Zinc in PDB 2oy4: Uninhibited Human Mmp-8

All present enzymatic activity of Uninhibited Human Mmp-8:
3.4.24.34;

The structure of Uninhibited Human Mmp-8, PDB code: 2oy4 was solved by V.Calderone, I.Bertini, M.Fragai, C.Luchinat, M.Maletta, K.J.Yeo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.17 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.294, 47.110, 61.325, 77.73, 80.04, 77.01
R / Rfree (%)	22.5 / 29.3

The structure of Uninhibited Human Mmp-8 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Uninhibited Human Mmp-8 (pdb code 2oy4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Uninhibited Human Mmp-8, PDB code: 2oy4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Uninhibited Human Mmp-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Uninhibited Human Mmp-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn998 b:5.2 occ:1.00 OD2 A:ASP149 2.0 13.3 1.0 NE2 A:HIS162 2.1 12.1 1.0 NE2 A:HIS147 2.3 11.7 1.0 ND1 A:HIS175 2.4 14.0 1.0 CG A:ASP149 2.9 14.5 1.0 CD2 A:HIS147 3.0 10.0 1.0 CE1 A:HIS162 3.1 9.5 1.0 OD1 A:ASP149 3.1 15.1 1.0 CD2 A:HIS162 3.2 8.8 1.0 CG A:HIS175 3.3 13.2 1.0 CE1 A:HIS175 3.4 14.8 1.0 CE1 A:HIS147 3.4 11.2 1.0 CB A:HIS175 3.4 11.4 1.0 O A:SER151 4.1 16.4 1.0 CG A:HIS147 4.2 12.0 1.0 CB A:ASP149 4.2 20.0 1.0 ND1 A:HIS162 4.2 10.3 1.0 CG A:HIS162 4.3 7.8 1.0 CE1 A:PHE164 4.4 17.1 1.0 ND1 A:HIS147 4.4 10.3 1.0 CD2 A:HIS175 4.4 12.8 1.0 NE2 A:HIS175 4.5 15.3 1.0 CZ A:PHE164 4.7 16.3 1.0 CZ A:PHE153 4.8 10.6 1.0 CE2 A:PHE153 4.8 9.2 1.0 CA A:HIS175 4.9 10.6 1.0 CB A:SER151 5.0 19.3 1.0

Zinc binding site 2 out of 4 in the Uninhibited Human Mmp-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Uninhibited Human Mmp-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:5.8 occ:1.00 NE2 A:HIS197 2.1 16.4 1.0 NE2 A:HIS207 2.1 20.4 1.0 NE2 A:HIS201 2.2 12.2 1.0 O A:HOH1143 2.7 15.0 1.0 O A:HOH1095 2.8 32.5 1.0 O A:HOH1140 2.8 26.1 1.0 CD2 A:HIS197 3.0 14.8 1.0 CD2 A:HIS207 3.0 18.7 1.0 CE1 A:HIS197 3.1 13.1 1.0 CE1 A:HIS207 3.1 21.4 1.0 CD2 A:HIS201 3.1 13.1 1.0 CE1 A:HIS201 3.3 14.9 1.0 ND1 A:HIS207 4.1 19.2 1.0 CG A:HIS207 4.1 18.0 1.0 ND1 A:HIS197 4.2 10.5 1.0 CG A:HIS197 4.2 12.8 1.0 O A:HOH1001 4.3 11.3 1.0 CG A:HIS201 4.3 13.7 1.0 ND1 A:HIS201 4.4 15.4 1.0 OE2 A:GLU198 4.5 18.1 1.0 OE1 A:GLU198 4.7 17.6 1.0 O A:HOH1116 4.8 28.1 1.0 O A:HOH1141 4.9 40.1 1.0 CE A:MET215 4.9 16.7 1.0 CD A:GLU198 4.9 16.3 1.0

Zinc binding site 3 out of 4 in the Uninhibited Human Mmp-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Uninhibited Human Mmp-8 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn998 b:5.3 occ:1.00 OD2 F:ASP149 1.8 14.0 1.0 NE2 F:HIS162 2.1 18.1 1.0 NE2 F:HIS147 2.2 8.3 1.0 ND1 F:HIS175 2.4 16.9 1.0 CG F:ASP149 2.8 19.2 1.0 CD2 F:HIS147 3.0 5.7 1.0 CE1 F:HIS162 3.1 14.5 1.0 CD2 F:HIS162 3.1 15.7 1.0 CE1 F:HIS147 3.2 8.3 1.0 OD1 F:ASP149 3.2 20.9 1.0 CE1 F:HIS175 3.3 15.4 1.0 CG F:HIS175 3.4 11.7 1.0 CB F:HIS175 3.7 12.0 1.0 CB F:ASP149 4.2 20.9 1.0 O F:SER151 4.2 17.8 1.0 ND1 F:HIS162 4.2 15.5 1.0 CG F:HIS162 4.2 12.6 1.0 CG F:HIS147 4.2 12.0 1.0 ND1 F:HIS147 4.3 7.3 1.0 CE1 F:PHE164 4.3 19.5 1.0 NE2 F:HIS175 4.4 12.7 1.0 CD2 F:HIS175 4.5 12.6 1.0 CZ F:PHE164 4.5 19.3 1.0 CE2 F:PHE153 4.7 13.8 1.0 CZ F:PHE153 4.7 12.7 1.0 CB F:SER151 4.8 20.9 1.0

Zinc binding site 4 out of 4 in the Uninhibited Human Mmp-8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Uninhibited Human Mmp-8 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn999 b:5.8 occ:1.00 NE2 F:HIS201 2.1 19.8 1.0 NE2 F:HIS197 2.1 15.4 1.0 NE2 F:HIS207 2.2 19.7 1.0 O F:HOH1072 2.7 29.4 1.0 CE1 F:HIS201 3.0 15.3 1.0 CE1 F:HIS197 3.1 14.7 1.0 CD2 F:HIS207 3.1 20.4 1.0 CD2 F:HIS197 3.1 18.6 1.0 CE1 F:HIS207 3.1 20.2 1.0 CD2 F:HIS201 3.1 17.8 1.0 ND1 F:HIS201 4.1 18.0 1.0 ND1 F:HIS207 4.1 20.4 1.0 CG F:HIS207 4.2 19.8 1.0 ND1 F:HIS197 4.2 15.9 1.0 CG F:HIS201 4.2 13.8 1.0 CG F:HIS197 4.2 15.9 1.0 O F:HOH1002 4.3 14.4 1.0 O F:HOH1054 4.4 23.0 1.0 OE2 F:GLU198 4.5 19.2 1.0 OE1 F:GLU198 4.6 20.5 1.0 O F:HOH1121 4.8 23.2 1.0 O F:HOH1106 4.9 21.2 1.0 CD F:GLU198 4.9 16.1 1.0

I.Bertini, V.Calderone, M.Fragai, C.Luchinat, M.Maletta, K.J.Yeo. Snapshots of the Reaction Mechanism of Matrix Metalloproteinases. Angew.Chem.Int.Ed.Engl. V. 45 7952 2006.
ISSN: ISSN 1433-7851
PubMed: 17096442
DOI: 10.1002/ANIE.200603100