Calcium in PDB 1pex: Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain

The structure of Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain, PDB code: 1pex was solved by F.X.Gomis-Ruth, U.Gohlke, M.Betz, V.Knauper, G.Murphy, C.Lopez-Otin, W.Bode, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.940, 52.940, 144.020, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / n/a

The structure of Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain (pdb code 1pex). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain, PDB code: 1pex:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:45.4 occ:1.01 O A:ASP329 2.1 36.3 1.0 O A:ASP285 2.1 35.6 1.0 O A:SER378 2.3 37.0 1.0 O A:ASP427 2.4 38.9 1.0 C A:ASP285 3.3 35.2 1.0 C A:ASP329 3.3 35.6 1.0 C A:SER378 3.5 35.8 1.0 C A:ASP427 3.5 37.4 1.0 CA A:ASP285 4.0 36.1 1.0 CA A:SER378 4.1 36.8 1.0 CA A:ASP329 4.1 36.6 1.0 CA A:ASP427 4.2 36.7 1.0 N A:ALA330 4.3 34.3 1.0 N A:ALA286 4.3 34.1 1.0 CA A:ALA330 4.5 33.3 1.0 N A:ALA428 4.5 36.7 1.0 O A:ILE328 4.5 36.7 1.0 N A:ALA379 4.5 32.8 1.0 CB A:SER378 4.6 36.7 1.0 CA A:ALA286 4.6 33.5 1.0 CA A:ALA428 4.8 35.1 1.0 CB A:ALA286 4.8 32.4 1.0 O A:LEU284 4.8 33.0 1.0 CA A:ALA379 4.8 30.6 1.0 CB A:ASP285 4.8 38.5 1.0 CB A:ASP427 4.9 36.9 1.0 CB A:ALA330 4.9 33.0 1.0 O A:ILE377 4.9 41.2 1.0

Calcium binding site 2 out of 2 in the Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Collagenase-3 (Mmp-13) C-Terminal Hemopexin-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:37.2 occ:1.03 O A:ALA331 2.2 34.5 1.0 O A:ALA380 2.2 31.6 1.0 O A:VAL429 2.2 34.3 1.0 O A:ILE287 2.4 37.8 1.0 CL A:CL501 2.9 30.5 1.0 CL A:CL504 3.3 29.7 1.1 C A:ALA331 3.4 34.3 1.0 C A:ALA380 3.4 31.4 1.0 C A:VAL429 3.5 34.1 1.0 C A:ILE287 3.6 36.9 1.0 CA A:TYR332 4.1 35.2 1.0 CB A:TYR332 4.2 34.2 1.0 N A:TYR332 4.2 34.7 1.0 N A:VAL381 4.3 31.5 1.0 N A:TYR430 4.3 35.0 1.0 CA A:TYR430 4.4 35.1 1.0 CB A:TYR430 4.4 35.0 1.0 N A:ALA380 4.4 31.4 1.0 CA A:ALA380 4.4 32.0 1.0 CG1 A:VAL429 4.4 32.6 1.0 CA A:VAL381 4.4 32.7 1.0 N A:VAL429 4.4 34.4 1.0 N A:ALA331 4.4 32.7 1.0 CA A:ALA331 4.5 33.4 1.0 CA A:VAL429 4.5 33.8 1.0 N A:THR288 4.5 37.6 1.0 CA A:THR288 4.5 38.4 1.0 CA A:ILE287 4.6 36.0 1.0 N A:ILE287 4.6 35.2 1.0 CB A:ILE287 4.7 35.8 1.0 CB A:VAL381 4.8 31.5 1.0 CB A:ALA380 4.9 31.6 1.0

F.X.Gomis-Ruth, U.Gohlke, M.Betz, V.Knauper, G.Murphy, C.Lopez-Otin, W.Bode. The Helping Hand of Collagenase-3 (Mmp-13): 2.7 A Crystal Structure of Its C-Terminal Haemopexin-Like Domain. J.Mol.Biol. V. 264 556 1996.
ISSN: ISSN 0022-2836
PubMed: 8969305
DOI: 10.1006/JMBI.1996.0661