Calcium in PDB 1ck7: Gelatinase A (Full-Length)

All present enzymatic activity of Gelatinase A (Full-Length):
3.4.24.24;

The structure of Gelatinase A (Full-Length), PDB code: 1ck7 was solved by E.Morgunova, A.Tuuttila, U.Bergmann, M.Isupov, Y.Lindqvist, G.Schneider, K.Tryggvason, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.00 / 2.80
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	121.320, 121.320, 345.110, 90.00, 90.00, 90.00
R / Rfree (%)	28.6 / 32.7

The structure of Gelatinase A (Full-Length) also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Gelatinase A (Full-Length) (pdb code 1ck7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Gelatinase A (Full-Length), PDB code: 1ck7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Gelatinase A (Full-Length)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Gelatinase A (Full-Length) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca992 b:23.9 occ:1.00 O A:GLY186 2.4 22.6 1.0 O A:LEU190 2.5 18.5 1.0 O A:ASP188 2.6 20.7 1.0 OD2 A:ASP208 2.6 26.7 1.0 OE2 A:GLU211 2.7 26.0 1.0 O A:ASP185 2.9 37.8 1.0 CG A:ASP208 3.4 24.1 1.0 C A:LEU190 3.6 17.0 1.0 C A:GLY186 3.6 24.7 1.0 C A:ASP188 3.8 19.8 1.0 N A:LEU190 3.8 16.7 1.0 OD1 A:ASP185 3.8 26.6 1.0 CD A:GLU211 3.9 24.5 1.0 CB A:ASP208 3.9 8.9 1.0 C A:ASP185 3.9 29.0 1.0 N A:ASP188 4.1 22.7 1.0 C A:LYS187 4.1 27.0 1.0 CA A:LEU190 4.1 14.5 1.0 C A:GLY189 4.2 22.4 1.0 OD1 A:ASP208 4.4 27.6 1.0 CG A:GLU211 4.4 2.6 1.0 CA A:GLY186 4.4 26.1 1.0 N A:LYS187 4.5 26.7 1.0 N A:GLY186 4.5 25.8 1.0 CA A:LYS187 4.5 26.5 1.0 CA A:ASP188 4.5 20.9 1.0 O A:LYS187 4.5 26.1 1.0 CB A:LEU190 4.5 12.7 1.0 N A:LEU191 4.6 17.6 1.0 N A:ASP185 4.6 21.6 1.0 CA A:GLY189 4.7 21.1 1.0 N A:GLY189 4.7 19.1 1.0 CA A:LEU191 4.7 14.2 1.0 O A:GLY189 4.9 24.6 1.0 OE1 A:GLU211 4.9 33.0 1.0 CA A:ASP185 5.0 26.8 1.0

Calcium binding site 2 out of 3 in the Gelatinase A (Full-Length)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Gelatinase A (Full-Length) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca993 b:0.7 occ:1.00 O A:GLY200 2.7 47.1 1.0 O A:ALA167 2.9 34.1 1.0 O A:ASP168 2.9 33.5 1.0 OE1 A:GLU166 3.2 58.5 1.0 O A:GLY202 3.4 27.5 1.0 OD1 A:ASP204 3.5 36.5 1.0 C A:ASP168 3.6 33.5 1.0 C A:GLY200 3.8 46.5 1.0 CG A:ASP204 4.0 37.9 1.0 OD2 A:ASP204 4.0 37.4 1.0 C A:ALA167 4.0 35.2 1.0 CD A:GLU166 4.1 58.5 1.0 CA A:ASP168 4.2 33.5 1.0 OE2 A:GLU166 4.2 55.2 1.0 CG A:MET170 4.4 9.8 1.0 N A:ILE169 4.5 36.2 1.0 CA A:GLY200 4.5 51.1 1.0 O A:HOH1003 4.5 29.0 1.0 C A:GLY202 4.5 32.5 1.0 N A:ASP168 4.6 34.3 1.0 N A:GLY200 4.7 55.0 1.0 N A:MET170 4.7 34.5 1.0 N A:GLY202 4.7 39.4 1.0 N A:VAL201 4.8 43.3 1.0 C A:VAL201 4.8 43.0 1.0 CA A:ILE169 4.8 35.4 1.0 CA A:VAL201 5.0 40.2 1.0

Calcium binding site 3 out of 3 in the Gelatinase A (Full-Length)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Gelatinase A (Full-Length) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca994 b:63.8 occ:1.00 O A:ASP476 2.5 59.2 1.0 O A:ASP569 2.7 68.5 1.0 O A:ASP618 2.7 0.7 1.0 O A:ASP521 2.8 52.3 1.0 C A:ASP618 3.6 0.8 1.0 C A:ASP569 3.7 66.9 1.0 CB A:ASP618 3.7 99.0 1.0 CA A:ASP618 3.7 0.3 1.0 C A:ASP476 3.7 60.5 1.0 C A:ASP521 3.8 49.9 1.0 CA A:ASP569 4.0 68.0 1.0 CB A:ASP569 4.3 74.6 1.0 CA A:ASP476 4.5 65.5 1.0 CA A:GLY477 4.6 58.0 1.0 N A:GLY477 4.6 58.4 1.0 CA A:ASP521 4.6 49.2 1.0 N A:ALA570 4.7 64.6 1.0 CL A:CL995 4.7 58.6 1.0 N A:ALA619 4.7 0.8 1.0 N A:ALA522 4.8 50.1 1.0 CA A:ALA522 4.8 51.9 1.0 CA A:ALA570 4.9 64.3 1.0 O A:PHE475 4.9 75.4 1.0 CB A:ALA522 5.0 53.2 1.0

E.Morgunova, A.Tuuttila, U.Bergmann, M.Isupov, Y.Lindqvist, G.Schneider, K.Tryggvason. Structure of Human Pro-Matrix Metalloproteinase-2: Activation Mechanism Revealed. Science V. 284 1667 1999.
ISSN: ISSN 0036-8075
PubMed: 10356396
DOI: 10.1126/SCIENCE.284.5420.1667