A:HIS165 2.9 23.4 1.0 CD2 A:HIS155 3.0 22.2 1.0 CA C:ALA201 3.0 41.0 1.0 C C:ALA201 3.0 42.0 1.0 CD2 A:HIS159 3.1 22.2 1.0 CE1 A:HIS165 3.1 26.8 1.0 CE1 A:HIS159 3.2 22.5 1.0 ND1 A:HIS155 4.0 21.3 1.0 CB C:ALA201 4.0 41.3 1.0 CG A:HIS155 4.1 20.8 1.0 CG A:HIS165 4.1 21.9 1.0 ND1 A:HIS165 4.2 23.4 1.0 CG A:HIS159 4.3 21.2 1.0 N C:PHE202 4.3 43.7 1.0 ND1 A:HIS159 4.3 21.7 1.0 OE2 A:GLU156 4.5 29.6 1.0 O A:HOH2037 4.8 21.4 1.0 CE A:MET173 4.9 16.8 1.0 OE1 A:GLU156 4.9 33.1 1.0

Zinc binding site 3 out of 4 in the Structure of Karilysin Catalytic Mmp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Karilysin Catalytic Mmp Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn998 b:49.0 occ:1.00 OD2 B:ASP104 2.0 41.2 1.0 NE2 B:HIS117 2.0 32.4 1.0 ND1 B:HIS133 2.2 30.7 1.0 NE2 B:HIS102 2.2 38.5 1.0 CG B:ASP104 2.9 45.8 1.0 CE1 B:HIS117 3.0 33.8 1.0 CD2 B:HIS102 3.0 40.8 1.0 CD2 B:HIS117 3.1 29.8 1.0 CE1 B:HIS133 3.1 30.6 1.0 CG B:HIS133 3.2 29.2 1.0 OD1 B:ASP104 3.3 50.0 1.0 CE1 B:HIS102 3.3 40.4 1.0 CB B:HIS133 3.6 27.4 1.0 ND1 B:HIS117 4.1 32.5 1.0 O B:TYR106 4.1 51.5 1.0 CG B:HIS117 4.2 29.9 1.0 CG B:HIS102 4.2 44.6 1.0 NE2 B:HIS133 4.3 28.0 1.0 CB B:ASP104 4.3 47.0 1.0 CD2 B:HIS133 4.3 28.4 1.0 ND1 B:HIS102 4.4 41.4 1.0 CE2 B:PHE119 4.4 27.3 1.0 CZ B:PHE108 4.7 44.0 1.0 CE2 B:PHE108 4.7 46.6 1.0 CZ B:PHE119 4.9 31.1 1.0

Zinc binding site 4 out of 4 in the Structure of Karilysin Catalytic Mmp Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Karilysin Catalytic Mmp Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn999 b:32.2 occ:1.00 NE2 B:HIS165 2.0 25.6 1.0 N D:ALA201 2.0 44.1 1.0 NE2 B:HIS155 2.1 19.0 1.0 NE2 B:HIS159 2.3 18.3 1.0 O D:ALA201 2.3 46.3 1.0 CE1 B:HIS165 3.0 27.5 1.0 CE1 B:HIS155 3.0 21.8 1.0 C D:ALA201 3.0 46.8 1.0 CD2 B:HIS165 3.0 21.8 1.0 CA D:ALA201 3.0 45.8 1.0 CD2 B:HIS155 3.1 20.2 1.0 CD2 B:HIS159 3.1 17.2 1.0 CE1 B:HIS159 3.3 21.2 1.0 CB D:ALA201 4.0 46.0 1.0 OE2 B:GLU156 4.1 24.0 1.0 ND1 B:HIS165 4.1 24.6 1.0 ND1 B:HIS155 4.1 20.0 1.0 CG B:HIS165 4.2 23.6 1.0 CG B:HIS155 4.2 19.1 1.0 N D:PHE202 4.3 49.0 1.0 CG B:HIS159 4.3 17.2 1.0 ND1 B:HIS159 4.4 17.2 1.0 O B:HOH2016 4.5 40.1 1.0 O B:HOH2059 4.6 32.0 1.0 CD B:GLU156 4.8 24.2 1.0 OE1 B:GLU156 4.8 24.7 1.0 CE B:MET173 4.8 16.0 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