Calcium 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:

Zinc

(Zn)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution, PDB code: 1jk3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca402 b:16.5 occ:1.00 OE2 A:GLU201 2.2 16.1 1.0 OD1 A:ASP198 2.3 13.4 1.0 OD2 A:ASP175 2.3 16.8 1.0 O A:ILE180 2.3 14.2 1.0 O A:GLY176 2.3 14.7 1.0 O A:GLY178 2.4 14.6 1.0 CG A:ASP198 3.4 11.0 1.0 C A:ILE180 3.4 12.5 1.0 CD A:GLU201 3.5 13.3 1.0 CG A:ASP175 3.5 16.4 1.0 C A:GLY176 3.5 14.6 1.0 C A:GLY178 3.6 15.0 1.0 N A:GLY178 3.9 15.3 1.0 N A:ILE180 3.9 12.8 1.0 CB A:ASP198 4.0 9.5 1.0 N A:GLY176 4.0 15.3 1.0 OD1 A:ASP175 4.1 18.5 1.0 N A:ASP175 4.2 15.3 1.0 CA A:ILE180 4.2 13.3 1.0 C A:LYS177 4.2 15.1 1.0 OE1 A:GLU201 4.2 16.8 1.0 C A:ASP175 4.3 16.1 1.0 OD2 A:ASP198 4.3 11.1 1.0 C A:GLY179 4.4 15.1 1.0 CA A:GLY178 4.4 15.4 1.0 CA A:GLY176 4.4 14.9 1.0 N A:LEU181 4.4 10.9 1.0 CA A:LYS177 4.4 15.1 1.0 N A:LYS177 4.4 14.7 1.0 CG A:GLU201 4.5 10.6 1.0 CB A:ILE180 4.6 13.2 1.0 CA A:ASP175 4.6 15.9 1.0 CB A:ASP175 4.6 16.7 1.0 CA A:LEU181 4.6 10.1 1.0 N A:GLY179 4.7 15.0 1.0 O A:ASP175 4.7 16.7 1.0 O A:LYS177 4.8 17.1 1.0 CA A:GLY179 4.8 15.1 1.0 O A:GLY179 4.8 15.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca403 b:13.0 occ:1.00 O A:GLY192 2.3 11.0 1.0 O A:HOH1109 2.3 17.7 1.0 O A:GLY190 2.3 15.2 1.0 O A:ASP158 2.4 11.0 1.0 O A:HOH1037 2.4 13.3 1.0 OD2 A:ASP194 2.4 12.4 1.0 CG A:ASP194 3.4 11.4 1.0 C A:GLY192 3.4 10.5 1.0 C A:ASP158 3.5 9.7 1.0 C A:GLY190 3.5 15.4 1.0 O A:HOH1223 3.6 44.0 1.0 OD1 A:ASP194 3.8 12.9 1.0 C A:ILE191 3.9 12.8 1.0 O A:ALA157 4.0 12.9 1.0 N A:GLY192 4.0 12.5 1.0 O A:ILE191 4.1 12.0 1.0 N A:ASP194 4.3 9.5 1.0 CA A:ASP158 4.3 9.7 1.0 CA A:GLY192 4.3 12.0 1.0 CA A:ILE191 4.3 14.7 1.0 N A:ILE191 4.4 15.0 1.0 O A:GLY188 4.4 14.0 1.0 N A:GLY193 4.4 10.4 1.0 N A:ILE159 4.4 9.6 1.0 O A:HOH1068 4.4 27.0 1.0 CA A:GLY190 4.5 16.4 1.0 N A:GLY190 4.5 16.8 1.0 CA A:GLY193 4.5 9.6 1.0 CA A:ILE159 4.6 9.7 1.0 C A:GLY193 4.6 9.3 1.0 CB A:ASP194 4.7 10.6 1.0 N A:LEU160 4.7 9.6 1.0 O A:HOH1064 4.8 13.8 1.0 CE A:MET156 4.8 26.1 0.5 CA A:ASP194 4.8 9.7 1.0 C A:SER189 4.9 16.4 1.0 C A:ALA157 5.0 11.5 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 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:Ca404 b:8.5 occ:1.00 O A:HOH1017 2.4 11.6 1.0 OE2 A:GLU199 2.4 9.5 1.0 O A:GLU199 2.4 9.3 1.0 O A:GLU201 2.4 9.5 1.0 OD1 A:ASP124 2.4 8.7 1.0 O A:HOH1015 2.4 12.1 1.0 OD2 A:ASP124 2.5 9.3 1.0 CG A:ASP124 2.8 8.6 1.0 CD A:GLU199 3.4 9.3 1.0 C A:GLU199 3.5 9.2 1.0 C A:GLU201 3.6 8.9 1.0 CG A:GLU199 3.9 10.0 1.0 CA A:GLU199 4.1 8.8 1.0 OG1 A:THR122 4.2 8.7 1.0 CA A:PHE202 4.2 9.2 1.0 CB A:ASP124 4.3 8.0 1.0 N A:PHE202 4.3 9.1 1.0 CD1 A:TRP203 4.4 8.4 1.0 N A:GLU201 4.4 9.7 1.0 C A:ASP200 4.5 10.4 1.0 N A:ASP200 4.5 10.0 1.0 OE1 A:GLU199 4.6 10.6 1.0 CB A:GLU199 4.6 9.3 1.0 CA A:GLU201 4.7 9.3 1.0 O A:HOH1026 4.7 12.7 1.0 CA A:ASP200 4.7 10.6 1.0 NH2 A:ARG165 4.8 16.6 0.8 NE1 A:TRP203 4.8 8.2 1.0 N A:TRP203 4.9 8.5 1.0 CD1 A:PHE202 4.9 12.0 1.0 O A:ASP200 5.0 11.4 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