Calcium in PDB 3ba0: Crystal Structure of Full-Length Human Mmp-12

All present enzymatic activity of Crystal Structure of Full-Length Human Mmp-12:
3.4.24.65;

The structure of Crystal Structure of Full-Length Human Mmp-12, PDB code: 3ba0 was solved by I.Bertini, V.Calderone, M.Fragai, R.Jaiswal, C.Luchinat, M.Melikian, E.Myonas, D.I.Svergun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.70 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.037, 60.148, 59.611, 90.00, 90.74, 90.00
R / Rfree (%)	23.6 / 31.9

The structure of Crystal Structure of Full-Length Human Mmp-12 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Full-Length Human Mmp-12 (pdb code 3ba0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Full-Length Human Mmp-12, PDB code: 3ba0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Full-Length Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Full-Length Human Mmp-12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca473 b:2.0 occ:1.00 O A:GLY192 2.2 2.4 1.0 O A:ASP158 2.6 6.9 1.0 OD2 A:ASP194 3.1 2.7 1.0 C A:GLY192 3.5 6.9 1.0 C A:ASP158 3.6 6.6 1.0 N A:GLY192 3.8 10.4 1.0 N A:ILE191 4.0 7.9 1.0 CG A:ASP194 4.1 2.0 1.0 CA A:ASP158 4.2 9.4 1.0 CA A:ILE191 4.2 9.8 1.0 C A:GLY190 4.3 8.7 1.0 CA A:GLY192 4.4 7.9 1.0 N A:GLY193 4.4 4.8 1.0 N A:ILE159 4.4 6.2 1.0 N A:ASP194 4.4 2.0 1.0 C A:ILE191 4.5 11.8 1.0 OD1 A:ASP194 4.6 2.0 1.0 O A:GLY188 4.6 5.7 1.0 N A:GLY190 4.6 6.5 1.0 O A:ALA157 4.6 11.3 1.0 CA A:ILE159 4.6 4.5 1.0 CB A:ASP158 4.7 10.9 1.0 N A:LEU160 4.8 2.0 1.0 O A:GLY190 4.9 12.6 1.0 CH2 A:TRP109 4.9 2.0 1.0 C A:GLY193 4.9 2.0 1.0 CA A:GLY190 4.9 8.4 1.0 CA A:GLY193 4.9 2.0 1.0 CD1 A:LEU160 5.0 2.0 1.0 C A:ILE159 5.0 2.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Full-Length Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Full-Length Human Mmp-12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca474 b:2.0 occ:1.00 O A:GLU201 2.2 2.0 1.0 O A:GLU199 2.3 4.0 1.0 OD2 A:ASP124 2.5 2.0 1.0 OE2 A:GLU199 3.0 2.0 1.0 OD1 A:ASP124 3.1 10.9 1.0 CG A:ASP124 3.2 7.5 1.0 C A:GLU201 3.4 3.2 1.0 C A:GLU199 3.5 2.0 1.0 CG A:GLU199 3.9 2.0 1.0 CD A:GLU199 4.0 2.0 1.0 C A:ASP200 4.0 6.5 1.0 N A:GLU201 4.2 6.8 1.0 CA A:ASP200 4.2 5.2 1.0 N A:PHE202 4.3 3.6 1.0 O A:ASP200 4.3 7.7 1.0 CA A:PHE202 4.3 2.0 1.0 N A:ASP200 4.4 2.7 1.0 CA A:GLU199 4.4 2.0 1.0 CA A:GLU201 4.4 4.0 1.0 CD1 A:PHE202 4.6 11.4 1.0 CB A:GLU199 4.7 2.0 1.0 CB A:ASP124 4.8 2.0 1.0 NH2 A:ARG165 4.8 2.0 1.0 CD1 A:TRP203 5.0 2.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Full-Length Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Full-Length Human Mmp-12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca475 b:2.0 occ:1.00 OD2 A:ASP198 1.7 3.0 1.0 O A:ILE180 2.2 2.0 1.0 OE2 A:GLU201 2.5 2.0 1.0 O A:GLY178 2.6 2.0 1.0 CG A:ASP198 2.8 4.8 1.0 OD2 A:ASP175 2.9 2.6 1.0 N A:GLY176 3.2 2.0 1.0 C A:ILE180 3.5 2.0 1.0 CB A:ASP198 3.6 2.2 1.0 OD1 A:ASP198 3.7 2.0 1.0 N A:GLY178 3.7 2.8 1.0 CD A:GLU201 3.7 2.0 1.0 C A:GLY178 3.7 2.0 1.0 C A:GLY176 3.7 2.0 1.0 N A:LYS177 3.7 2.0 1.0 C A:ASP175 3.9 2.0 1.0 CA A:GLY176 3.9 2.0 1.0 CG A:ASP175 4.0 2.0 1.0 CA A:LYS177 4.2 2.0 1.0 N A:ASP175 4.2 2.0 1.0 O A:GLY176 4.2 2.0 1.0 CA A:GLY178 4.3 2.5 1.0 N A:ILE180 4.3 2.0 1.0 C A:LYS177 4.3 2.2 1.0 OE1 A:GLU201 4.3 4.5 1.0 N A:LEU181 4.4 2.0 1.0 CA A:ILE180 4.4 2.0 1.0 CA A:LEU181 4.5 2.0 1.0 CA A:ASP175 4.5 2.0 1.0 O A:ASP175 4.5 2.0 1.0 OD1 A:ASP175 4.6 2.0 1.0 C A:GLY179 4.7 2.0 1.0 CG A:GLU201 4.7 4.9 1.0 N A:GLY179 4.8 2.0 1.0 CB A:ASP175 4.9 2.0 1.0 O A:GLY179 4.9 2.6 1.0 CD2 A:LEU181 5.0 2.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Full-Length Human Mmp-12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Full-Length Human Mmp-12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca476 b:15.3 occ:1.00 O A:ASP289 2.2 2.0 1.0 O A:ASP381 2.6 2.0 1.0 O A:GLU333 2.8 2.0 1.0 O A:ASP430 2.8 2.7 1.0 C A:ASP289 3.5 2.0 1.0 C A:ASP430 3.6 2.0 1.0 CA A:ASP430 3.8 2.0 1.0 C A:ASP381 3.8 2.0 1.0 C A:GLU333 3.9 2.0 1.0 O A:PHE288 4.1 2.0 1.0 O A:ILE429 4.3 2.5 1.0 OD1 A:ASP430 4.3 2.4 1.0 CA A:ASP381 4.4 2.0 1.0 N A:ALA290 4.4 2.0 1.0 CA A:ASP289 4.4 2.0 1.0 CB A:ASP430 4.4 2.0 1.0 CA A:GLU333 4.5 2.0 1.0 CB A:ASP381 4.5 2.0 1.0 CA A:ALA290 4.7 2.0 1.0 N A:ALA382 4.9 2.0 1.0 N A:ALA431 4.9 2.0 1.0 CB A:GLU333 4.9 2.7 1.0 CG A:ASP430 4.9 2.0 1.0 C A:PHE288 5.0 2.0 1.0 N A:ASP430 5.0 2.0 1.0

I.Bertini, V.Calderone, M.Fragai, R.Jaiswal, C.Luchinat, M.Melikian, E.Mylonas, D.I.Svergun. Evidence of Reciprocal Reorientation of the Catalytic and Hemopexin-Like Domains of Full-Length Mmp-12. J.Am.Chem.Soc. V. 130 7011 2008.
ISSN: ISSN 0002-7863
PubMed: 18465858
DOI: 10.1021/JA710491Y