Zinc in PDB 2pjt: Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344, PDB code: 2pjt was solved by Z.Xu, A.Huang, F.Lovering, J.I.Levin, L.Mosyak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.352, 35.789, 139.405, 90.00, 108.94, 90.00
R / Rfree (%)	21.2 / 27

The structure of Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344 also contains other interesting chemical elements:

Calcium

(Ca)

10 atoms

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344 (pdb code 2pjt). 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-344, PDB code: 2pjt:
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-344


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-344 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:35.7 occ:1.00 NE2 A:HIS197 2.1 42.7 1.0 O5 A:347401 2.2 47.9 1.0 NE2 A:HIS207 2.2 40.1 1.0 NE2 A:HIS201 2.2 36.4 1.0 O6 A:347401 2.3 48.2 1.0 C22 A:347401 2.9 51.0 1.0 CD2 A:HIS197 2.9 42.8 1.0 N3 A:347401 3.0 47.9 1.0 CD2 A:HIS207 3.1 38.2 1.0 CE1 A:HIS197 3.2 42.6 1.0 CE1 A:HIS201 3.2 36.3 1.0 CD2 A:HIS201 3.2 37.2 1.0 CE1 A:HIS207 3.3 39.4 1.0 CG A:HIS197 4.1 41.7 1.0 OE2 A:GLU198 4.1 39.4 1.0 ND1 A:HIS197 4.2 42.7 1.0 CG A:HIS207 4.3 38.6 1.0 ND1 A:HIS201 4.3 36.8 1.0 ND1 A:HIS207 4.3 38.8 1.0 CG A:HIS201 4.4 37.1 1.0 C12 A:347401 4.4 54.2 1.0 CE A:MET215 4.6 43.9 1.0 C16 A:347401 4.9 55.0 1.0 CD A:GLU198 5.0 39.9 1.0 C7 A:347401 5.0 53.3 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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-344 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:35.8 occ:1.00 ND1 A:HIS175 2.0 32.2 1.0 NE2 A:HIS147 2.1 34.1 1.0 OD2 A:ASP149 2.2 39.4 1.0 NE2 A:HIS162 2.2 32.2 1.0 CE1 A:HIS162 3.0 32.4 1.0 CE1 A:HIS175 3.0 33.5 1.0 CD2 A:HIS147 3.0 34.0 1.0 CG A:HIS175 3.0 31.6 1.0 CE1 A:HIS147 3.1 34.8 1.0 CG A:ASP149 3.1 39.4 1.0 OD1 A:ASP149 3.3 39.6 1.0 CD2 A:HIS162 3.4 32.2 1.0 CB A:HIS175 3.4 30.5 1.0 NE2 A:HIS175 4.1 33.2 1.0 CG A:HIS147 4.1 33.9 1.0 ND1 A:HIS147 4.1 34.6 1.0 ND1 A:HIS162 4.1 33.0 1.0 CD2 A:HIS175 4.1 32.2 1.0 CG A:HIS162 4.4 32.3 1.0 O A:TYR151 4.4 40.8 1.0 CB A:ASP149 4.5 38.0 1.0 CZ A:PHE164 4.5 39.4 1.0 CZ A:PHE153 4.8 37.8 1.0 CE2 A:PHE153 4.9 38.5 1.0 CA A:HIS175 4.9 31.2 1.0 CE2 A:PHE164 4.9 38.8 1.0 CB A:TYR151 5.0 42.6 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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-344 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:34.0 occ:1.00 NE2 B:HIS207 2.0 34.9 1.0 NE2 B:HIS197 2.2 34.5 1.0 O5 B:347401 2.2 66.6 1.0 NE2 B:HIS201 2.3 25.8 1.0 O6 B:347401 2.4 61.9 1.0 CD2 B:HIS207 2.9 33.8 1.0 C22 B:347401 2.9 65.4 1.0 CD2 B:HIS197 3.1 34.3 1.0 N3 B:347401 3.1 63.7 1.0 CD2 B:HIS201 3.1 27.2 1.0 CE1 B:HIS207 3.1 35.7 1.0 CE1 B:HIS197 3.2 34.6 1.0 CE1 B:HIS201 3.3 25.0 1.0 CG B:HIS207 4.1 34.0 1.0 ND1 B:HIS207 4.2 35.1 1.0 CG B:HIS197 4.2 34.7 1.0 ND1 B:HIS197 4.3 35.4 1.0 CG B:HIS201 4.3 27.7 1.0 ND1 B:HIS201 4.4 26.2 1.0 C12 B:347401 4.4 66.8 1.0 OE2 B:GLU198 4.4 30.0 1.0 OE1 B:GLU198 4.8 24.5 1.0 C16 B:347401 4.8 66.1 1.0 CE B:MET215 4.9 34.1 1.0 C9 B:347401 4.9 62.7 1.0 C8 B:347401 5.0 64.5 1.0 CD B:GLU198 5.0 27.4 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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-344 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:30.8 occ:1.00 NE2 B:HIS147 2.1 26.2 1.0 NE2 B:HIS162 2.2 39.7 1.0 OD2 B:ASP149 2.2 28.8 1.0 ND1 B:HIS175 2.2 25.6 1.0 CE1 B:HIS162 2.7 39.5 1.0 CE1 B:HIS147 3.0 27.4 1.0 CG B:ASP149 3.1 30.5 1.0 CD2 B:HIS147 3.1 27.2 1.0 CE1 B:HIS175 3.2 24.6 1.0 OD1 B:ASP149 3.2 28.7 1.0 CG B:HIS175 3.2 25.0 1.0 CD2 B:HIS162 3.5 38.4 1.0 CB B:HIS175 3.6 24.2 1.0 ND1 B:HIS162 3.9 38.7 1.0 ND1 B:HIS147 4.1 27.8 1.0 O B:TYR151 4.1 29.3 1.0 CG B:HIS147 4.1 27.9 1.0 NE2 B:HIS175 4.3 24.3 1.0 CG B:HIS162 4.3 37.4 1.0 CD2 B:HIS175 4.3 25.3 1.0 CZ B:PHE164 4.4 36.0 1.0 CE2 B:PHE164 4.5 34.5 1.0 CB B:ASP149 4.5 31.6 1.0 CB B:TYR151 4.6 31.1 1.0 CZ B:PHE153 4.8 24.4 1.0 CE2 B:PHE153 4.8 24.9 1.0 C B:TYR151 4.9 30.1 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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-344 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:36.8 occ:1.00 NE2 C:HIS201 2.1 33.5 1.0 O5 C:347401 2.1 63.8 1.0 NE2 C:HIS207 2.2 39.0 1.0 NE2 C:HIS197 2.3 24.1 1.0 O6 C:347401 2.3 63.3 1.0 C22 C:347401 2.9 63.4 1.0 CD2 C:HIS197 3.0 25.2 1.0 CD2 C:HIS201 3.0 34.3 1.0 N3 C:347401 3.0 63.0 1.0 CD2 C:HIS207 3.1 38.7 1.0 CE1 C:HIS201 3.1 34.0 1.0 CE1 C:HIS207 3.2 38.6 1.0 CE1 C:HIS197 3.4 25.9 1.0 OE2 C:GLU198 4.0 30.4 1.0 CG C:HIS201 4.2 35.5 1.0 ND1 C:HIS201 4.2 34.8 1.0 CG C:HIS197 4.2 26.1 1.0 CG C:HIS207 4.3 40.0 1.0 ND1 C:HIS207 4.3 39.9 1.0 ND1 C:HIS197 4.4 26.1 1.0 C12 C:347401 4.4 63.4 1.0 C9 C:347401 4.7 57.2 1.0 CD C:GLU198 4.7 29.1 1.0 C10 C:347401 4.8 54.8 1.0 OE1 C:GLU198 4.8 30.1 1.0 C8 C:347401 4.8 59.3 1.0 C16 C:347401 5.0 62.9 1.0 CE C:MET215 5.0 32.6 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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-344 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:33.4 occ:1.00 NE2 C:HIS147 2.1 38.8 1.0 NE2 C:HIS162 2.1 34.8 1.0 ND1 C:HIS175 2.2 33.5 1.0 OD2 C:ASP149 2.2 35.7 1.0 CE1 C:HIS162 2.5 36.4 1.0 CE1 C:HIS147 3.0 39.0 1.0 CG C:ASP149 3.0 38.2 1.0 CE1 C:HIS175 3.0 32.7 1.0 CD2 C:HIS147 3.0 38.2 1.0 OD1 C:ASP149 3.1 35.4 1.0 CG C:HIS175 3.2 34.0 1.0 CD2 C:HIS162 3.4 35.3 1.0 CB C:HIS175 3.6 34.0 1.0 ND1 C:HIS162 3.8 36.6 1.0 O C:TYR151 4.0 42.1 1.0 ND1 C:HIS147 4.0 39.5 1.0 CG C:HIS147 4.1 38.7 1.0 NE2 C:HIS175 4.2 34.1 1.0 CG C:HIS162 4.2 35.2 1.0 CZ C:PHE164 4.3 35.1 1.0 CD2 C:HIS175 4.3 34.4 1.0 CE2 C:PHE164 4.4 33.3 1.0 CB C:ASP149 4.4 40.0 1.0 O C:HOH421 4.7 18.5 1.0 CZ C:PHE153 4.8 36.3 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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-344 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:39.9 occ:1.00 NE2 D:HIS201 2.2 40.5 1.0 O6 D:347401 2.2 52.2 1.0 O5 D:347401 2.2 55.0 1.0 NE2 D:HIS197 2.3 44.1 1.0 CE1 D:HIS207 2.3 50.1 1.0 C22 D:347401 2.9 56.1 1.0 N3 D:347401 3.0 53.9 1.0 CE1 D:HIS201 3.1 39.7 1.0 NE2 D:HIS207 3.1 50.8 1.0 CD2 D:HIS201 3.1 41.6 1.0 CD2 D:HIS197 3.2 43.1 1.0 CE1 D:HIS197 3.2 44.4 1.0 ND1 D:HIS207 3.4 49.7 1.0 ND1 D:HIS201 4.1 40.7 1.0 CG D:HIS201 4.2 41.4 1.0 OE2 D:GLU198 4.3 38.7 1.0 ND1 D:HIS197 4.3 43.2 1.0 CD2 D:HIS207 4.3 50.4 1.0 CG D:HIS197 4.3 41.9 1.0 C12 D:347401 4.4 58.6 1.0 CG D:HIS207 4.5 50.1 1.0 CD D:GLU198 4.9 40.6 1.0 C16 D:347401 5.0 58.9 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-13 Complexed with Way-344


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-344 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn303 b:39.3 occ:1.00 ND1 D:HIS175 2.0 33.8 1.0 OD2 D:ASP149 2.2 48.5 1.0 NE2 D:HIS147 2.3 34.0 1.0 NE2 D:HIS162 2.4 49.4 1.0 CE1 D:HIS162 2.8 49.1 1.0 CE1 D:HIS175 2.8 34.3 1.0 CD2 D:HIS147 2.8 35.1 1.0 CG D:ASP149 3.1 50.1 1.0 CG D:HIS175 3.2 34.5 1.0 OD1 D:ASP149 3.2 52.7 1.0 CE1 D:HIS147 3.5 34.0 1.0 CD2 D:HIS162 3.6 47.8 1.0 CB D:HIS175 3.7 34.5 1.0 NE2 D:HIS175 4.0 36.3 1.0 ND1 D:HIS162 4.0 48.3 1.0 CG D:HIS147 4.1 35.6 1.0 O D:TYR151 4.1 55.1 1.0 CD2 D:HIS175 4.2 35.3 1.0 ND1 D:HIS147 4.4 34.7 1.0 CG D:HIS162 4.4 46.9 1.0 CB D:ASP149 4.5 49.0 1.0 CZ D:PHE164 4.6 45.6 1.0 CE2 D:PHE164 4.6 43.8 1.0 CE2 D:PHE153 4.8 43.9 1.0 O D:HOH433 4.8 23.2 1.0

A.Huang, D.Joseph-Mccarthy, F.Lovering, L.Sun, W.Wang, W.Xu, Y.Zhu, J.Cui, Y.Zhang, J.I.Levin. Structure-Based Design of Tace Selective Inhibitors: Manipulations in the S1'-S3' Pocket. Bioorg.Med.Chem. V. 15 6170 2007.
ISSN: ISSN 0968-0896
PubMed: 17606376
DOI: 10.1016/J.BMC.2007.06.031