Zinc in PDB 1ztq: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033, PDB code: 1ztq was solved by J.Wu, T.S.Rush Iii, R.Hotchandani, X.Du, M.Geck, E.Collins, Z.B.Xu, J.Skotnicki, J.I.Levin, F.Lovering, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.46 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.937, 135.252, 69.385, 90.00, 104.95, 90.00
R / Rfree (%)	23.6 / 28.7

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 also contains other interesting chemical elements:

Calcium

(Ca)

12 atoms

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 (pdb code 1ztq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033, PDB code: 1ztq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn550 b:15.0 occ:1.00 O50 A:033601 2.1 13.2 1.0 NE2 A:HIS197 2.2 5.0 1.0 NE2 A:HIS201 2.2 8.9 1.0 NE2 A:HIS207 2.2 11.0 1.0 C42 A:033601 2.9 15.5 1.0 CD2 A:HIS207 3.0 8.2 1.0 O45 A:033601 3.0 16.6 1.0 CE1 A:HIS201 3.1 6.9 1.0 CD2 A:HIS197 3.1 6.6 1.0 CE1 A:HIS197 3.2 9.9 1.0 CD2 A:HIS201 3.2 3.0 1.0 CE1 A:HIS207 3.3 8.8 1.0 CG A:HIS207 4.2 8.9 1.0 ND1 A:HIS201 4.2 5.2 1.0 ND1 A:HIS197 4.3 5.9 1.0 CG A:HIS197 4.3 6.0 1.0 C41 A:033601 4.3 13.3 1.0 ND1 A:HIS207 4.3 9.9 1.0 CG A:HIS201 4.3 8.5 1.0 C32 A:033601 4.4 7.1 1.0 CE A:MET215 4.6 9.9 1.0 C31 A:033601 4.6 7.0 1.0 C27 A:033601 4.7 5.4 1.0 OE1 A:GLU198 4.7 5.4 1.0 C9 A:033601 4.8 15.7 1.0 O A:HOH635 4.9 8.7 1.0 O A:HOH715 4.9 19.8 1.0 C30 A:033601 5.0 7.7 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn551 b:7.5 occ:1.00 ND1 A:HIS175 2.1 2.2 1.0 OD2 A:ASP149 2.2 13.8 1.0 NE2 A:HIS147 2.3 2.2 1.0 NE2 A:HIS162 2.4 17.2 1.0 CD2 A:HIS147 3.0 3.4 1.0 CG A:ASP149 3.0 13.3 1.0 O A:HOH701 3.0 27.3 1.0 CE1 A:HIS175 3.1 6.3 1.0 OD1 A:ASP149 3.1 10.9 1.0 CG A:HIS175 3.1 3.9 1.0 CE1 A:HIS162 3.3 19.5 1.0 CE1 A:HIS147 3.4 3.0 1.0 CB A:HIS175 3.5 3.3 1.0 CD2 A:HIS162 3.5 15.7 1.0 O A:HOH702 4.0 14.7 1.0 O A:TYR151 4.1 14.7 1.0 NE2 A:HIS175 4.2 7.8 1.0 CG A:HIS147 4.2 2.6 1.0 CD2 A:HIS175 4.3 5.5 1.0 ND1 A:HIS147 4.4 6.0 1.0 CB A:ASP149 4.5 12.2 1.0 ND1 A:HIS162 4.5 20.3 1.0 O A:HOH666 4.6 2.2 1.0 CB A:TYR151 4.6 21.4 1.0 CG A:HIS162 4.6 17.2 1.0 CE2 A:PHE164 4.6 4.3 1.0 CE2 A:PHE153 4.6 14.5 1.0 CZ A:PHE153 4.8 14.5 1.0 CZ A:PHE164 4.9 5.6 1.0 CA A:HIS175 4.9 5.5 1.0 C A:TYR151 5.0 17.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn552 b:15.1 occ:1.00 O50 B:033602 2.1 17.5 1.0 NE2 B:HIS197 2.2 2.2 1.0 NE2 B:HIS207 2.2 15.2 1.0 NE2 B:HIS201 2.2 7.5 1.0 CD2 B:HIS207 3.0 13.8 1.0 CD2 B:HIS197 3.0 7.5 1.0 C42 B:033602 3.1 16.3 1.0 CE1 B:HIS201 3.1 9.3 1.0 CE1 B:HIS197 3.3 8.0 1.0 O45 B:033602 3.3 18.0 1.0 CD2 B:HIS201 3.3 7.8 1.0 CE1 B:HIS207 3.3 13.9 1.0 CG B:HIS207 4.2 13.6 1.0 CG B:HIS197 4.2 9.2 1.0 ND1 B:HIS201 4.3 8.4 1.0 ND1 B:HIS197 4.3 7.5 1.0 ND1 B:HIS207 4.3 15.9 1.0 C41 B:033602 4.4 15.8 1.0 CG B:HIS201 4.4 10.0 1.0 OE1 B:GLU198 4.4 4.1 1.0 C27 B:033602 4.6 11.1 1.0 C32 B:033602 4.7 11.3 1.0 C28 B:033602 4.8 14.1 1.0 CE B:MET215 4.8 5.8 1.0 C31 B:033602 4.9 10.5 1.0 O B:HOH690 5.0 12.2 1.0 C29 B:033602 5.0 11.6 1.0 C9 B:033602 5.0 15.6 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn553 b:12.4 occ:1.00 OD2 B:ASP149 2.1 10.5 1.0 NE2 B:HIS147 2.2 2.2 1.0 ND1 B:HIS175 2.3 2.2 1.0 NE2 B:HIS162 2.3 12.4 1.0 CE1 B:HIS162 2.5 11.8 1.0 CD2 B:HIS147 2.9 2.2 1.0 CG B:ASP149 2.9 12.0 1.0 OD1 B:ASP149 3.0 6.6 1.0 CG B:HIS175 3.2 4.5 1.0 CE1 B:HIS175 3.3 5.1 1.0 CB B:HIS175 3.4 3.7 1.0 CE1 B:HIS147 3.4 4.5 1.0 CD2 B:HIS162 3.6 14.2 1.0 ND1 B:HIS162 3.8 12.8 1.0 O B:TYR151 4.1 20.4 1.0 CG B:HIS147 4.1 6.7 1.0 CB B:ASP149 4.3 9.0 1.0 CD2 B:HIS175 4.3 4.7 1.0 ND1 B:HIS147 4.3 6.7 1.0 NE2 B:HIS175 4.4 2.2 1.0 CG B:HIS162 4.4 13.2 1.0 CE2 B:PHE164 4.6 14.1 1.0 CB B:TYR151 4.7 22.3 1.0 O B:HOH603 4.7 4.1 1.0 CZ B:PHE164 4.7 12.8 1.0 CE2 B:PHE153 4.8 16.0 1.0 O B:HOH662 4.8 32.0 1.0 CZ B:PHE153 4.8 18.0 1.0 CA B:HIS175 4.9 8.3 1.0 CD2 B:TYR151 4.9 27.0 1.0 C B:TYR151 5.0 20.7 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn554 b:12.1 occ:1.00 O50 C:033603 2.1 5.0 1.0 NE2 C:HIS197 2.2 10.3 1.0 NE2 C:HIS201 2.3 11.8 1.0 NE2 C:HIS207 2.3 16.5 1.0 CE1 C:HIS201 2.9 13.3 1.0 CD2 C:HIS197 3.0 8.9 1.0 C42 C:033603 3.1 7.6 1.0 CD2 C:HIS207 3.1 17.7 1.0 CE1 C:HIS197 3.3 9.4 1.0 O45 C:033603 3.3 7.0 1.0 CE1 C:HIS207 3.4 17.5 1.0 CD2 C:HIS201 3.5 12.7 1.0 CG C:HIS197 4.2 10.0 1.0 ND1 C:HIS201 4.2 13.1 1.0 ND1 C:HIS197 4.3 10.1 1.0 CG C:HIS207 4.3 14.6 1.0 OE2 C:GLU198 4.3 14.4 1.0 O C:HOH612 4.4 16.1 1.0 C41 C:033603 4.4 5.6 1.0 ND1 C:HIS207 4.4 16.9 1.0 CG C:HIS201 4.5 14.1 1.0 C27 C:033603 4.8 8.7 1.0 CA C:PRO217 4.8 14.8 1.0 C28 C:033603 4.8 7.8 1.0 C32 C:033603 4.9 9.9 1.0 O C:PHE216 5.0 13.3 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn555 b:12.4 occ:1.00 OD2 C:ASP149 2.1 11.1 1.0 ND1 C:HIS175 2.1 7.3 1.0 NE2 C:HIS147 2.2 5.4 1.0 NE2 C:HIS162 2.3 16.6 1.0 CD2 C:HIS147 2.9 7.2 1.0 CG C:HIS175 3.1 7.8 1.0 CG C:ASP149 3.1 12.6 1.0 CE1 C:HIS162 3.1 15.6 1.0 CE1 C:HIS175 3.2 8.8 1.0 CB C:HIS175 3.3 7.8 1.0 CD2 C:HIS162 3.4 15.4 1.0 CE1 C:HIS147 3.4 4.7 1.0 OD1 C:ASP149 3.5 8.9 1.0 O C:TYR151 4.0 19.1 1.0 CG C:HIS147 4.2 6.4 1.0 CD2 C:HIS175 4.2 3.6 1.0 NE2 C:HIS175 4.3 8.3 1.0 ND1 C:HIS162 4.3 14.7 1.0 ND1 C:HIS147 4.4 4.8 1.0 CG C:HIS162 4.4 15.1 1.0 CB C:ASP149 4.5 11.0 1.0 CB C:TYR151 4.5 21.5 1.0 CZ C:PHE164 4.5 20.5 1.0 CE2 C:PHE164 4.6 21.8 1.0 CD1 C:TYR151 4.7 26.0 1.0 CZ C:PHE153 4.7 10.9 1.0 C C:TYR151 4.8 18.6 1.0 CA C:HIS175 4.8 8.3 1.0 CE2 C:PHE153 4.8 7.0 1.0 CG C:TYR151 5.0 25.3 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn556 b:12.4 occ:1.00 O50 D:033604 2.1 5.2 1.0 NE2 D:HIS201 2.1 5.9 1.0 NE2 D:HIS197 2.2 10.8 1.0 NE2 D:HIS207 2.5 12.7 1.0 CE1 D:HIS201 3.0 7.7 1.0 CD2 D:HIS197 3.0 9.3 1.0 C42 D:033604 3.0 7.7 1.0 CD2 D:HIS201 3.2 6.8 1.0 CD2 D:HIS207 3.2 14.4 1.0 O45 D:033604 3.2 5.9 1.0 CE1 D:HIS197 3.3 9.2 1.0 CE1 D:HIS207 3.4 9.7 1.0 ND1 D:HIS201 4.1 6.7 1.0 CG D:HIS197 4.2 10.3 1.0 O D:HOH623 4.3 5.5 1.0 O D:HOH638 4.3 24.3 1.0 CG D:HIS201 4.3 6.2 1.0 ND1 D:HIS197 4.3 9.8 1.0 CG D:HIS207 4.3 13.2 1.0 ND1 D:HIS207 4.4 12.4 1.0 C41 D:033604 4.4 6.2 1.0 OE1 D:GLU198 4.6 9.0 1.0 C32 D:033604 4.7 9.1 1.0 CE D:MET215 4.8 4.8 1.0 C27 D:033604 4.8 9.3 1.0 O D:HOH683 4.8 19.6 1.0 C9 D:033604 4.8 7.9 1.0 C31 D:033604 4.9 10.7 1.0 O D:PHE216 5.0 15.4 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-033 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn557 b:13.9 occ:1.00 ND1 D:HIS175 2.2 2.9 1.0 OD1 D:ASP149 2.2 6.7 1.0 NE2 D:HIS147 2.3 8.2 1.0 CE1 D:HIS162 2.3 6.4 1.0 NE2 D:HIS162 2.5 9.2 1.0 CD2 D:HIS147 2.8 8.0 1.0 CG D:ASP149 3.0 7.9 1.0 CE1 D:HIS175 3.1 5.6 1.0 CG D:HIS175 3.2 2.3 1.0 OD2 D:ASP149 3.2 2.2 1.0 CB D:HIS175 3.5 2.2 1.0 CE1 D:HIS147 3.5 8.7 1.0 ND1 D:HIS162 3.6 10.9 1.0 CD2 D:HIS162 3.9 6.9 1.0 O D:TYR151 4.0 14.5 1.0 CG D:HIS147 4.1 8.8 1.0 NE2 D:HIS175 4.2 4.7 1.0 CD2 D:HIS175 4.3 2.2 1.0 CB D:ASP149 4.3 7.8 1.0 ND1 D:HIS147 4.4 8.8 1.0 CG D:HIS162 4.4 5.9 1.0 CB D:TYR151 4.6 16.7 1.0 CE2 D:PHE164 4.7 11.9 1.0 C D:TYR151 4.7 13.3 1.0 CZ D:PHE164 4.8 10.6 1.0 CE2 D:PHE153 4.8 2.5 1.0 CZ D:PHE153 4.9 5.4 1.0 CA D:HIS175 5.0 5.2 1.0

J.Wu, T.S.Rush Iii, R.Hotchandani, X.Du, M.Geck, E.Collins, Z.B.Xu, J.Skotnicki, J.I.Levin, F.E.Lovering. Identification of Potent and Selective Mmp-13 Inhibitors Bioorg.Med.Chem.Lett. V. 15 4105 2005.
ISSN: ISSN 0960-894X
PubMed: 16005220
DOI: 10.1016/J.BMCL.2005.06.019