Calcium 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:

Zinc

(Zn)

4 atoms

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Uninhibited Human Mmp-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca996 b:6.2 occ:1.00 O A:HOH1038 2.4 17.0 1.0 O A:GLY171 2.4 13.5 1.0 O A:ASP137 2.4 14.3 1.0 OD1 A:ASP173 2.4 17.2 1.0 O A:GLY169 2.5 16.8 1.0 O A:HOH1018 2.6 16.1 1.0 CG A:ASP173 3.5 13.9 1.0 C A:GLY171 3.5 14.5 1.0 C A:ASP137 3.6 14.0 1.0 C A:GLY169 3.7 18.5 1.0 OD2 A:ASP173 4.0 13.0 1.0 C A:ILE170 4.1 15.4 1.0 N A:GLY171 4.2 14.8 1.0 O A:ALA136 4.2 16.0 1.0 O A:ILE170 4.2 14.7 1.0 N A:ASP173 4.2 12.4 1.0 CA A:GLY171 4.3 15.1 1.0 CA A:ASP137 4.3 14.3 1.0 N A:ILE138 4.5 15.2 1.0 N A:GLY172 4.5 14.0 1.0 CA A:ILE170 4.5 15.8 1.0 N A:ILE170 4.6 16.6 1.0 ND2 A:ASN139 4.6 19.7 1.0 CA A:ILE138 4.6 14.6 1.0 N A:GLY169 4.6 19.0 1.0 C A:GLY172 4.6 11.8 1.0 CB A:ASP173 4.7 11.0 1.0 CA A:GLY169 4.7 18.1 1.0 CA A:GLY172 4.7 13.0 1.0 O A:GLY167 4.7 17.1 1.0 CH2 A:TRP88 4.8 21.8 1.0 CA A:ASP173 4.8 12.2 1.0 N A:ASN139 4.8 15.6 1.0 O A:HOH1015 4.9 15.6 1.0 C A:GLN168 5.0 19.7 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Uninhibited Human Mmp-8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca997 b:4.1 occ:1.00 O A:ASN157 2.4 16.3 1.0 O A:GLY155 2.4 13.3 1.0 OD2 A:ASP177 2.4 11.3 1.0 O A:ILE159 2.4 12.3 1.0 OE2 A:GLU180 2.5 14.7 1.0 OD1 A:ASP154 2.5 12.8 1.0 CG A:ASP177 3.4 10.4 1.0 C A:ASN157 3.5 14.4 1.0 C A:GLY155 3.6 14.7 1.0 C A:ILE159 3.6 13.2 1.0 CD A:GLU180 3.7 16.5 1.0 CG A:ASP154 3.7 12.9 1.0 N A:ASN157 4.0 15.7 1.0 N A:ILE159 4.0 13.7 1.0 CB A:ASP177 4.0 10.6 1.0 N A:GLY155 4.0 13.5 1.0 C A:PRO156 4.2 15.8 1.0 OD2 A:ASP154 4.3 13.2 1.0 CA A:ASN157 4.3 16.0 1.0 CA A:ILE159 4.3 14.1 1.0 C A:GLY158 4.3 12.9 1.0 C A:ASP154 4.3 14.0 1.0 N A:ASP154 4.3 14.3 1.0 CA A:GLY155 4.3 14.5 1.0 OD1 A:ASP177 4.4 13.0 1.0 OE1 A:GLU180 4.4 17.1 1.0 CG A:GLU180 4.5 15.6 1.0 N A:GLY158 4.5 13.4 1.0 N A:PRO156 4.6 15.4 1.0 CA A:PRO156 4.6 15.9 1.0 N A:LEU160 4.6 11.6 1.0 O A:PRO156 4.6 14.7 1.0 CA A:GLY158 4.7 13.5 1.0 CA A:ASP154 4.7 13.3 1.0 CB A:ILE159 4.7 15.3 1.0 O A:ASP154 4.8 12.9 1.0 CA A:LEU160 4.8 10.6 1.0 O A:GLY158 4.8 13.3 1.0 CB A:ASP154 4.8 15.3 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Uninhibited Human Mmp-8 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca996 b:5.5 occ:1.00 OD1 F:ASP173 2.4 13.2 1.0 O F:ASP137 2.4 15.8 1.0 O F:GLY169 2.4 15.2 1.0 O F:GLY171 2.5 13.6 1.0 O F:HOH1050 2.6 23.1 1.0 O F:HOH1064 2.6 17.5 1.0 CG F:ASP173 3.3 11.4 1.0 C F:ASP137 3.5 14.8 1.0 C F:GLY169 3.6 16.9 1.0 C F:GLY171 3.6 13.8 1.0 OD2 F:ASP173 3.9 13.0 1.0 C F:ILE170 4.0 15.1 1.0 ND2 F:ASN139 4.1 19.5 1.0 N F:GLY171 4.1 15.3 1.0 O F:ILE170 4.1 12.8 1.0 N F:ASP173 4.2 11.8 1.0 O F:ALA136 4.3 16.8 1.0 CA F:GLY171 4.3 13.9 1.0 CA F:ASP137 4.3 14.4 1.0 N F:ILE138 4.5 15.4 1.0 N F:ILE170 4.5 15.7 1.0 CA F:ILE170 4.5 16.1 1.0 CB F:ASP173 4.5 11.8 1.0 CA F:GLY169 4.6 16.1 1.0 N F:GLY169 4.6 17.9 1.0 O F:GLY167 4.6 17.1 1.0 CA F:ILE138 4.6 16.2 1.0 N F:GLY172 4.7 13.2 1.0 C F:GLY172 4.7 12.5 1.0 CA F:ASP173 4.7 12.1 1.0 N F:ASN139 4.7 15.1 1.0 O F:HOH1131 4.8 28.1 1.0 CA F:GLY172 4.9 12.3 1.0 CH2 F:TRP88 4.9 20.1 1.0 O F:HOH1011 4.9 12.4 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Uninhibited Human Mmp-8 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca997 b:3.8 occ:1.00 O F:GLY155 2.2 14.4 1.0 O F:ILE159 2.3 15.2 1.0 OD1 F:ASP154 2.3 12.1 1.0 OE2 F:GLU180 2.3 13.2 1.0 OD2 F:ASP177 2.3 14.4 1.0 O F:ASN157 2.4 13.3 1.0 CG F:ASP177 3.4 10.2 1.0 C F:ILE159 3.4 14.9 1.0 C F:GLY155 3.5 16.4 1.0 CG F:ASP154 3.5 15.7 1.0 CD F:GLU180 3.5 15.4 1.0 C F:ASN157 3.6 14.1 1.0 N F:ILE159 3.8 16.4 1.0 CB F:ASP177 4.0 9.9 1.0 N F:ASN157 4.0 15.5 1.0 N F:GLY155 4.0 14.7 1.0 OD2 F:ASP154 4.1 17.0 1.0 CA F:ILE159 4.1 16.6 1.0 C F:PRO156 4.2 16.2 1.0 OE1 F:GLU180 4.3 17.8 1.0 C F:GLY158 4.3 16.3 1.0 C F:ASP154 4.3 14.6 1.0 CA F:GLY155 4.3 15.6 1.0 CA F:ASN157 4.3 14.9 1.0 OD1 F:ASP177 4.4 9.7 1.0 N F:ASP154 4.4 13.6 1.0 N F:PRO156 4.4 16.0 1.0 CA F:PRO156 4.5 16.9 1.0 CB F:ILE159 4.5 17.9 1.0 CG F:GLU180 4.5 15.1 1.0 N F:LEU160 4.5 13.3 1.0 N F:GLY158 4.6 14.6 1.0 O F:PRO156 4.6 16.1 1.0 CA F:ASP154 4.6 14.2 1.0 CB F:ASP154 4.7 14.4 1.0 CA F:LEU160 4.7 11.9 1.0 CA F:GLY158 4.7 14.9 1.0 O F:ASP154 4.7 13.5 1.0 O F:GLY158 4.8 15.4 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