Calcium in PDB 4g0d: Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain

The structure of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain, PDB code: 4g0d was solved by E.A.Stura, L.Vera, R.Visse, H.Nagase, V.Dive, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.50 / 2.54
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	101.260, 105.900, 101.180, 90.00, 102.11, 90.00
R / Rfree (%)	16.9 / 24.1

The structure of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain also contains other interesting chemical elements:

Chlorine	(Cl)	8 atoms
Zinc	(Zn)	8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Calcium atom in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain (pdb code 4g0d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 23 binding sites of Calcium where determined in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain, PDB code: 4g0d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 23 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:42.1 occ:1.00 OD1 A:ASP128 2.2 41.2 1.0 O A:ASP203 2.3 24.9 1.0 OD2 A:ASP203 2.3 20.8 1.0 O A:GLU205 2.7 25.3 1.0 CG A:ASP128 2.9 38.9 1.0 OD2 A:ASP128 2.9 44.1 1.0 C A:ASP203 3.4 30.1 1.0 CG A:ASP203 3.4 34.6 1.0 OG1 A:THR126 3.8 32.9 1.0 C A:GLU205 3.8 26.3 1.0 CA A:ASP203 3.9 27.6 1.0 CB A:ASP203 4.1 24.6 1.0 OD1 A:ASP203 4.3 41.9 1.0 CB A:ASP128 4.4 31.0 1.0 CD1 A:TRP207 4.4 27.5 1.0 N A:ASP204 4.5 27.7 1.0 N A:GLU205 4.5 20.1 1.0 CA A:THR206 4.5 30.8 1.0 N A:THR206 4.6 21.4 1.0 C A:ASP204 4.7 38.5 1.0 CA A:ASP204 4.7 26.7 1.0 CD A:PRO127 4.8 27.3 1.0 CA A:GLU205 4.8 30.5 1.0 N A:TRP207 4.9 26.1 1.0 NE1 A:TRP207 4.9 23.0 1.0

Calcium binding site 2 out of 23 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:33.4 occ:1.00 OE2 A:GLU205 2.2 29.1 1.0 O A:GLY180 2.3 34.1 1.0 OD1 A:ASP179 2.3 25.7 1.0 O A:SER182 2.3 29.4 1.0 OD2 A:ASP202 2.3 36.9 1.0 O A:LEU184 2.4 23.3 1.0 CG A:ASP179 3.4 36.7 1.0 CD A:GLU205 3.5 34.2 1.0 C A:GLY180 3.5 34.3 1.0 C A:LEU184 3.5 27.7 1.0 CG A:ASP202 3.5 33.8 1.0 C A:SER182 3.6 30.8 1.0 N A:LEU184 3.8 26.2 1.0 OD2 A:ASP179 3.9 36.4 1.0 N A:GLY180 4.0 29.0 1.0 CB A:ASP202 4.0 17.0 1.0 N A:SER182 4.0 45.3 1.0 CA A:LEU184 4.1 24.4 1.0 C A:PRO181 4.2 38.9 1.0 C A:ASP179 4.2 26.0 1.0 C A:GLY183 4.2 26.7 1.0 N A:ASP179 4.2 33.2 1.0 OE1 A:GLU205 4.2 33.8 1.0 CA A:GLY180 4.3 27.8 1.0 CA A:SER182 4.4 32.2 1.0 N A:PRO181 4.4 44.1 1.0 CB A:LEU184 4.4 20.6 1.0 CG A:GLU205 4.4 22.3 1.0 N A:GLY183 4.5 25.2 1.0 O A:PRO181 4.5 38.2 1.0 CA A:PRO181 4.5 38.9 1.0 CA A:ASP179 4.5 23.7 1.0 N A:LEU185 4.5 18.8 1.0 OD1 A:ASP202 4.5 32.5 1.0 CA A:GLY183 4.5 35.0 1.0 CB A:ASP179 4.6 35.2 1.0 O A:ASP179 4.7 38.0 1.0 CA A:LEU185 4.8 17.9 1.0 O A:GLY183 4.8 23.8 1.0 CD1 A:LEU185 4.8 25.6 1.0 CB A:PHE178 5.0 28.3 1.0

Calcium binding site 3 out of 23 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:31.1 occ:1.00 O A:ASN194 2.2 28.1 1.0 O A:ASP162 2.3 22.6 1.0 O A:HOH750 2.4 30.7 1.0 OD1 A:ASP198 2.5 28.2 1.0 O A:GLY196 2.6 35.5 1.0 C A:ASN194 3.4 38.3 1.0 C A:ASP162 3.4 28.9 1.0 CG A:ASP198 3.5 29.3 1.0 C A:GLY196 3.7 32.7 1.0 O A:ALA161 3.8 28.6 1.0 OD2 A:ASP198 3.8 32.6 1.0 C A:TYR195 4.0 31.5 1.0 CA A:ASP162 4.0 27.1 1.0 N A:GLY196 4.1 26.9 1.0 O A:GLY192 4.1 38.8 1.0 N A:ASN194 4.2 41.9 1.0 O A:TYR195 4.2 29.4 1.0 CA A:ASN194 4.2 41.4 1.0 N A:TYR195 4.3 32.4 1.0 O A:HOH808 4.3 26.4 1.0 N A:ASP198 4.5 21.3 1.0 N A:ILE163 4.5 21.4 1.0 CA A:TYR195 4.5 26.7 1.0 CA A:GLY196 4.5 31.4 1.0 C A:PRO193 4.5 40.1 1.0 N A:MET164 4.6 24.8 1.0 N A:GLY197 4.7 26.8 1.0 O A:HOH782 4.7 32.7 1.0 CA A:ILE163 4.7 18.4 1.0 CG A:MET164 4.7 37.3 1.0 C A:ALA161 4.7 30.1 1.0 CB A:ASP198 4.7 27.7 1.0 C A:GLY197 4.8 19.1 1.0 CA A:GLY197 4.8 22.2 1.0 O A:PRO193 4.8 36.4 1.0 N A:ASP162 4.9 31.5 1.0 O A:HOH784 4.9 24.6 1.0 CH2 A:TRP113 4.9 33.9 1.0 CA A:ASP198 5.0 28.1 1.0

Calcium binding site 4 out of 23 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:12.6 occ:1.00 O A:ASP432 2.3 19.6 1.0 O A:ASP291 2.4 17.0 1.0 O A:ASP335 2.4 19.1 1.0 O A:SER383 2.5 13.4 1.0 O A:HOH680 2.5 8.3 1.0 O A:HOH625 2.5 17.1 1.0 O A:HOH820 2.7 32.5 1.0 C A:ASP291 3.4 12.6 1.0 C A:ASP432 3.4 12.7 1.0 C A:ASP335 3.6 20.4 1.0 C A:SER383 3.6 10.9 1.0 CA A:ASP291 3.9 7.1 1.0 CA A:ASP432 4.0 10.0 1.0 O A:HOH646 4.1 29.8 1.0 CA A:ASP335 4.1 14.2 1.0 CA A:SER383 4.3 20.3 1.0 O A:HOH644 4.5 24.6 1.0 N A:ALA433 4.6 10.0 1.0 O A:LEU290 4.6 18.5 1.0 N A:ALA292 4.6 11.3 1.0 N A:ALA336 4.7 17.3 1.0 N A:ALA384 4.7 9.2 1.0 CB A:ASP291 4.7 13.7 1.0 CB A:ASP432 4.7 11.5 1.0 O A:ILE334 4.8 12.9 1.0 O A:VAL431 4.8 12.8 1.0 CB A:SER383 4.9 12.4 1.0 CB A:ASP335 4.9 12.2 1.0 CA A:ALA433 4.9 10.8 1.0 CA A:ALA292 5.0 11.3 1.0 CA A:ALA384 5.0 8.6 1.0

Calcium binding site 5 out of 23 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:34.1 occ:1.00 O A:VAL434 2.2 10.2 1.0 O A:ALA385 2.3 19.8 1.0 O A:ALA337 2.4 18.1 1.0 O A:ILE293 2.5 16.2 1.0 CL A:CL508 2.9 14.9 1.0 O A:HOH746 3.0 6.8 1.0 C A:VAL434 3.5 13.5 1.0 C A:ALA385 3.5 13.7 1.0 C A:ALA337 3.6 18.8 1.0 C A:ILE293 3.7 12.5 1.0 CG1 A:VAL434 4.1 7.6 1.0 N A:VAL434 4.2 8.6 1.0 N A:ILE293 4.2 13.5 1.0 N A:ALA385 4.3 12.4 1.0 CA A:VAL434 4.3 11.7 1.0 CA A:VAL386 4.4 9.4 1.0 N A:VAL386 4.4 12.4 1.0 N A:TYR435 4.4 13.1 1.0 CA A:TYR338 4.4 23.2 1.0 CA A:ILE293 4.4 12.3 1.0 CA A:TYR435 4.4 16.8 1.0 N A:TYR338 4.4 22.6 1.0 CA A:ALA385 4.5 10.3 1.0 N A:ALA337 4.5 10.8 1.0 CB A:VAL386 4.5 13.2 1.0 CB A:TYR338 4.6 19.2 1.0 CA A:ALA337 4.6 20.0 1.0 CB A:TYR435 4.6 15.3 1.0 N A:THR294 4.6 7.0 1.0 CA A:THR294 4.8 17.2 1.0 CB A:ILE293 4.8 11.4 1.0 OG1 A:THR294 4.8 27.9 1.0 CB A:VAL434 4.9 10.0 1.0 CG2 A:THR294 5.0 19.6 1.0

Calcium binding site 6 out of 23 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:33.9 occ:1.00 OD2 B:ASP203 2.4 16.4 1.0 O B:GLU205 2.4 16.1 1.0 OD2 B:ASP128 2.5 20.7 1.0 O B:ASP203 2.5 12.6 1.0 O B:HOH653 2.6 31.8 1.0 OD1 B:ASP128 2.7 32.5 1.0 CG B:ASP128 2.9 20.5 1.0 CG B:ASP203 3.5 19.1 1.0 C B:ASP203 3.5 15.2 1.0 C B:GLU205 3.6 18.7 1.0 CA B:ASP203 4.0 12.1 1.0 OG1 B:THR126 4.1 21.0 1.0 CB B:ASP203 4.2 17.2 1.0 OD1 B:ASP203 4.3 17.5 1.0 CA B:THR206 4.4 18.5 1.0 N B:GLU205 4.4 15.9 1.0 N B:THR206 4.4 17.6 1.0 CB B:ASP128 4.4 21.2 1.0 O B:HOH742 4.4 32.6 1.0 C B:ASP204 4.5 21.7 1.0 CD1 B:TRP207 4.5 19.9 1.0 N B:ASP204 4.6 20.7 1.0 CA B:GLU205 4.7 14.5 1.0 CA B:ASP204 4.8 22.4 1.0 N B:TRP207 4.9 18.4 1.0 CD B:PRO127 5.0 22.6 1.0

Calcium binding site 7 out of 23 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:17.0 occ:1.00 O B:SER182 2.1 17.1 1.0 OD2 B:ASP202 2.2 17.2 1.0 O B:GLY180 2.3 28.4 1.0 O B:LEU184 2.3 11.1 1.0 OD1 B:ASP179 2.4 21.8 1.0 OE2 B:GLU205 2.5 19.2 1.0 C B:SER182 3.3 28.2 1.0 CG B:ASP179 3.3 18.9 1.0 C B:LEU184 3.4 15.9 1.0 CG B:ASP202 3.4 18.1 1.0 C B:GLY180 3.5 24.2 1.0 N B:LEU184 3.6 14.5 1.0 CD B:GLU205 3.7 15.1 1.0 OD2 B:ASP179 3.7 28.4 1.0 N B:GLY180 3.9 21.9 1.0 N B:SER182 3.9 33.5 1.0 CA B:LEU184 3.9 14.7 1.0 C B:GLY183 4.0 19.1 1.0 C B:ASP179 4.1 15.9 1.0 C B:PRO181 4.1 31.9 1.0 CA B:SER182 4.2 28.1 1.0 CB B:LEU184 4.2 16.6 1.0 N B:ASP179 4.2 17.7 1.0 CB B:ASP202 4.2 14.3 1.0 N B:GLY183 4.2 19.0 1.0 CA B:GLY180 4.3 17.7 1.0 CA B:GLY183 4.3 10.6 1.0 OD1 B:ASP202 4.3 20.4 1.0 N B:PRO181 4.4 33.6 1.0 O B:PRO181 4.5 28.2 1.0 O B:ASP179 4.5 24.0 1.0 CA B:ASP179 4.5 11.7 1.0 CB B:ASP179 4.5 18.4 1.0 CA B:PRO181 4.5 26.1 1.0 CG B:GLU205 4.5 14.7 1.0 OE1 B:GLU205 4.6 14.1 1.0 N B:LEU185 4.6 23.3 1.0 O B:HOH716 4.6 38.5 1.0 O B:GLY183 4.7 14.3 1.0 CA B:LEU185 5.0 8.8 1.0

Calcium binding site 8 out of 23 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:23.0 occ:1.00 O B:ASN194 2.1 30.4 1.0 O B:HOH643 2.4 22.5 1.0 O B:ASP162 2.4 17.1 1.0 O B:GLY196 2.5 19.0 1.0 O B:HOH720 2.5 27.4 1.0 OD1 B:ASP198 2.5 22.5 1.0 C B:ASN194 3.3 33.5 1.0 C B:ASP162 3.6 17.8 1.0 CG B:ASP198 3.6 20.6 1.0 C B:GLY196 3.6 17.0 1.0 C B:TYR195 3.9 22.4 1.0 OD2 B:ASP198 4.0 28.6 1.0 O B:ALA161 4.0 20.2 1.0 O B:TYR195 4.1 21.0 1.0 N B:GLY196 4.1 27.7 1.0 CA B:ASN194 4.2 30.1 1.0 N B:TYR195 4.2 34.0 1.0 N B:ASN194 4.3 31.3 1.0 O B:GLY192 4.3 26.1 1.0 N B:ASP198 4.3 16.7 1.0 CA B:TYR195 4.4 21.6 1.0 CA B:ASP162 4.4 23.8 1.0 O B:HOH721 4.4 32.0 1.0 O B:HOH648 4.4 21.0 1.0 CA B:GLY196 4.4 19.5 1.0 N B:MET164 4.5 17.7 1.0 N B:ILE163 4.5 13.8 1.0 N B:GLY197 4.5 16.3 1.0 CA B:GLY197 4.6 18.8 1.0 CA B:ILE163 4.6 16.6 1.0 O B:HOH762 4.6 32.5 1.0 C B:PRO193 4.7 30.1 1.0 CG B:MET164 4.7 17.9 1.0 C B:GLY197 4.7 22.0 1.0 CB B:ASP198 4.8 15.7 1.0 CA B:ASP198 5.0 16.7 1.0

Calcium binding site 9 out of 23 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:16.9 occ:1.00 O B:HOH605 2.4 22.2 1.0 O B:ASP335 2.4 19.9 1.0 O B:ASP432 2.5 21.0 1.0 O B:SER383 2.5 20.4 1.0 O B:HOH801 2.5 40.6 1.0 O B:ASP291 2.5 18.8 1.0 O B:HOH675 2.7 23.0 1.0 C B:ASP432 3.5 19.6 1.0 C B:ASP335 3.5 25.3 1.0 C B:SER383 3.6 17.2 1.0 C B:ASP291 3.6 18.6 1.0 CA B:ASP432 4.0 18.4 1.0 O B:HOH661 4.0 27.4 1.0 CA B:ASP335 4.1 25.3 1.0 CA B:ASP291 4.1 19.4 1.0 CA B:SER383 4.2 24.0 1.0 N B:ALA433 4.6 19.4 1.0 CB B:ASP432 4.7 19.3 1.0 N B:ALA336 4.7 24.4 1.0 CB B:SER383 4.7 14.9 1.0 O B:ILE334 4.7 19.8 1.0 N B:ALA384 4.7 15.9 1.0 O B:VAL431 4.7 22.1 1.0 N B:ALA292 4.8 14.2 1.0 O B:LEU290 4.8 22.8 1.0 CB B:ASP335 4.9 27.3 1.0 CB B:ASP291 4.9 22.1 1.0 CA B:ALA433 5.0 15.1 1.0

Calcium binding site 10 out of 23 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca507 b:42.1 occ:1.00 O B:ALA337 2.3 23.2 1.0 O B:VAL434 2.3 20.8 1.0 O B:ILE293 2.3 16.7 1.0 O B:ALA385 2.4 28.2 1.0 CL B:CL508 2.8 28.6 1.0 CL B:CL510 3.0 34.3 1.0 C B:ALA337 3.5 25.8 1.0 C B:VAL434 3.5 21.3 1.0 C B:ILE293 3.6 20.1 1.0 C B:ALA385 3.6 15.1 1.0 N B:VAL434 4.2 14.8 1.0 CG1 B:VAL434 4.2 17.5 1.0 CA B:TYR338 4.3 25.6 1.0 N B:ALA337 4.3 18.4 1.0 N B:TYR338 4.3 25.7 1.0 N B:ILE293 4.3 14.1 1.0 CB B:TYR338 4.3 18.1 1.0 CA B:VAL434 4.3 19.7 1.0 CB B:THR294 4.4 23.1 1.0 N B:ALA385 4.4 14.6 1.0 CA B:VAL386 4.4 18.1 1.0 CA B:ALA337 4.4 19.4 1.0 CA B:THR294 4.4 25.7 1.0 N B:TYR435 4.4 17.8 1.0 N B:THR294 4.5 12.1 1.0 CA B:ILE293 4.5 22.5 1.0 N B:VAL386 4.5 13.0 1.0 CA B:TYR435 4.5 18.5 1.0 CA B:ALA385 4.6 17.9 1.0 CB B:VAL386 4.6 20.8 1.0 CB B:TYR435 4.6 10.7 1.0 OG1 B:THR294 4.7 22.4 1.0 CB B:ILE293 4.9 10.8 1.0 CB B:ALA337 4.9 15.1 1.0 CB B:VAL434 4.9 19.5 1.0

E.A.Stura, R.Visse, P.Cuniasse, V.Dive, H.Nagase. Crystal Structure of Full-Length Human Collagenase 3 (Mmp-13) with Peptides in the Active Site Defines Exosites in the Catalytic Domain. Faseb J. V. 27 4395 2013.
ISSN: ISSN 0892-6638
PubMed: 23913860
DOI: 10.1096/FJ.13-233601