Zinc 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:

Calcium (Ca) 3 atoms
Bromine (Br) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7ovy

Go back to Zinc Binding Sites List in 7ovy
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn301

b:10.7
occ:1.00
O78 A:2IF306 2.0 13.9 0.3
NE2 A:HIS218 2.0 12.1 1.0
NE2 A:HIS222 2.1 9.5 1.0
NE2 A:HIS228 2.1 10.7 1.0
O77 A:2IF306 2.3 11.3 0.5
C75 A:2IF306 2.8 15.4 0.4
N76 A:2IF306 3.0 11.5 0.3
CD2 A:HIS218 3.0 10.8 1.0
CE1 A:HIS218 3.0 10.9 1.0
CE1 A:HIS228 3.0 16.2 1.0
CD2 A:HIS222 3.0 10.0 1.0
CE1 A:HIS222 3.1 11.4 1.0
CD2 A:HIS228 3.1 11.6 1.0
ND1 A:HIS218 4.1 12.9 1.0
CG A:HIS218 4.1 8.8 1.0
ND1 A:HIS228 4.2 13.2 1.0
ND1 A:HIS222 4.2 11.1 1.0
CG A:HIS222 4.2 8.6 1.0
CG A:HIS228 4.2 11.4 1.0
C15 A:2IF306 4.2 18.3 0.5
OE2 A:GLU219 4.4 18.5 1.0
C132 A:2IF306 4.8 25.5 0.4
C19 A:2IF306 4.8 21.4 0.4
C14 A:2IF306 4.8 22.1 0.5
N16 A:2IF306 4.8 18.7 0.3
CE A:MET236 4.9 11.3 1.0
C20 A:2IF306 5.0 21.2 0.5

Zinc binding site 2 out of 2 in 7ovy

Go back to Zinc Binding Sites List in 7ovy
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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:Zn302

b:11.7
occ:1.00
OD2 A:ASP170 2.0 14.0 0.5
NE2 A:HIS168 2.0 11.5 1.0
NE2 A:HIS183 2.0 14.3 1.0
ND1 A:HIS196 2.0 9.8 1.0
OD2 A:ASP170 2.1 14.1 0.5
CG A:ASP170 2.9 15.0 0.5
CD2 A:HIS168 2.9 9.5 1.0
CE1 A:HIS183 2.9 14.8 1.0
CE1 A:HIS196 2.9 10.8 1.0
CG A:ASP170 3.0 15.2 0.5
CE1 A:HIS168 3.0 10.3 1.0
CD2 A:HIS183 3.1 12.1 1.0
CG A:HIS196 3.1 10.4 1.0
OD1 A:ASP170 3.2 13.0 0.5
OD1 A:ASP170 3.2 13.5 0.5
CB A:HIS196 3.5 8.9 1.0
ND1 A:HIS183 4.1 13.7 1.0
CG A:HIS168 4.1 10.5 1.0
NE2 A:HIS196 4.1 10.6 1.0
ND1 A:HIS168 4.1 10.8 1.0
O A:HIS172 4.2 14.4 1.0
CG A:HIS183 4.2 10.8 1.0
CD2 A:HIS196 4.2 10.8 1.0
CB A:ASP170 4.3 16.1 0.5
CE1 A:PHE185 4.3 15.9 1.0
CB A:ASP170 4.4 15.9 0.5
CZ A:PHE185 4.5 23.0 1.0
CZ A:PHE174 4.7 10.2 1.0
CE2 A:PHE174 4.7 10.0 1.0
O A:HOH518 4.8 36.8 1.0
O A:HOH460 5.0 14.1 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 16:56:00 2021

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