Zinc in PDB 2oy2: Human Mmp-8 in Complex with Peptide Iag

All present enzymatic activity of Human Mmp-8 in Complex with Peptide Iag:
3.4.24.34;

The structure of Human Mmp-8 in Complex with Peptide Iag, PDB code: 2oy2 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)	38.75 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.207, 68.533, 78.281, 90.00, 98.10, 90.00
R / Rfree (%)	16.4 / 19.2

The structure of Human Mmp-8 in Complex with Peptide Iag also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Human Mmp-8 in Complex with Peptide Iag (pdb code 2oy2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Mmp-8 in Complex with Peptide Iag, PDB code: 2oy2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human Mmp-8 in Complex with Peptide Iag


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Mmp-8 in Complex with Peptide Iag within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn998 b:6.1 occ:1.00 OD2 A:ASP149 1.9 8.4 1.0 NE2 A:HIS147 2.0 4.3 1.0 NE2 A:HIS162 2.0 5.7 1.0 ND1 A:HIS175 2.1 5.1 1.0 CG A:ASP149 2.9 10.6 1.0 CD2 A:HIS147 2.9 4.9 1.0 CE1 A:HIS162 2.9 6.0 1.0 CE1 A:HIS175 3.0 5.3 1.0 CE1 A:HIS147 3.1 4.7 1.0 CD2 A:HIS162 3.1 4.8 1.0 CG A:HIS175 3.1 4.4 1.0 OD1 A:ASP149 3.2 11.2 1.0 CB A:HIS175 3.5 5.4 1.0 ND1 A:HIS162 4.1 6.6 1.0 CG A:HIS147 4.1 4.3 1.0 ND1 A:HIS147 4.1 4.0 1.0 NE2 A:HIS175 4.2 6.1 1.0 CG A:HIS162 4.2 5.2 1.0 CB A:ASP149 4.2 11.1 1.0 CD2 A:HIS175 4.2 5.6 1.0 CE1 A:PHE164 4.3 8.9 1.0 O A:SER151 4.3 10.1 1.0 CZ A:PHE164 4.6 9.4 1.0 CZ A:PHE153 4.6 4.0 1.0 CE2 A:PHE153 4.6 4.2 1.0 O A:HOH1006 4.8 12.0 1.0 CA A:HIS175 5.0 4.4 1.0

Zinc binding site 2 out of 4 in the Human Mmp-8 in Complex with Peptide Iag


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Mmp-8 in Complex with Peptide Iag within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:9.7 occ:1.00 NE2 A:HIS207 2.0 9.3 1.0 NE2 A:HIS197 2.1 5.5 1.0 NE2 A:HIS201 2.1 7.0 1.0 O A:HOH1059 2.3 10.6 1.0 O A:HOH1183 2.3 17.1 1.0 CD2 A:HIS207 3.0 8.0 1.0 CD2 A:HIS201 3.0 5.6 1.0 CE1 A:HIS197 3.0 4.8 1.0 CE1 A:HIS207 3.1 9.6 1.0 CD2 A:HIS197 3.1 4.8 1.0 CE1 A:HIS201 3.1 6.5 1.0 N W:ILE207 3.9 12.7 1.0 CG A:HIS207 4.1 8.3 1.0 ND1 A:HIS207 4.1 9.1 1.0 O A:HOH1001 4.1 9.0 1.0 ND1 A:HIS197 4.2 4.3 1.0 CG A:HIS197 4.2 4.9 1.0 CG A:HIS201 4.2 5.0 1.0 ND1 A:HIS201 4.2 6.4 1.0 CA W:ILE207 4.3 12.3 1.0 OE1 A:GLU198 4.4 9.1 1.0 O A:HOH1060 4.5 11.4 1.0 O A:HOH1132 4.6 25.3 1.0 O A:HOH1138 4.7 27.1 1.0 O A:HOH1231 4.7 32.1 1.0 OE2 A:GLU198 4.7 9.7 1.0 O A:HOH1236 4.8 42.6 1.0 CE A:MET215 4.8 5.8 1.0 CB W:ILE207 4.8 12.2 1.0 CD A:GLU198 4.9 7.8 1.0

Zinc binding site 3 out of 4 in the Human Mmp-8 in Complex with Peptide Iag


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Mmp-8 in Complex with Peptide Iag within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn998 b:7.1 occ:1.00 OD2 F:ASP149 1.9 9.6 1.0 NE2 F:HIS162 2.0 7.6 1.0 NE2 F:HIS147 2.0 6.1 1.0 ND1 F:HIS175 2.1 6.0 1.0 CE1 F:HIS162 2.9 7.8 1.0 CG F:ASP149 2.9 12.1 1.0 CD2 F:HIS147 2.9 5.2 1.0 CE1 F:HIS175 3.0 6.0 1.0 CE1 F:HIS147 3.1 6.1 1.0 CG F:HIS175 3.1 5.2 1.0 CD2 F:HIS162 3.1 6.7 1.0 OD1 F:ASP149 3.2 11.4 1.0 CB F:HIS175 3.5 5.1 1.0 ND1 F:HIS162 4.1 7.8 1.0 CG F:HIS147 4.1 5.8 1.0 NE2 F:HIS175 4.1 6.0 1.0 ND1 F:HIS147 4.2 6.3 1.0 CG F:HIS162 4.2 6.7 1.0 CD2 F:HIS175 4.2 6.3 1.0 CB F:ASP149 4.2 12.9 1.0 O F:SER151 4.2 12.1 1.0 CE1 F:PHE164 4.3 9.7 1.0 CZ F:PHE164 4.5 10.3 1.0 CE2 F:PHE153 4.6 6.0 1.0 CZ F:PHE153 4.6 5.9 1.0 O F:HOH1005 4.9 10.2 1.0 CA F:HIS175 5.0 4.6 1.0 CB F:SER151 5.0 14.7 1.0

Zinc binding site 4 out of 4 in the Human Mmp-8 in Complex with Peptide Iag


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Mmp-8 in Complex with Peptide Iag within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn999 b:9.5 occ:1.00 NE2 F:HIS207 2.0 10.7 1.0 NE2 F:HIS197 2.1 6.4 1.0 NE2 F:HIS201 2.1 7.7 1.0 O Y:HOH59 2.2 11.3 1.0 O Y:HOH401 2.5 23.9 1.0 CD2 F:HIS207 2.9 9.5 1.0 CE1 F:HIS207 3.0 10.7 1.0 CD2 F:HIS197 3.0 5.4 1.0 CE1 F:HIS197 3.0 5.8 1.0 CD2 F:HIS201 3.1 6.6 1.0 CE1 F:HIS201 3.1 8.1 1.0 N Y:ILE207 3.9 16.0 1.0 CG F:HIS207 4.1 9.7 1.0 ND1 F:HIS207 4.1 11.0 1.0 O F:HOH1000 4.1 10.5 1.0 ND1 F:HIS197 4.1 5.5 1.0 CG F:HIS197 4.2 5.2 1.0 ND1 F:HIS201 4.2 7.5 1.0 CG F:HIS201 4.2 6.4 1.0 CA Y:ILE207 4.3 15.7 1.0 OE1 F:GLU198 4.4 9.8 1.0 OE2 F:GLU198 4.5 11.0 1.0 O F:HOH1126 4.6 21.2 1.0 O F:HOH1215 4.7 39.4 1.0 O F:HOH1082 4.7 17.7 1.0 CE F:MET215 4.7 7.8 1.0 O F:HOH1137 4.8 29.0 1.0 CD F:GLU198 4.8 8.5 1.0 CB Y:ILE207 4.9 15.7 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: ESSN 0570-0833
PubMed: 17096442
DOI: 10.1002/ANIE.200603100