Calcium in PDB 7ovy: Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain

Enzymatic activity of Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain

All present enzymatic activity of Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain, PDB code: 7ovy was solved by L.Ciccone, A.Rossello, L.Vera, E.Nuti, E.A.Stura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.89 / 1.24
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.34, 60.45, 54.05, 90, 115.24, 90
R / Rfree (%) 18.4 / 20.9

Other elements in 7ovy:

The structure of Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Bromine (Br) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain (pdb code 7ovy). 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 A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain, PDB code: 7ovy:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7ovy

Go back to Calcium Binding Sites List in 7ovy
Calcium binding site 1 out of 3 in the Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 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 A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:12.8
occ:1.00
O A:GLY192 2.3 10.6 1.0
O A:ASP158 2.3 13.6 1.0
O A:GLY190 2.3 16.1 1.0
O A:HOH425 2.4 19.0 1.0
O A:HOH464 2.4 13.3 1.0
OD1 A:ASP194 2.4 11.2 1.0
CG A:ASP194 3.4 10.1 1.0
C A:ASP158 3.4 12.2 1.0
C A:GLY192 3.5 10.6 1.0
C A:GLY190 3.6 16.4 1.0
OD2 A:ASP194 3.8 12.8 1.0
O A:HOH495 4.0 26.2 1.0
C A:ILE191 4.0 13.0 1.0
N A:GLY192 4.1 11.1 1.0
O A:ALA157 4.1 17.5 1.0
O A:ILE191 4.2 12.4 1.0
CA A:ASP158 4.2 11.6 1.0
N A:ASP194 4.3 9.7 1.0
CA A:GLY192 4.4 12.0 1.0
N A:ILE159 4.4 10.7 1.0
CA A:ILE191 4.4 15.3 1.0
N A:ILE191 4.4 15.7 1.0
O A:GLY188 4.4 16.0 1.0
N A:GLY193 4.4 9.9 1.0
CA A:GLY190 4.5 21.7 1.0
CA A:ILE159 4.5 9.7 1.0
CA A:GLY193 4.5 11.2 1.0
N A:GLY190 4.5 19.3 1.0
N A:LEU160 4.6 11.2 1.0
CB A:ASP194 4.6 10.4 1.0
C A:GLY193 4.7 9.4 1.0
O A:HOH458 4.8 15.9 1.0
CA A:ASP194 4.8 8.8 1.0
C A:SER189 4.8 16.9 0.7
C A:SER189 4.9 17.1 0.3

Calcium binding site 2 out of 3 in 7ovy

Go back to Calcium Binding Sites List in 7ovy
Calcium binding site 2 out of 3 in the Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 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 A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:9.5
occ:1.00
O A:GLU199 2.3 9.9 1.0
O A:HOH570 2.4 13.5 1.0
O A:HOH533 2.4 15.2 1.0
O A:GLU201 2.4 10.0 1.0
OE2 A:GLU199 2.4 8.1 1.0
OD2 A:ASP124 2.4 8.9 1.0
OD1 A:ASP124 2.6 10.5 1.0
CG A:ASP124 2.9 10.6 1.0
C A:GLU199 3.4 10.2 1.0
CD A:GLU199 3.5 9.1 1.0
C A:GLU201 3.6 9.1 1.0
CG A:GLU199 3.9 9.6 1.0
CA A:GLU199 4.1 7.8 1.0
OG1 A:THR122 4.1 8.7 1.0
CA A:PHE202 4.2 10.5 1.0
O A:HOH620 4.3 24.5 1.0
N A:PHE202 4.3 8.8 1.0
CD1 A:TRP203 4.3 7.5 1.0
CB A:ASP124 4.4 9.4 1.0
N A:GLU201 4.4 9.8 1.0
N A:ASP200 4.5 9.1 1.0
C A:ASP200 4.5 13.8 1.0
OE1 A:GLU199 4.6 11.8 1.0
CB A:GLU199 4.6 9.0 1.0
NH1 A:ARG165 4.6 18.6 1.0
CA A:ASP200 4.7 10.5 1.0
CA A:GLU201 4.7 8.9 1.0
O A:HOH474 4.8 17.8 1.0
N A:TRP203 4.8 8.4 1.0
NE1 A:TRP203 4.8 9.3 1.0
CD1 A:PHE202 4.9 11.2 1.0
O A:ASP200 5.0 14.6 1.0

Calcium binding site 3 out of 3 in 7ovy

Go back to Calcium Binding Sites List in 7ovy
Calcium binding site 3 out of 3 in the Crystal Structure of A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 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 A Dimeric Based Inhibitor JG34 in Complex with the Mmp-12 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:10.5
occ:1.00
OE2 A:GLU201 2.2 16.2 1.0
O A:ILE180 2.3 12.3 1.0
O A:GLY176 2.3 13.1 1.0
O A:GLY178 2.3 13.9 1.0
OD1 A:ASP175 2.4 11.4 1.0
OD2 A:ASP198 2.4 11.0 1.0
C A:ILE180 3.5 11.5 1.0
CG A:ASP198 3.5 9.7 1.0
CD A:GLU201 3.5 15.1 1.0
C A:GLY178 3.5 15.7 1.0
CG A:ASP175 3.5 14.1 1.0
C A:GLY176 3.5 14.8 1.0
N A:GLY178 3.8 13.4 1.0
N A:ILE180 3.9 11.1 1.0
OD2 A:ASP175 4.1 14.7 1.0
CB A:ASP198 4.1 8.3 1.0
C A:LYS177 4.1 13.5 1.0
N A:GLY176 4.1 11.3 1.0
CA A:ILE180 4.2 10.9 1.0
OE1 A:GLU201 4.2 13.5 1.0
C A:GLY179 4.2 12.2 1.0
CA A:GLY178 4.3 15.9 1.0
N A:ASP175 4.3 11.8 1.0
C A:ASP175 4.3 13.8 1.0
OD1 A:ASP198 4.4 9.9 1.0
CA A:LYS177 4.4 13.8 1.0
N A:LYS177 4.4 12.8 1.0
CG A:GLU201 4.4 10.9 1.0
CA A:GLY176 4.5 13.9 1.0
N A:LEU181 4.5 11.1 1.0
N A:GLY179 4.5 15.6 1.0
CA A:GLY179 4.7 16.5 1.0
CA A:LEU181 4.7 9.6 1.0
CA A:ASP175 4.7 12.9 1.0
CB A:ASP175 4.7 14.8 1.0
O A:GLY179 4.7 16.7 1.0
O A:LYS177 4.8 20.5 1.0
CB A:ILE180 4.8 12.1 1.0
O A:ASP175 4.8 15.9 1.0
O A:HOH571 4.9 28.4 1.0

Reference:

D.Cuffaro, C.Camodeca, T.Tuccinardi, L.Ciccone, J.W.Bartsch, T.Kellermann, L.Cook, E.Nuti, A.Rossello. Discovery of Dimeric Arylsulfonamides As Potent ADAM8 Inhibitors Acs Med.Chem.Lett. 2021.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.1C00411
Page generated: Fri Nov 5 11:40:13 2021

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