Zinc in PDB 1i73: Complex of Pro-Leu-L-Trp Phosphonate with the Catalitic Domain of Matrix Metallo Proteinase-8 (MET80 Form)

All present enzymatic activity of Complex of Pro-Leu-L-Trp Phosphonate with the Catalitic Domain of Matrix Metallo Proteinase-8 (MET80 Form):
3.4.24.34;

The structure of Complex of Pro-Leu-L-Trp Phosphonate with the Catalitic Domain of Matrix Metallo Proteinase-8 (MET80 Form), PDB code: 1i73 was solved by E.Gavuzzo, G.Pochetti, F.Mazza, C.Gallina, B.Gorini, S.D'alessio, M.Pieper, H.Tschesche, P.A.Tucker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	32.983, 68.673, 70.486, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 19.4

The structure of Complex of Pro-Leu-L-Trp Phosphonate with the Catalitic Domain of Matrix Metallo Proteinase-8 (MET80 Form) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Complex of Pro-Leu-L-Trp Phosphonate with the Catalitic Domain of Matrix Metallo Proteinase-8 (MET80 Form) (pdb code 1i73). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Complex of Pro-Leu-L-Trp Phosphonate with the Catalitic Domain of Matrix Metallo Proteinase-8 (MET80 Form), PDB code: 1i73:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Complex of Pro-Leu-L-Trp Phosphonate with the Catalitic Domain of Matrix Metallo Proteinase-8 (MET80 Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of Pro-Leu-L-Trp Phosphonate with the Catalitic Domain of Matrix Metallo Proteinase-8 (MET80 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn998 b:8.4 occ:1.00 NE2 A:HIS162 2.0 7.1 1.0 OD1 A:ASP149 2.0 9.5 1.0 NE2 A:HIS147 2.0 7.5 1.0 ND1 A:HIS175 2.1 7.8 1.0 CE1 A:HIS162 2.9 7.9 1.0 CG A:ASP149 2.9 10.5 1.0 CD2 A:HIS147 2.9 8.3 1.0 CE1 A:HIS175 3.0 8.2 1.0 CD2 A:HIS162 3.0 8.2 1.0 CE1 A:HIS147 3.1 6.2 1.0 CG A:HIS175 3.1 6.5 1.0 OD2 A:ASP149 3.2 10.8 1.0 CB A:HIS175 3.5 6.9 1.0 ND1 A:HIS162 4.0 9.2 1.0 CG A:HIS147 4.1 6.6 1.0 ND1 A:HIS147 4.1 7.8 1.0 NE2 A:HIS175 4.1 8.4 1.0 CG A:HIS162 4.2 7.7 1.0 O A:SER151 4.2 12.3 1.0 CD2 A:HIS175 4.2 7.2 1.0 CB A:ASP149 4.2 9.6 1.0 CE1 A:PHE164 4.3 10.8 1.0 CZ A:PHE164 4.6 15.6 1.0 CZ A:PHE153 4.7 7.9 1.0 CE2 A:PHE153 4.7 7.1 1.0 O A:HOH396 4.8 11.8 1.0 CA A:HIS175 5.0 5.9 1.0

Zinc binding site 2 out of 2 in the Complex of Pro-Leu-L-Trp Phosphonate with the Catalitic Domain of Matrix Metallo Proteinase-8 (MET80 Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of Pro-Leu-L-Trp Phosphonate with the Catalitic Domain of Matrix Metallo Proteinase-8 (MET80 Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:8.7 occ:1.00 O2P B:PAT3 1.9 29.1 1.0 NE2 A:HIS207 2.0 8.2 1.0 NE2 A:HIS197 2.0 7.2 1.0 NE2 A:HIS201 2.1 7.4 1.0 O1P B:PAT3 2.7 32.2 1.0 P B:PAT3 2.8 24.5 1.0 CE1 A:HIS197 3.0 7.2 1.0 CD2 A:HIS207 3.0 8.7 1.0 CE1 A:HIS207 3.0 10.5 1.0 CD2 A:HIS197 3.0 7.3 1.0 CD2 A:HIS201 3.1 6.5 1.0 CE1 A:HIS201 3.1 9.1 1.0 O3P B:PAT3 3.6 31.9 1.0 ND1 A:HIS197 4.1 6.2 1.0 ND1 A:HIS207 4.1 9.9 1.0 CG A:HIS207 4.1 7.6 1.0 CG A:HIS197 4.1 6.7 1.0 ND1 A:HIS201 4.2 8.6 1.0 CG A:HIS201 4.2 6.7 1.0 CA B:PAT3 4.3 20.1 1.0 N B:PAT3 4.3 18.8 1.0 C B:LEU2 4.6 13.8 1.0 OE2 A:GLU198 4.7 12.9 1.0 CE A:MET215 4.7 8.1 1.0 CD2 B:LEU2 4.7 46.2 1.0 O B:LEU2 4.7 17.5 1.0 OE1 A:GLU198 4.7 13.7 1.0 CB B:LEU2 4.7 22.2 1.0 O A:PRO217 4.9 12.3 1.0 O A:HOH541 4.9 34.2 1.0 O B:HOH500 5.0 29.5 1.0

E.Gavuzzo, G.Pochetti, F.Mazza, C.Gallina, B.Gorini, S.D'alessio, M.Pieper, H.Tschesche, P.A.Tucker. Two Crystal Structures of Human Neutrophil Collagenase, One Complexed with A Primed- and the Other with An Unprimed-Side Inhibitor: Implications For Drug Design. J.Med.Chem. V. 43 3377 2000.
ISSN: ISSN 0022-2623
PubMed: 10978185
DOI: 10.1021/JM9909589