Zinc in PDB 1cxv: Structure of Recombinant Mouse Collagenase-3 (Mmp-13)

The structure of Structure of Recombinant Mouse Collagenase-3 (Mmp-13), PDB code: 1cxv was solved by I.Botos, E.Meyer, S.M.Swanson, V.Lemaitre, Y.Eeckhout, E.F.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.360, 48.460, 74.940, 90.00, 108.15, 90.00
R / Rfree (%)	19.6 / 23.4

The structure of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	4 atoms

The binding sites of Zinc atom in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13) (pdb code 1cxv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13), PDB code: 1cxv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:20.4 occ:1.00 NE2 A:HIS201 2.0 20.0 1.0 NE2 A:HIS205 2.0 19.1 1.0 NE2 A:HIS211 2.1 20.6 1.0 O1 A:CBP10 2.1 21.6 1.0 O4 A:CBP10 2.6 23.6 1.0 N2 A:CBP10 2.7 25.8 1.0 CD2 A:HIS201 2.9 19.1 1.0 CD2 A:HIS205 3.0 17.7 1.0 C3 A:CBP10 3.1 25.2 1.0 CD2 A:HIS211 3.1 20.8 1.0 CE1 A:HIS211 3.1 20.8 1.0 CE1 A:HIS201 3.1 19.7 1.0 CE1 A:HIS205 3.1 18.3 1.0 O A:HOH849 3.9 18.7 1.0 CG A:HIS201 4.1 19.1 1.0 ND1 A:HIS201 4.2 19.4 1.0 CG A:HIS205 4.2 16.9 1.0 CG A:HIS211 4.2 21.1 1.0 OE2 A:GLU202 4.2 18.9 1.0 ND1 A:HIS211 4.2 20.3 1.0 ND1 A:HIS205 4.3 17.1 1.0 C5 A:CBP10 4.6 26.0 1.0 C16 A:CBP10 4.7 26.4 1.0 C17 A:CBP10 4.7 26.0 1.0 CE A:MET219 4.9 19.6 1.0 CD A:GLU202 4.9 18.1 1.0 OE1 A:GLU202 5.0 17.3 1.0

Zinc binding site 2 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:23.7 occ:1.00 ND1 A:HIS179 2.0 22.4 1.0 NE2 A:HIS151 2.0 24.5 1.0 OD2 A:ASP153 2.0 25.5 1.0 NE2 A:HIS166 2.0 21.6 1.0 CD2 A:HIS151 2.9 25.6 1.0 CG A:ASP153 2.9 26.7 1.0 CE1 A:HIS179 3.0 22.1 1.0 CE1 A:HIS166 3.0 21.8 1.0 CG A:HIS179 3.0 21.7 1.0 CD2 A:HIS166 3.0 21.7 1.0 CE1 A:HIS151 3.1 25.2 1.0 OD1 A:ASP153 3.2 25.9 1.0 CB A:HIS179 3.4 20.9 1.0 O A:TYR155 4.1 32.2 1.0 CG A:HIS151 4.1 26.5 1.0 CD2 A:HIS179 4.1 21.9 1.0 NE2 A:HIS179 4.1 22.2 1.0 ND1 A:HIS166 4.1 21.6 1.0 ND1 A:HIS151 4.2 26.0 1.0 CG A:HIS166 4.2 21.2 1.0 CB A:ASP153 4.3 28.2 1.0 CZ A:PHE168 4.5 23.1 1.0 CB A:TYR155 4.6 34.6 1.0 CZ A:PHE157 4.6 28.3 1.0 CE2 A:PHE157 4.7 28.6 1.0 CE1 A:PHE168 4.7 23.1 1.0 CA A:HIS179 4.9 20.1 1.0 C A:TYR155 4.9 32.2 1.0

Zinc binding site 3 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:20.4 occ:1.00 NE2 B:HIS501 2.0 20.2 1.0 NE2 B:HIS505 2.0 19.1 1.0 NE2 B:HIS511 2.0 20.8 1.0 O1 B:CBP11 2.1 21.9 1.0 O4 B:CBP11 2.6 23.4 1.0 N2 B:CBP11 2.7 25.9 1.0 CD2 B:HIS501 2.9 19.3 1.0 CD2 B:HIS505 3.0 17.5 1.0 CD2 B:HIS511 3.0 21.0 1.0 CE1 B:HIS511 3.1 21.1 1.0 C3 B:CBP11 3.1 25.2 1.0 CE1 B:HIS505 3.1 17.9 1.0 CE1 B:HIS501 3.1 20.2 1.0 CG B:HIS501 4.1 18.8 1.0 O B:HOH759 4.1 27.2 1.0 OE2 B:GLU502 4.2 18.9 1.0 CG B:HIS505 4.2 16.8 1.0 ND1 B:HIS501 4.2 19.5 1.0 CG B:HIS511 4.2 21.2 1.0 ND1 B:HIS511 4.2 20.8 1.0 ND1 B:HIS505 4.2 16.7 1.0 C5 B:CBP11 4.6 26.3 1.0 C16 B:CBP11 4.7 26.3 1.0 C17 B:CBP11 4.7 26.3 1.0 O B:HOH738 4.8 48.2 1.0 CE B:MET519 4.8 19.5 1.0 CD B:GLU502 5.0 18.1 1.0

Zinc binding site 4 out of 4 in the Structure of Recombinant Mouse Collagenase-3 (Mmp-13)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Recombinant Mouse Collagenase-3 (Mmp-13) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4 b:23.1 occ:1.00 OD2 B:ASP453 1.9 24.9 1.0 NE2 B:HIS451 2.0 24.3 1.0 NE2 B:HIS466 2.0 21.6 1.0 ND1 B:HIS479 2.1 22.1 1.0 CG B:ASP453 2.8 26.5 1.0 CD2 B:HIS451 2.9 25.4 1.0 CE1 B:HIS466 3.0 21.9 1.0 CE1 B:HIS451 3.0 24.8 1.0 CE1 B:HIS479 3.0 22.1 1.0 OD1 B:ASP453 3.1 25.6 1.0 CD2 B:HIS466 3.1 21.8 1.0 CG B:HIS479 3.1 21.5 1.0 CB B:HIS479 3.5 20.6 1.0 CG B:HIS451 4.1 26.4 1.0 ND1 B:HIS451 4.1 25.7 1.0 O B:TYR455 4.1 32.5 1.0 ND1 B:HIS466 4.2 21.3 1.0 CD2 B:HIS479 4.2 21.6 1.0 NE2 B:HIS479 4.2 22.1 1.0 CG B:HIS466 4.2 21.1 1.0 CB B:ASP453 4.2 27.8 1.0 CZ B:PHE468 4.4 23.3 1.0 CE1 B:PHE468 4.7 23.3 1.0 CZ B:PHE457 4.7 28.1 1.0 CE2 B:PHE457 4.7 28.6 1.0 O B:HOH622 5.0 24.8 1.0 C B:TYR455 5.0 32.7 1.0 CB B:TYR455 5.0 35.8 1.0 CA B:HIS479 5.0 20.2 1.0

I.Botos, E.Meyer, S.M.Swanson, V.Lemaitre, Y.Eeckhout, E.F.Meyer. Structure of Recombinant Mouse Collagenase-3 (Mmp-13). J.Mol.Biol. V. 292 837 1999.
ISSN: ISSN 0022-2836
PubMed: 10525409
DOI: 10.1006/JMBI.1999.3068