Calcium in PDB 6qig: Metalloproteinase

All present enzymatic activity of Metalloproteinase:
3.4.24.87;

The structure of Metalloproteinase, PDB code: 6qig was solved by H.J.Kim, J.Emsley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.20 / 2.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.532, 87.532, 407.342, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 24.7

The structure of Metalloproteinase also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Metalloproteinase (pdb code 6qig). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Metalloproteinase, PDB code: 6qig:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Metalloproteinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Metalloproteinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca717 b:51.7 occ:1.00 O A:LEU183 2.3 50.2 1.0 OD1 A:ASP182 2.3 58.8 1.0 OE1 A:GLU212 2.3 59.8 1.0 O A:ARG190 2.3 49.2 1.0 O A:HOH805 2.3 35.4 1.0 O A:VAL192 2.4 51.4 1.0 CD A:GLU212 3.2 62.1 1.0 N A:LEU183 3.2 51.8 1.0 OE2 A:GLU212 3.3 60.6 1.0 C A:LEU183 3.4 55.0 1.0 CG A:ASP182 3.5 60.4 1.0 C A:ARG190 3.5 54.0 1.0 C A:ASP182 3.5 52.9 1.0 C A:VAL192 3.6 50.4 1.0 CA A:LEU183 3.7 52.7 1.0 CA A:ASP182 3.8 54.4 1.0 CB A:LEU183 4.0 55.6 1.0 CA A:ARG190 4.2 58.3 1.0 CB A:ASP182 4.2 55.2 1.0 N A:VAL192 4.3 54.0 1.0 O A:ASP182 4.3 45.4 1.0 OD2 A:ASP182 4.4 57.2 1.0 C A:GLN191 4.4 52.2 1.0 CG1 A:VAL192 4.5 53.5 1.0 N A:GLU184 4.5 53.4 1.0 N A:GLN191 4.6 53.5 1.0 CA A:VAL192 4.6 53.4 1.0 CB A:ARG190 4.6 56.5 1.0 N A:ARG193 4.6 52.5 1.0 CG A:GLU212 4.6 64.8 1.0 O A:GLN191 4.7 58.1 1.0 CA A:ARG193 4.8 49.3 1.0 CA A:GLN191 4.9 56.2 1.0 CA A:GLU184 5.0 50.8 1.0

Calcium binding site 2 out of 3 in the Metalloproteinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Metalloproteinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca718 b:73.6 occ:1.00 OE1 A:GLU83 2.3 79.6 1.0 O A:CYS281 2.3 79.6 1.0 OD2 A:ASP173 2.3 75.4 1.0 OD2 A:ASP166 2.3 69.8 1.0 OD1 A:ASP173 2.8 73.6 1.0 CD A:GLU83 2.8 83.3 1.0 OE2 A:GLU83 2.8 80.1 1.0 CG A:ASP173 2.9 79.1 1.0 OD1 A:ASP166 2.9 81.2 1.0 OD2 A:ASP284 2.9 89.0 1.0 CG A:ASP166 3.0 75.1 1.0 OD1 A:ASP284 3.4 86.2 1.0 C A:CYS281 3.4 70.3 1.0 CG A:ASP284 3.5 89.3 1.0 CA A:CA719 3.7 79.9 1.0 CG A:GLU83 4.2 82.3 1.0 CA A:CYS281 4.2 80.0 1.0 N A:VAL282 4.3 66.7 1.0 CB A:ASP173 4.4 76.3 1.0 O A:ASP284 4.4 84.1 1.0 CA A:VAL282 4.5 80.2 1.0 CB A:ASP166 4.5 71.1 1.0 O A:HIS81 4.5 67.3 1.0 CB A:CYS281 4.6 89.7 1.0 CB A:GLU83 4.7 76.3 1.0 CB A:ASP284 4.9 84.9 1.0

Calcium binding site 3 out of 3 in the Metalloproteinase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Metalloproteinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca719 b:79.9 occ:1.00 OE2 A:GLU83 2.3 80.1 1.0 O A:ASP166 2.3 0.2 1.0 OD1 A:ASP166 2.3 81.2 1.0 OD2 A:ASP284 3.2 89.0 1.0 CG A:ASP166 3.3 75.1 1.0 CD A:GLU83 3.4 83.3 1.0 C A:ASP166 3.5 97.5 1.0 CA A:CA718 3.7 73.6 1.0 OE1 A:GLU83 4.0 79.6 1.0 OD2 A:ASP166 4.0 69.8 1.0 CG A:ARG287 4.0 0.6 1.0 CA A:ASP166 4.2 82.1 1.0 CB A:ASP166 4.2 71.1 1.0 O A:PRO285 4.3 61.1 1.0 CG A:ASP284 4.4 89.3 1.0 CG A:GLU83 4.6 82.3 1.0 CD A:ARG287 4.6 0.5 1.0 N A:THR167 4.6 0.0 1.0 N A:ARG287 4.7 75.0 1.0 O A:ASP168 4.7 96.1 1.0 CA A:PRO286 4.8 65.3 1.0 CA A:THR167 5.0 0.4 1.0

A.Petri, H.J.Kim, Y.Xu, R.De Groot, C.Li, A.Vandenbulcke, K.Vanhoorelbeke, J.Emsley, J.T.B.Crawley. Crystal Structure and Substrate-Induced Activation of ADAMTS13. Nat Commun V. 10 3781 2019.
ISSN: ESSN 2041-1723
PubMed: 31439947
DOI: 10.1038/S41467-019-11474-5