Calcium in PDB 9csx: Matrix Metalloproteinase-10 Proenzyme

All present enzymatic activity of Matrix Metalloproteinase-10 Proenzyme:
3.4.24.22;

The structure of Matrix Metalloproteinase-10 Proenzyme, PDB code: 9csx was solved by E.A.Isiorho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.12 / 1.67
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.841, 72.003, 54.495, 90, 130.82, 90
R / Rfree (%)	18.9 / 21.3

The structure of Matrix Metalloproteinase-10 Proenzyme also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Matrix Metalloproteinase-10 Proenzyme (pdb code 9csx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Matrix Metalloproteinase-10 Proenzyme, PDB code: 9csx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Matrix Metalloproteinase-10 Proenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Matrix Metalloproteinase-10 Proenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:11.5 occ:1.00 O A:TYR191 2.3 10.4 1.0 O A:GLY189 2.3 12.0 1.0 O A:ASP157 2.3 13.6 1.0 O A:HOH422 2.4 13.4 1.0 OD1 A:ASP193 2.4 9.7 1.0 O A:HOH441 2.5 15.6 1.0 H5 A:IMD301 3.4 12.1 1.0 CG A:ASP193 3.5 15.1 1.0 C A:GLY189 3.5 14.6 1.0 C A:ASP157 3.5 17.1 1.0 C A:TYR191 3.5 15.7 1.0 HA A:ASP157 3.8 15.8 1.0 H A:MET159 3.8 15.0 1.0 HG2 A:MET159 3.9 21.0 1.0 OD2 A:ASP193 4.0 9.8 1.0 HA3 A:GLY192 4.0 16.3 1.0 H A:ASP193 4.1 15.5 1.0 O A:ALA156 4.1 13.2 1.0 C A:LEU190 4.1 11.8 1.0 HA A:ILE158 4.1 15.3 1.0 HA A:LEU190 4.2 16.3 1.0 N A:ASP193 4.2 12.9 1.0 H A:GLY189 4.2 13.4 1.0 HH2 A:TRP108 4.2 16.2 1.0 CA A:ASP157 4.2 13.2 1.0 N A:GLY189 4.2 11.2 1.0 N A:TYR191 4.3 11.6 1.0 O A:LEU190 4.3 14.3 1.0 C5 A:IMD301 4.3 10.1 1.0 CA A:GLY189 4.4 16.9 1.0 N A:LEU190 4.4 12.7 1.0 N A:GLY192 4.4 12.8 1.0 C A:GLY192 4.4 15.3 1.0 O A:GLY187 4.4 11.5 1.0 CA A:LEU190 4.5 13.6 1.0 CA A:TYR191 4.5 11.1 1.0 CA A:GLY192 4.5 13.5 1.0 HA A:ASP193 4.5 14.7 1.0 N A:ILE158 4.5 12.7 1.0 HG3 A:MET159 4.5 21.0 1.0 H A:TYR191 4.6 13.9 1.0 HA2 A:GLY189 4.6 20.3 1.0 N A:MET159 4.6 12.5 1.0 CB A:ASP193 4.6 13.5 1.0 CG A:MET159 4.6 17.4 1.0 CA A:ASP193 4.7 12.2 1.0 C A:PRO188 4.7 15.1 1.0 HB2 A:MET159 4.7 19.1 1.0 CA A:ILE158 4.8 12.7 1.0 HB2 A:TYR191 4.8 14.6 1.0 OE2 A:GLU155 4.8 16.2 1.0 O A:HOH477 4.8 17.6 1.0 O A:HOH439 4.8 20.4 1.0 HN1 A:IMD301 4.9 18.5 1.0 HD13 A:ILE158 4.9 38.7 1.0 HB2 A:ASP193 4.9 16.3 1.0 HA A:PRO188 4.9 15.3 1.0 HB3 A:ASP157 5.0 20.4 1.0

Calcium binding site 2 out of 4 in the Matrix Metalloproteinase-10 Proenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Matrix Metalloproteinase-10 Proenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:14.3 occ:1.00 O A:GLY175 2.2 15.0 1.0 O A:SER179 2.2 14.2 1.0 OE2 A:GLU200 2.3 16.3 1.0 OD2 A:ASP197 2.4 8.3 1.0 OD1 A:ASP174 2.4 15.6 1.0 O A:GLY177 2.4 13.8 1.0 C A:SER179 3.4 13.4 1.0 CG A:ASP197 3.4 13.5 1.0 C A:GLY175 3.4 17.1 1.0 H A:ASP174 3.5 19.9 1.0 C A:GLY177 3.5 18.1 1.0 CD A:GLU200 3.6 16.2 1.0 CG A:ASP174 3.6 18.3 1.0 H A:GLY177 3.9 16.1 1.0 HB3 A:ASP197 3.9 12.9 1.0 N A:GLY177 3.9 13.4 1.0 HA A:LEU180 3.9 14.5 1.0 H A:SER179 3.9 17.9 1.0 N A:SER179 3.9 14.9 1.0 HB2 A:HIS178 4.0 26.1 1.0 N A:GLY175 4.0 15.7 1.0 H A:GLY175 4.0 18.8 1.0 CB A:ASP197 4.1 10.7 1.0 HB2 A:ASP197 4.1 12.9 1.0 C A:PRO176 4.1 14.9 1.0 HB3 A:SER179 4.1 21.7 1.0 HA A:PRO176 4.2 20.1 1.0 OD2 A:ASP174 4.2 21.9 1.0 CA A:SER179 4.2 15.6 1.0 HD23 A:LEU180 4.2 20.7 1.0 C A:ASP174 4.2 17.3 1.0 OE1 A:GLU200 4.2 15.2 1.0 N A:ASP174 4.3 16.5 1.0 CA A:GLY177 4.3 13.6 1.0 CA A:GLY175 4.3 17.8 1.0 C A:HIS178 4.3 15.1 1.0 OD1 A:ASP197 4.3 14.4 1.0 N A:PRO176 4.4 18.9 1.0 N A:LEU180 4.4 11.6 1.0 CA A:PRO176 4.4 16.8 1.0 HG2 A:GLU200 4.5 25.2 1.0 HB3 A:PHE173 4.5 14.7 1.0 HB2 A:ASP199 4.6 20.1 1.0 CA A:LEU180 4.6 12.1 1.0 N A:HIS178 4.6 12.3 1.0 CA A:ASP174 4.6 15.1 1.0 O A:PRO176 4.6 17.6 1.0 CG A:GLU200 4.6 21.0 1.0 O A:ASP174 4.7 18.5 1.0 CB A:ASP174 4.7 17.9 1.0 CB A:SER179 4.7 18.1 1.0 HA2 A:GLY177 4.8 16.4 1.0 CB A:HIS178 4.8 21.7 1.0 CA A:HIS178 4.8 14.5 1.0 O A:HIS178 4.8 13.9 1.0 HD1 A:PHE173 4.8 19.4 1.0 HA2 A:GLY175 4.8 21.4 1.0 HG3 A:GLU200 4.9 25.2 1.0

Calcium binding site 3 out of 4 in the Matrix Metalloproteinase-10 Proenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Matrix Metalloproteinase-10 Proenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:34.9 occ:1.00 O A:HOH545 2.4 30.3 1.0 O A:ASP198 2.5 19.9 1.0 O A:GLU200 2.6 17.8 1.0 OD2 A:ASP123 2.7 26.4 1.0 OD1 A:ASP198 2.7 20.3 1.0 OD1 A:ASP123 3.1 30.9 1.0 CG A:ASP123 3.2 27.8 1.0 HG1 A:THR121 3.4 18.2 1.0 C A:ASP198 3.4 17.4 1.0 HD1 A:TRP202 3.6 19.1 1.0 HA A:ASP198 3.7 18.4 1.0 CG A:ASP198 3.7 19.3 1.0 HA A:LYS201 3.7 28.2 1.0 C A:GLU200 3.7 18.8 1.0 OG1 A:THR121 3.9 15.1 1.0 CA A:ASP198 4.0 15.3 1.0 HD2 A:PRO122 4.0 28.1 1.0 HA A:ASP199 4.1 19.0 1.0 H A:TRP202 4.2 17.6 1.0 CB A:ASP198 4.3 18.0 1.0 CD1 A:TRP202 4.4 15.9 1.0 N A:GLU200 4.4 14.3 1.0 N A:ASP199 4.4 12.1 1.0 H A:GLU200 4.5 17.2 1.0 C A:ASP199 4.5 18.4 1.0 HB3 A:ASP198 4.5 21.6 1.0 OD2 A:ASP198 4.5 21.3 1.0 O A:HOH410 4.5 30.6 1.0 CA A:LYS201 4.5 23.5 1.0 CA A:ASP199 4.5 15.8 1.0 N A:LYS201 4.6 17.8 1.0 CB A:ASP123 4.6 22.9 1.0 HB2 A:ASP123 4.6 27.5 1.0 HE1 A:TRP202 4.7 18.2 1.0 HG2 A:PRO122 4.7 33.9 1.0 CA A:GLU200 4.7 18.2 1.0 H A:ASP123 4.8 20.0 1.0 O A:HOH520 4.8 28.7 1.0 NE1 A:TRP202 4.9 15.1 1.0 CD A:PRO122 4.9 23.4 1.0 N A:TRP202 5.0 14.7 1.0

Calcium binding site 4 out of 4 in the Matrix Metalloproteinase-10 Proenzyme


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Matrix Metalloproteinase-10 Proenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca307 b:33.6 occ:1.00 O A:HOH567 2.3 34.3 1.0 OD2 A:ASP127 2.5 37.4 1.0 CG A:ASP127 3.0 31.5 1.0 O A:HOH443 3.1 41.7 1.0 OD1 A:ASP127 3.1 28.9 1.0 HH11 A:ARG126 3.8 51.8 1.0 HH12 A:ARG126 3.9 51.8 1.0 NH1 A:ARG126 4.1 43.1 1.0 HB3 A:ASP127 4.1 37.9 1.0 CB A:ASP127 4.2 31.6 1.0 HB2 A:ASP127 4.5 37.9 1.0 O A:HOH474 4.9 27.5 1.0

E.A.Isiorho, E.A.Isiorho. N/A N/A.