Zinc in PDB 4r3v: Structure of Karilysin Propeptide and Catalytic Mmp Domain

The structure of Structure of Karilysin Propeptide and Catalytic Mmp Domain, PDB code: 4r3v was solved by M.Lopez-Pelegrin, M.Ksiazek, A.Y.Karim, T.Guevara, 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)	60.80 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.180, 121.690, 41.880, 90.00, 105.26, 90.00
R / Rfree (%)	16.5 / 19.4

The structure of Structure of Karilysin Propeptide and Catalytic Mmp Domain also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Structure of Karilysin Propeptide and Catalytic Mmp Domain (pdb code 4r3v). 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 Propeptide and Catalytic Mmp Domain, PDB code: 4r3v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Karilysin Propeptide and 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 Propeptide and Catalytic Mmp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:23.1 occ:1.00 NE2 A:HIS165 2.0 19.4 1.0 NE2 A:HIS155 2.0 21.3 1.0 OD1 A:ASP25 2.0 22.6 1.0 NE2 A:HIS159 2.1 18.9 1.0 CG A:ASP25 2.8 22.2 1.0 OD2 A:ASP25 2.9 29.9 1.0 O A:HOH452 2.9 27.5 1.0 CD2 A:HIS165 2.9 20.0 1.0 CE1 A:HIS155 3.0 20.8 1.0 CD2 A:HIS159 3.0 19.2 1.0 CD2 A:HIS155 3.0 21.4 1.0 CE1 A:HIS165 3.0 19.7 1.0 CE1 A:HIS159 3.1 18.5 1.0 CG A:HIS165 4.1 21.0 1.0 ND1 A:HIS155 4.1 21.1 1.0 ND1 A:HIS165 4.1 22.0 1.0 CG A:HIS155 4.1 20.4 1.0 CG A:HIS159 4.1 18.3 1.0 ND1 A:HIS159 4.2 19.9 1.0 CB A:ASP25 4.2 21.4 1.0 N A:GLY27 4.3 25.6 1.0 CB A:TYR24 4.3 21.5 1.0 CA A:GLY27 4.5 25.2 1.0 N A:ASP25 4.5 22.9 1.0 O A:ASP25 4.5 26.2 1.0 C A:ASP25 4.7 27.8 1.0 CE A:MET173 4.7 19.3 1.0 CA A:ASP25 4.7 21.9 1.0 CD1 A:TYR24 4.9 21.4 1.0 CG A:TYR24 4.9 21.5 1.0 CA A:PRO175 5.0 21.3 1.0

Zinc binding site 2 out of 4 in the Structure of Karilysin Propeptide and 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 Propeptide and Catalytic Mmp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:23.9 occ:1.00 OD2 A:ASP104 2.0 23.4 1.0 NE2 A:HIS117 2.0 21.1 1.0 NE2 A:HIS102 2.1 22.9 1.0 ND1 A:HIS133 2.1 22.1 1.0 CE1 A:HIS117 2.9 21.0 1.0 CD2 A:HIS102 2.9 23.2 1.0 CG A:ASP104 2.9 27.6 1.0 CE1 A:HIS133 3.0 21.8 1.0 CD2 A:HIS117 3.1 20.9 1.0 CG A:HIS133 3.1 20.8 1.0 CE1 A:HIS102 3.2 22.2 1.0 OD1 A:ASP104 3.3 24.0 1.0 CB A:HIS133 3.5 18.6 1.0 ND1 A:HIS117 4.1 21.8 1.0 CG A:HIS102 4.1 22.6 1.0 CG A:HIS117 4.2 19.6 1.0 NE2 A:HIS133 4.2 22.0 1.0 O A:TYR106 4.2 25.8 1.0 ND1 A:HIS102 4.2 23.4 1.0 CB A:ASP104 4.2 25.3 1.0 CE1 A:PHE119 4.2 23.1 1.0 CD2 A:HIS133 4.2 21.7 1.0 CE2 A:PHE108 4.5 25.0 1.0 CZ A:PHE108 4.7 22.8 1.0 CZ A:PHE119 4.7 23.2 1.0 CA A:HIS133 4.9 17.8 1.0

Zinc binding site 3 out of 4 in the Structure of Karilysin Propeptide and 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 Propeptide and Catalytic Mmp Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:23.8 occ:1.00 OD1 B:ASP25 2.0 27.1 1.0 NE2 B:HIS159 2.0 23.8 1.0 NE2 B:HIS165 2.0 23.3 1.0 NE2 B:HIS155 2.0 21.1 1.0 CG B:ASP25 2.7 25.7 1.0 OD2 B:ASP25 2.9 28.5 1.0 CD2 B:HIS159 2.9 23.0 1.0 CD2 B:HIS165 3.0 24.5 1.0 CE1 B:HIS155 3.0 20.5 1.0 CD2 B:HIS155 3.0 21.8 1.0 CE1 B:HIS165 3.1 22.9 1.0 CE1 B:HIS159 3.1 22.4 1.0 O B:HOH426 3.3 24.0 1.0 CG B:HIS159 4.1 20.6 1.0 CG B:HIS165 4.1 22.9 1.0 ND1 B:HIS155 4.1 21.6 1.0 ND1 B:HIS165 4.2 23.9 1.0 CG B:HIS155 4.2 20.0 1.0 CB B:ASP25 4.2 23.8 1.0 ND1 B:HIS159 4.2 21.3 1.0 N B:GLY27 4.3 28.6 1.0 CB B:TYR24 4.3 21.7 1.0 CA B:GLY27 4.4 27.4 1.0 N B:ASP25 4.5 22.4 1.0 O B:ASP25 4.5 27.3 1.0 C B:ASP25 4.7 28.7 1.0 CA B:ASP25 4.7 22.9 1.0 CE B:MET173 4.7 18.4 1.0 CD2 B:TYR24 4.9 21.2 1.0 CG B:TYR24 5.0 20.3 1.0 CA B:PRO175 5.0 21.4 1.0

Zinc binding site 4 out of 4 in the Structure of Karilysin Propeptide and 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 Propeptide and Catalytic Mmp Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:30.5 occ:1.00 NE2 B:HIS117 2.0 33.4 1.0 OD2 B:ASP104 2.0 28.8 1.0 NE2 B:HIS102 2.0 31.2 1.0 ND1 B:HIS133 2.0 24.6 1.0 CD2 B:HIS102 2.9 32.4 1.0 CE1 B:HIS117 2.9 33.3 1.0 CG B:ASP104 3.0 33.2 1.0 CE1 B:HIS133 3.0 24.7 1.0 CD2 B:HIS117 3.1 32.3 1.0 CG B:HIS133 3.1 22.7 1.0 CE1 B:HIS102 3.1 31.9 1.0 OD1 B:ASP104 3.3 35.7 1.0 CB B:HIS133 3.5 19.7 1.0 CG B:HIS102 4.1 33.2 1.0 ND1 B:HIS117 4.1 33.5 1.0 NE2 B:HIS133 4.2 24.5 1.0 CG B:HIS117 4.2 30.6 1.0 ND1 B:HIS102 4.2 33.9 1.0 CD2 B:HIS133 4.2 24.1 1.0 CB B:ASP104 4.3 31.9 1.0 O B:TYR106 4.3 36.5 1.0 CE1 B:PHE119 4.3 26.1 1.0 CE2 B:PHE108 4.5 28.0 1.0 CZ B:PHE108 4.6 25.4 1.0 CZ B:PHE119 4.8 28.3 1.0 CA B:HIS133 4.9 19.4 1.0 O B:HOH427 5.0 28.8 1.0

M.L Oacutepez-Pelegrin, M.Ksiazek, A.Y.Karim, T.Guevara, J.L.Arolas, J.Potempa, F.X.Gomis-R Uumlth. A Novel Mechanism of Latency in Matrix Metalloproteinases. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
PubMed: 25555916
DOI: 10.1074/JBC.M114.605956