Zinc in PDB 5lab: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh:
3.4.24.65;

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh, PDB code: 5lab was solved by E.Ravera, V.Calderone, C.Luchinat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.34
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.190, 62.560, 37.260, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 19.5

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh (pdb code 5lab). 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 the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh, PDB code: 5lab:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh


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 Human MMP12 Complexed with the Inhibitor Nngh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:13.3 occ:1.00 O5 A:NGH306 2.1 19.5 1.0 NE2 A:HIS222 2.1 11.9 1.0 NE2 A:HIS218 2.1 11.9 1.0 NE2 A:HIS228 2.1 13.4 1.0 O4 A:NGH306 2.2 14.2 1.0 C11 A:NGH306 2.9 21.3 1.0 N1 A:NGH306 2.9 14.4 1.0 CE1 A:HIS228 3.0 14.9 1.0 CE1 A:HIS222 3.0 10.9 1.0 CD2 A:HIS218 3.0 11.5 1.0 CE1 A:HIS218 3.1 12.2 1.0 CD2 A:HIS228 3.1 13.3 1.0 CD2 A:HIS222 3.1 10.3 1.0 O A:HOH485 4.0 13.7 1.0 ND1 A:HIS228 4.1 14.9 1.0 ND1 A:HIS218 4.2 12.6 1.0 ND1 A:HIS222 4.2 12.5 1.0 CG A:HIS218 4.2 11.5 1.0 CG A:HIS228 4.2 13.6 1.0 CG A:HIS222 4.2 11.6 1.0 OE1 A:GLU219 4.3 13.8 1.0 C10 A:NGH306 4.3 23.1 1.0 O A:HOH560 4.8 29.3 1.0 C5 A:NGH306 4.8 16.5 1.0 N A:NGH306 4.8 25.7 1.0 O A:HOH577 4.9 34.7 1.0 CE A:MET236 4.9 14.3 1.0 C9 A:NGH306 4.9 28.3 1.0 C4 A:NGH306 4.9 15.8 1.0 OE2 A:GLU219 5.0 15.3 1.0 CD A:GLU219 5.0 13.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh


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 Human MMP12 Complexed with the Inhibitor Nngh within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:14.3 occ:1.00 OD1 A:ASP170 1.8 11.8 0.7 ND1 A:HIS196 1.8 16.6 1.0 CE1 A:HIS196 2.0 18.8 1.0 NE2 A:HIS168 2.1 14.4 1.0 NE2 A:HIS183 2.1 14.3 1.0 CG A:ASP170 2.8 14.5 0.7 CD2 A:HIS168 3.0 13.1 1.0 CE1 A:HIS183 3.0 17.6 1.0 CE1 A:HIS168 3.1 15.5 1.0 CG A:HIS196 3.1 14.4 1.0 CD2 A:HIS183 3.1 17.8 1.0 NE2 A:HIS196 3.2 17.1 1.0 OD2 A:ASP170 3.2 13.5 0.7 CB A:HIS196 3.6 13.4 1.0 CD2 A:HIS196 3.9 14.9 1.0 ND1 A:HIS183 4.1 17.1 1.0 CG A:HIS168 4.1 14.4 1.0 ND1 A:HIS168 4.2 14.3 1.0 CB A:ASP170 4.2 14.6 0.7 CG A:HIS183 4.2 14.5 1.0 O A:HIS172 4.3 19.2 1.0 CE2 A:PHE185 4.3 18.8 1.0 CZ A:PHE185 4.6 18.6 1.0 CZ A:PHE174 4.6 15.3 1.0 CE1 A:PHE174 4.8 16.1 1.0 CB A:HIS172 4.9 22.6 1.0 O A:HOH466 4.9 16.0 1.0 O A:HOH545 5.0 36.8 1.0

L.Benda, J.Mares, E.Ravera, G.Parigi, C.Luchinat, M.Kaupp, J.Vaara. First-Principles Calculation of Pseudo-Contact Shifts in A Paramagnetic Metalloprotein To Be Published.