Calcium 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:

Zinc

(Zn)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Human Mmp-8 in Complex with Peptide Iag, PDB code: 2oy2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca996 b:7.5 occ:1.00 O A:GLY169 2.3 9.6 1.0 O A:HOH1015 2.3 10.2 1.0 O A:GLY171 2.3 6.3 1.0 O A:ASP137 2.3 6.6 1.0 OD1 A:ASP173 2.4 5.4 1.0 O A:HOH1027 2.5 9.2 1.0 CG A:ASP173 3.4 5.0 1.0 C A:GLY171 3.5 6.2 1.0 C A:GLY169 3.5 9.5 1.0 C A:ASP137 3.5 6.0 1.0 OD2 A:ASP173 3.9 5.9 1.0 C A:ILE170 3.9 7.8 1.0 N A:GLY171 4.0 7.1 1.0 O A:ILE170 4.1 7.1 1.0 CA A:GLY171 4.3 6.7 1.0 N A:ASP173 4.3 4.9 1.0 O A:ALA136 4.3 8.4 1.0 N A:ILE170 4.4 9.0 1.0 CA A:ASP137 4.4 6.5 1.0 CA A:ILE170 4.4 8.8 1.0 N A:ILE138 4.4 5.7 1.0 O A:GLY167 4.4 9.7 1.0 CA A:GLY169 4.5 9.9 1.0 ND2 A:ASN139 4.5 12.2 1.0 N A:GLY169 4.5 10.9 1.0 N A:GLY172 4.5 5.7 1.0 CA A:ILE138 4.5 5.5 1.0 CB A:ASP173 4.6 4.7 1.0 CA A:GLY172 4.7 5.4 1.0 N A:ASN139 4.7 5.2 1.0 C A:GLY172 4.7 5.2 1.0 O A:HOH1012 4.8 12.2 1.0 CA A:ASP173 4.8 4.4 1.0 C A:GLN168 4.9 11.0 1.0 CH2 A:TRP88 4.9 9.7 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca997 b:4.6 occ:1.00 O A:GLY155 2.3 5.8 1.0 OE2 A:GLU180 2.3 6.5 1.0 O A:ILE159 2.3 5.3 1.0 O A:ASN157 2.3 5.1 1.0 OD1 A:ASP154 2.3 5.4 1.0 OD2 A:ASP177 2.4 4.7 1.0 CG A:ASP177 3.4 4.2 1.0 C A:ILE159 3.4 4.7 1.0 C A:GLY155 3.5 5.8 1.0 CD A:GLU180 3.5 5.9 1.0 C A:ASN157 3.5 5.2 1.0 CG A:ASP154 3.5 5.6 1.0 N A:ASN157 3.9 5.3 1.0 N A:ILE159 3.9 4.9 1.0 CB A:ASP177 4.0 3.1 1.0 N A:GLY155 4.0 5.7 1.0 C A:PRO156 4.1 5.8 1.0 OD2 A:ASP154 4.2 7.0 1.0 CA A:ILE159 4.2 5.3 1.0 OE1 A:GLU180 4.2 6.1 1.0 C A:ASP154 4.3 5.5 1.0 C A:GLY158 4.3 4.7 1.0 CA A:ASN157 4.3 5.6 1.0 N A:ASP154 4.3 5.3 1.0 CA A:GLY155 4.3 6.0 1.0 OD1 A:ASP177 4.4 4.7 1.0 N A:LEU160 4.4 4.2 1.0 N A:PRO156 4.4 6.0 1.0 O A:PRO156 4.5 6.0 1.0 CA A:PRO156 4.5 5.9 1.0 CG A:GLU180 4.5 5.0 1.0 N A:GLY158 4.5 4.7 1.0 CA A:LEU160 4.5 3.8 1.0 CA A:ASP154 4.6 5.1 1.0 CB A:ASP154 4.6 5.4 1.0 CA A:GLY158 4.7 4.7 1.0 CB A:ILE159 4.7 5.9 1.0 O A:GLY158 4.7 5.4 1.0 O A:ASP154 4.8 6.0 1.0 CD2 A:LEU160 5.0 6.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca996 b:8.3 occ:1.00 O F:GLY169 2.3 10.4 1.0 O F:GLY171 2.3 7.8 1.0 O F:ASP137 2.3 7.9 1.0 O F:HOH1010 2.3 11.5 1.0 O F:HOH1027 2.4 10.8 1.0 OD1 F:ASP173 2.5 6.2 1.0 CG F:ASP173 3.4 5.8 1.0 C F:ASP137 3.5 7.2 1.0 C F:GLY171 3.5 7.8 1.0 C F:GLY169 3.5 10.5 1.0 OD2 F:ASP173 3.9 7.0 1.0 C F:ILE170 3.9 9.2 1.0 N F:GLY171 4.0 8.9 1.0 O F:ILE170 4.1 8.7 1.0 N F:ASP173 4.2 5.2 1.0 CA F:GLY171 4.3 8.5 1.0 O F:ALA136 4.3 9.7 1.0 CA F:ASP137 4.4 7.6 1.0 N F:ILE170 4.4 10.0 1.0 CA F:ILE170 4.4 10.1 1.0 N F:ILE138 4.4 6.7 1.0 ND2 F:ASN139 4.4 13.1 1.0 O F:GLY167 4.5 10.7 1.0 CA F:GLY169 4.5 11.1 1.0 N F:GLY172 4.5 7.2 1.0 N F:GLY169 4.5 11.8 1.0 CA F:ILE138 4.5 6.5 1.0 CB F:ASP173 4.6 6.0 1.0 CA F:GLY172 4.6 6.5 1.0 N F:ASN139 4.7 6.1 1.0 C F:GLY172 4.7 5.8 1.0 O F:HOH1021 4.8 12.7 1.0 CA F:ASP173 4.8 5.3 1.0 CH2 F:TRP88 4.9 10.0 1.0 C F:GLN168 4.9 12.5 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca997 b:6.5 occ:1.00 O F:GLY155 2.2 8.4 1.0 OE2 F:GLU180 2.3 7.9 1.0 O F:ILE159 2.3 7.1 1.0 O F:ASN157 2.3 8.9 1.0 OD1 F:ASP154 2.4 7.7 1.0 OD2 F:ASP177 2.4 6.1 1.0 CG F:ASP177 3.4 5.7 1.0 C F:GLY155 3.4 8.7 1.0 C F:ILE159 3.5 6.4 1.0 C F:ASN157 3.5 8.5 1.0 CG F:ASP154 3.5 8.7 1.0 CD F:GLU180 3.5 7.7 1.0 N F:ASN157 3.9 8.4 1.0 N F:ILE159 3.9 6.6 1.0 N F:GLY155 4.0 8.3 1.0 CB F:ASP177 4.0 5.2 1.0 C F:PRO156 4.0 9.0 1.0 OD2 F:ASP154 4.1 9.4 1.0 CA F:ILE159 4.2 7.0 1.0 C F:GLY158 4.2 7.4 1.0 C F:ASP154 4.2 8.1 1.0 CA F:ASN157 4.3 8.7 1.0 OE1 F:GLU180 4.3 8.2 1.0 CA F:GLY155 4.3 8.7 1.0 N F:ASP154 4.3 7.9 1.0 OD1 F:ASP177 4.3 6.6 1.0 N F:PRO156 4.4 9.0 1.0 O F:PRO156 4.4 9.1 1.0 CA F:PRO156 4.4 9.0 1.0 N F:LEU160 4.5 5.6 1.0 N F:GLY158 4.5 8.2 1.0 CG F:GLU180 4.5 7.1 1.0 CA F:ASP154 4.6 8.0 1.0 CA F:LEU160 4.6 5.1 1.0 CA F:GLY158 4.6 7.3 1.0 CB F:ASP154 4.7 8.3 1.0 CB F:ILE159 4.7 7.3 1.0 O F:ASP154 4.7 8.3 1.0 O F:GLY158 4.7 8.2 1.0 CD2 F:LEU160 5.0 7.1 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: ESSN 0570-0833
PubMed: 17096442
DOI: 10.1002/ANIE.200603100