Zinc in PDB 3ayu: Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor

All present enzymatic activity of Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor:
3.4.24.24;

The structure of Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor, PDB code: 3ayu was solved by H.Hashimoto, T.Takeuchi, K.Komatsu, K.Miyazaki, M.Sato, S.Higashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.881, 76.060, 37.082, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20.5

The structure of Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor (pdb code 3ayu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor, PDB code: 3ayu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor


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 Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn415 b:12.7 occ:1.00 NE2 A:HIS120 2.1 14.5 1.0 NE2 A:HIS130 2.1 19.4 1.0 NE2 A:HIS124 2.1 14.3 1.0 OD1 B:ASP6 2.2 18.1 1.0 OD2 B:ASP6 2.3 19.2 1.0 CG B:ASP6 2.5 19.2 1.0 CD2 A:HIS130 3.0 19.6 1.0 CD2 A:HIS120 3.0 14.1 1.0 CE1 A:HIS120 3.0 14.7 1.0 CE1 A:HIS130 3.0 20.2 1.0 CD2 A:HIS124 3.1 13.9 1.0 CE1 A:HIS124 3.1 14.5 1.0 CB B:ASP6 4.0 19.4 1.0 ND1 A:HIS130 4.1 20.5 1.0 CG A:HIS130 4.1 20.3 1.0 ND1 A:HIS120 4.1 14.4 1.0 CB B:TYR3 4.1 18.1 1.0 CG A:HIS120 4.1 14.1 1.0 ND1 A:HIS124 4.2 14.3 1.0 CG A:HIS124 4.2 14.0 1.0 CG B:TYR3 4.3 18.0 1.0 CD2 B:TYR3 4.4 17.9 1.0 O B:HOH226 4.6 27.7 1.0 C B:ASP6 4.7 19.1 1.0 N B:ALA7 4.7 18.7 1.0 CA B:ASP6 4.8 19.5 1.0 CB B:ALA7 4.8 18.4 1.0 CE A:MET138 4.8 15.6 1.0 N B:ASP6 4.9 20.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor


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 Mmp-2 Active Site Mutant in Complex with App- Drived Decapeptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn416 b:12.1 occ:1.00 NE2 A:HIS69 2.0 15.8 1.0 OD2 A:ASP71 2.0 15.4 1.0 NE2 A:HIS84 2.0 15.1 1.0 ND1 A:HIS97 2.1 14.7 1.0 CE1 A:HIS84 2.9 15.4 1.0 CD2 A:HIS69 2.9 16.0 1.0 CG A:ASP71 3.0 16.2 1.0 CE1 A:HIS69 3.0 16.1 1.0 CE1 A:HIS97 3.1 14.9 1.0 CD2 A:HIS84 3.1 14.7 1.0 CG A:HIS97 3.1 14.4 1.0 OD1 A:ASP71 3.3 16.2 1.0 CB A:HIS97 3.5 14.3 1.0 ND1 A:HIS84 4.1 15.3 1.0 CG A:HIS69 4.1 16.3 1.0 ND1 A:HIS69 4.1 16.3 1.0 O A:TYR73 4.1 17.1 1.0 NE2 A:HIS97 4.2 14.8 1.0 CG A:HIS84 4.2 14.9 1.0 CD2 A:HIS97 4.3 14.3 1.0 CB A:ASP71 4.3 16.8 1.0 CZ A:PHE75 4.5 16.2 1.0 CE1 A:PHE86 4.6 16.5 1.0 O A:HOH347 4.6 35.5 1.0 CE2 A:PHE75 4.7 16.4 1.0 O A:HOH293 4.7 16.3 1.0 CA A:HIS97 4.9 14.0 1.0 CB A:TYR73 5.0 18.0 1.0

H.Hashimoto, T.Takeuchi, K.Komatsu, K.Miyazaki, M.Sato, S.Higashi. Structural Basis For Matrix Metalloproteinase-2 (Mmp-2)-Selective Inhibitory Action of {Beta}-Amyloid Precursor Protein-Derived Inhibitor J.Biol.Chem. 2011.
ISSN: ESSN 1083-351X
PubMed: 21813640
DOI: 10.1074/JBC.M111.264176