Zinc in PDB 1jk3: Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution

All present enzymatic activity of Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution:
3.4.24.65;

The structure of Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution, PDB code: 1jk3 was solved by R.Lang, A.Kocourek, M.Braun, H.Tschesche, R.Huber, W.Bode, K.Maskos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.36 / 1.09
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	51.905, 60.263, 54.612, 90.00, 114.65, 90.00
R / Rfree (%)	16.7 / 19.6

The structure of Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution (pdb code 1jk3). 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 Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution, PDB code: 1jk3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution


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 Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:11.0 occ:1.00 NE2 A:HIS228 2.1 10.3 1.0 NE2 A:HIS218 2.1 10.3 1.0 O2 A:BAT900 2.1 11.3 1.0 O1 A:BAT900 2.1 12.5 1.0 NE2 A:HIS222 2.1 10.4 1.0 C2 A:BAT900 2.8 10.5 1.0 N1 A:BAT900 2.8 10.0 1.0 CE1 A:HIS228 3.0 10.4 1.0 CD2 A:HIS218 3.0 9.7 1.0 CD2 A:HIS228 3.1 10.4 1.0 CE1 A:HIS218 3.1 11.4 1.0 CD2 A:HIS222 3.1 9.9 1.0 CE1 A:HIS222 3.1 11.1 1.0 O A:HOH1007 4.1 12.3 1.0 O A:HOH1066 4.2 24.2 1.0 ND1 A:HIS228 4.2 9.7 1.0 ND1 A:HIS218 4.2 10.6 1.0 CG A:HIS218 4.2 9.7 1.0 CG A:HIS228 4.2 10.4 1.0 C1 A:BAT900 4.2 11.2 1.0 ND1 A:HIS222 4.3 11.2 1.0 CG A:HIS222 4.3 9.6 1.0 S2 A:BAT900 4.4 18.6 0.5 C5 A:BAT900 4.7 14.9 0.5 C9 A:BAT900 4.7 11.1 1.0 C8 A:BAT900 4.7 10.9 1.0 O A:HOH1186 4.7 26.2 1.0 CE A:MET236 4.8 11.2 1.0 C6 A:BAT900 4.9 17.2 0.5 C3 A:BAT900 4.9 12.9 1.0 C4 A:BAT900 4.9 13.5 0.5 C4 A:BAT900 4.9 14.8 0.5 C7 A:BAT900 4.9 18.6 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution


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 Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:17.4 occ:1.00 NE2 A:HIS183 1.8 8.8 0.5 OD1 A:ASP170 2.0 14.4 0.7 NE2 A:HIS168 2.0 15.0 1.0 ND1 A:HIS196 2.1 13.0 1.0 NE2 A:HIS183 2.2 9.5 0.5 CE1 A:HIS183 2.5 11.2 0.5 CD2 A:HIS168 2.8 15.1 1.0 CG A:ASP170 2.9 14.4 0.7 CD2 A:HIS183 3.0 12.0 0.5 CE1 A:HIS196 3.0 14.4 1.0 CE1 A:HIS183 3.0 9.8 0.5 CE1 A:HIS168 3.1 14.4 1.0 CG A:HIS196 3.1 12.3 1.0 OD2 A:ASP170 3.1 15.4 0.7 CD2 A:HIS183 3.3 8.9 0.5 CB A:HIS196 3.5 10.9 1.0 ND1 A:HIS183 3.7 13.4 0.5 CG A:HIS183 4.0 11.1 0.5 CG A:HIS168 4.0 15.7 1.0 ND1 A:HIS168 4.1 14.9 1.0 NE2 A:HIS196 4.1 13.1 1.0 ND1 A:HIS183 4.2 9.9 0.5 CD2 A:HIS196 4.2 11.8 1.0 CB A:ASP170 4.3 13.8 0.7 CG A:HIS183 4.3 9.6 0.5 CE1 A:PHE185 4.5 15.7 1.0 O A:HIS172 4.5 15.0 1.0 CZ A:PHE174 4.7 12.1 1.0 CB A:HIS172 4.8 15.3 1.0 CZ A:PHE185 4.8 17.6 1.0 CE2 A:PHE174 4.8 13.1 1.0 CA A:HIS196 5.0 10.0 1.0

R.Lang, A.Kocourek, M.Braun, H.Tschesche, R.Huber, W.Bode, K.Maskos. Substrate Specificity Determinants of Human Macrophage Elastase (Mmp-12) Based on the 1.1 A Crystal Structure. J.Mol.Biol. V. 312 731 2001.
ISSN: ISSN 0022-2836
PubMed: 11575928
DOI: 10.1006/JMBI.2001.4954