Calcium in PDB 1qib: Crystal Structure of Gelatinase A Catalytic Domain

All present enzymatic activity of Crystal Structure of Gelatinase A Catalytic Domain:
3.4.24.24;

The structure of Crystal Structure of Gelatinase A Catalytic Domain, PDB code: 1qib was solved by V.Dhanaraj, M.G.Williams, Q.-Z.Ye, F.Molina, L.L.Johnson, D.F.Ortwine, A.Pavlovsky, J.R.Rubin, R.W.Skeean, A.D.White, C.Humblet, D.J.Hupe, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	84.830, 84.830, 57.900, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.4

The structure of Crystal Structure of Gelatinase A Catalytic Domain also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Gelatinase A Catalytic Domain (pdb code 1qib). 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 Gelatinase A Catalytic Domain, PDB code: 1qib:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Gelatinase A Catalytic Domain


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 Gelatinase A Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:14.9 occ:1.00 O A:GLY159 2.5 15.1 1.0 OD2 A:ASP181 2.6 17.1 1.0 O A:ASP161 2.6 19.7 1.0 OE2 A:GLU184 2.7 15.5 1.0 O A:LEU163 2.7 16.9 1.0 OD1 A:ASP158 2.9 18.4 1.0 CG A:ASP158 3.5 18.5 1.0 C A:GLY159 3.6 15.6 1.0 C A:ASP161 3.7 17.6 1.0 C A:ASP158 3.7 16.6 1.0 C A:LEU163 3.7 14.7 1.0 CG A:ASP181 3.8 18.6 1.0 N A:ASP158 3.8 17.3 1.0 N A:LEU163 3.8 16.8 1.0 CD A:GLU184 3.8 18.7 1.0 N A:GLY159 3.9 15.6 1.0 O A:ASP158 3.9 17.1 1.0 OD2 A:ASP158 4.0 20.4 1.0 CA A:ASP158 4.1 17.1 1.0 N A:ASP161 4.2 16.1 1.0 CA A:LEU163 4.2 15.7 1.0 C A:LYS160 4.3 15.9 1.0 CA A:GLY159 4.3 14.9 1.0 C A:GLY162 4.4 16.9 1.0 CB A:ASP158 4.4 17.0 1.0 CB A:ASP181 4.4 17.0 1.0 CA A:ASP161 4.5 17.0 1.0 CB A:LEU163 4.5 15.3 1.0 O A:LYS160 4.5 15.4 1.0 N A:GLY162 4.6 16.4 1.0 N A:LYS160 4.6 15.6 1.0 CG A:GLU184 4.6 17.7 1.0 CA A:GLY162 4.6 15.9 1.0 OE1 A:GLU184 4.7 20.6 1.0 OD1 A:ASP181 4.7 19.9 1.0 CA A:LYS160 4.8 15.8 1.0 N A:LEU164 4.9 11.5 1.0 C A:PHE157 5.0 17.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Gelatinase A Catalytic Domain


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 Gelatinase A Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:12.0 occ:1.00 O A:HOH303 2.5 22.0 1.0 O A:ASP141 2.5 11.9 1.0 O A:GLY173 2.6 15.9 1.0 O A:GLY175 2.7 12.7 1.0 O A:HOH304 2.7 17.6 1.0 OD1 A:ASP177 2.7 10.0 1.0 C A:ASP141 3.6 13.4 1.0 C A:GLY173 3.7 14.6 1.0 C A:GLY175 3.8 13.8 1.0 CG A:ASP177 3.8 13.8 1.0 C A:VAL174 4.0 15.3 1.0 O A:ALA140 4.0 9.9 1.0 O A:VAL174 4.0 15.6 1.0 N A:ASP177 4.2 9.8 1.0 N A:GLY175 4.3 13.6 1.0 CA A:VAL174 4.3 16.4 1.0 CA A:ASP141 4.3 12.4 1.0 N A:VAL174 4.4 16.1 1.0 N A:ILE142 4.4 15.1 1.0 OD2 A:ASP177 4.5 12.0 1.0 CA A:ILE142 4.5 15.3 1.0 CA A:GLY176 4.6 12.0 1.0 O A:GLY171 4.6 15.6 1.0 C A:GLY176 4.6 10.1 1.0 N A:GLY176 4.6 14.3 1.0 CA A:GLY175 4.7 12.6 1.0 CA A:GLY173 4.7 13.9 1.0 N A:GLY173 4.7 14.5 1.0 N A:MET143 4.7 14.8 1.0 CB A:ASP177 4.9 12.9 1.0 CA A:ASP177 4.9 12.0 1.0 CG A:MET143 4.9 13.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Gelatinase A Catalytic Domain


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 Gelatinase A Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:17.4 occ:1.00 O A:GLU184 2.5 13.1 1.0 OD2 A:ASP107 2.6 13.5 1.0 O A:ASP182 2.7 15.9 1.0 O A:HOH302 2.7 28.4 1.0 OD1 A:ASP182 2.8 10.9 1.0 O A:HOH301 2.9 29.8 1.0 OD1 A:ASP107 3.1 18.6 1.0 CG A:ASP107 3.2 15.7 1.0 C A:ASP182 3.5 15.2 1.0 C A:GLU184 3.7 16.1 1.0 CG A:ASP182 3.7 13.2 1.0 CA A:ASP182 4.1 15.4 1.0 OG1 A:THR105 4.2 16.6 1.0 N A:GLU184 4.2 16.9 1.0 CB A:ASP182 4.3 14.7 1.0 N A:ASP183 4.5 15.1 1.0 C A:ASP183 4.5 16.9 1.0 CA A:LEU185 4.6 15.2 1.0 N A:LEU185 4.6 16.1 1.0 CD1 A:TRP186 4.6 12.9 1.0 OD2 A:ASP182 4.6 14.2 1.0 CA A:GLU184 4.6 16.9 1.0 CB A:ASP107 4.6 15.3 1.0 CA A:ASP183 4.7 14.7 1.0

V.Dhanaraj, M.G.Williams, Q.-Z.Ye, F.Molina, L.L.Johnson, D.F.Ortwine, A.Pavlovsky, J.R.Rubin, R.W.Skeean, A.D.White, C.Humblet, D.J.Hupe, T.L.Blundell. X-Ray Structure of Gelatinase A Catalytic Domain Complexed with A Hydroxamate Inhibitor Croatica Chemica Acta V. 72 575 1999.
ISSN: ISSN 0011-1643