Zinc in PDB 4fvl: 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: 4fvl 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)	49.11 / 2.44
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	125.780, 157.270, 105.550, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 22.3

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

Chlorine	(Cl)	3 atoms
Calcium	(Ca)	10 atoms

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

Zinc binding site 1 out of 4 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn501 b:24.1 occ:1.00 NE2 A:HIS226 2.0 21.9 1.0 NE2 A:HIS232 2.1 31.3 1.0 NE2 A:HIS222 2.2 23.6 1.0 O C:HOH204 2.5 25.6 0.5 CD2 A:HIS226 2.9 25.8 1.0 CE1 A:HIS232 3.0 27.6 1.0 CD2 A:HIS232 3.0 26.6 1.0 CD2 A:HIS222 3.0 20.7 1.0 CE1 A:HIS226 3.0 27.3 1.0 CE1 A:HIS222 3.3 24.4 1.0 O C:HOH204 3.5 24.5 0.5 O C:SER45 3.6 33.8 1.0 C C:SER45 3.9 31.5 1.0 ND1 A:HIS232 4.0 32.1 1.0 CG A:HIS226 4.1 24.5 1.0 CG A:HIS232 4.1 29.5 1.0 N C:TYR46 4.1 34.5 1.0 ND1 A:HIS226 4.1 20.4 1.0 CA C:TYR46 4.1 26.2 1.0 CB C:ARG44 4.2 27.9 1.0 CB C:TYR46 4.2 28.0 1.0 CG A:HIS222 4.2 25.1 1.0 ND1 A:HIS222 4.3 27.5 1.0 N C:SER45 4.3 34.5 1.0 CD1 C:TYR46 4.4 23.1 1.0 C C:ARG44 4.5 27.2 1.0 CG C:TYR46 4.5 27.2 1.0 CA C:SER45 4.6 32.5 1.0 O C:ARG44 4.7 25.6 1.0 CE A:MET240 4.9 19.3 1.0 CA C:ARG44 5.0 28.3 1.0

Zinc binding site 2 out of 4 in the Human Collagenase 3 (Mmp-13) Full Form with Peptides From Pro-Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn502 b:36.1 occ:1.00 NE2 A:HIS172 1.8 33.5 1.0 ND1 A:HIS200 2.0 31.6 1.0 OD2 A:ASP174 2.0 42.9 1.0 NE2 A:HIS187 2.1 40.7 1.0 CE1 A:HIS172 2.7 38.9 1.0 CD2 A:HIS172 2.9 33.9 1.0 CG A:ASP174 2.9 42.5 1.0 CE1 A:HIS200 3.0 35.5 1.0 CG A:HIS200 3.0 29.9 1.0 CE1 A:HIS187 3.0 43.9 1.0 OD1 A:ASP174 3.1 46.9 1.0 CD2 A:HIS187 3.1 30.8 1.0 CB A:HIS200 3.4 26.6 1.0 ND1 A:HIS172 3.9 36.9 1.0 CG A:HIS172 4.0 36.2 1.0 NE2 A:HIS200 4.1 36.9 1.0 CD2 A:HIS200 4.1 31.7 1.0 ND1 A:HIS187 4.2 37.9 1.0 CG A:HIS187 4.3 36.5 1.0 CB A:ASP174 4.3 46.3 1.0 O A:TYR176 4.3 43.8 1.0 CZ A:PHE178 4.6 40.1 1.0 CE2 A:PHE178 4.7 35.0 1.0 CA A:HIS200 4.9 30.4 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 B:Zn501 b:19.4 occ:1.00 NE2 B:HIS222 2.0 14.1 1.0 NE2 B:HIS232 2.1 25.4 1.0 NE2 B:HIS226 2.1 14.4 1.0 CD2 B:HIS222 2.9 12.3 1.0 CE1 B:HIS232 3.0 18.9 1.0 CD2 B:HIS226 3.0 15.2 1.0 CD2 B:HIS232 3.1 17.9 1.0 CE1 B:HIS222 3.1 17.5 1.0 O D:HOH207 3.1 27.4 0.5 O D:HOH207 3.1 27.4 0.5 CE1 B:HIS226 3.2 20.8 1.0 O D:SER45 3.2 34.4 1.0 C D:SER45 3.7 29.3 1.0 CB D:TYR46 3.9 19.6 1.0 CA D:TYR46 4.1 24.3 1.0 ND1 B:HIS232 4.1 21.5 1.0 N D:TYR46 4.1 25.7 1.0 CG B:HIS222 4.1 15.6 1.0 ND1 B:HIS222 4.1 22.1 1.0 CG B:HIS232 4.1 26.4 1.0 CD1 D:TYR46 4.2 20.9 1.0 CG B:HIS226 4.2 17.2 1.0 ND1 B:HIS226 4.3 14.4 1.0 N D:SER45 4.3 26.0 1.0 CB D:ARG44 4.3 21.8 1.0 CG D:TYR46 4.3 19.3 1.0 CA D:SER45 4.5 23.3 1.0 C D:ARG44 4.5 22.6 1.0 CE B:MET240 4.6 14.5 1.0 O D:ARG44 4.8 23.9 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 B:Zn502 b:22.8 occ:1.00 NE2 B:HIS172 2.0 21.5 1.0 ND1 B:HIS200 2.0 21.7 1.0 OD2 B:ASP174 2.0 24.0 1.0 NE2 B:HIS187 2.1 20.4 1.0 CG B:ASP174 2.8 28.5 1.0 CE1 B:HIS200 2.9 26.3 1.0 CE1 B:HIS187 2.9 18.8 1.0 CD2 B:HIS172 2.9 16.6 1.0 OD1 B:ASP174 3.0 23.9 1.0 CE1 B:HIS172 3.0 20.9 1.0 CG B:HIS200 3.1 19.5 1.0 CD2 B:HIS187 3.2 18.4 1.0 CB B:HIS200 3.5 15.1 1.0 NE2 B:HIS200 4.1 25.5 1.0 CG B:HIS172 4.1 22.3 1.0 ND1 B:HIS187 4.1 19.2 1.0 ND1 B:HIS172 4.1 22.0 1.0 CD2 B:HIS200 4.2 22.5 1.0 CB B:ASP174 4.2 31.7 1.0 CG B:HIS187 4.3 16.9 1.0 O B:TYR176 4.3 28.6 1.0 CZ B:PHE178 4.6 18.4 1.0 O B:HOH638 4.8 32.9 1.0 CE2 B:PHE178 4.9 23.9 1.0 CA B:HIS200 5.0 15.2 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