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Calcium in PDB 4gr3: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A, PDB code: 4gr3 was solved by E.A.Stura, L.Vera, F.Beau, L.Devel, E.Cassar-Lajeunesse, V.Dive, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.56 / 1.49
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.960, 63.130, 37.310, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.6

Other elements in 4gr3:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A also contains other interesting chemical elements:

Bromine (Br) 1 atom
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A (pdb code 4gr3). 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 the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A, PDB code: 4gr3:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4gr3

Go back to Calcium Binding Sites List in 4gr3
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A


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 the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:10.5
occ:1.00
O A:GLY190 2.3 12.3 1.0
O A:GLY192 2.3 11.8 1.0
O A:ASP158 2.3 8.6 1.0
O A:HOH417 2.4 16.2 1.0
OD2 A:ASP194 2.4 8.1 1.0
O A:HOH424 2.4 11.2 1.0
CG A:ASP194 3.4 10.5 1.0
C A:ASP158 3.5 10.5 1.0
C A:GLY190 3.5 17.6 1.0
C A:GLY192 3.5 9.3 1.0
OD1 A:ASP194 3.8 9.7 1.0
C A:ILE191 4.0 9.9 1.0
N A:GLY192 4.0 11.9 1.0
O A:ILE191 4.2 12.2 1.0
N A:ASP194 4.2 6.7 1.0
O A:ALA157 4.3 12.1 1.0
CA A:ASP158 4.3 7.3 1.0
CA A:GLY192 4.3 12.3 1.0
CA A:ILE191 4.3 11.9 1.0
N A:ILE191 4.4 13.7 1.0
N A:ILE159 4.4 6.5 1.0
CA A:GLY190 4.4 13.2 1.0
N A:GLY190 4.4 14.3 1.0
O A:HOH592 4.5 33.4 1.0
N A:GLY193 4.5 10.5 1.0
O A:GLY188 4.5 12.4 1.0
CA A:ILE159 4.5 7.3 1.0
CA A:GLY193 4.6 9.5 1.0
O A:HOH613 4.6 34.7 1.0
CB A:ASP194 4.6 6.2 1.0
C A:GLY193 4.6 8.5 1.0
N A:LEU160 4.6 6.5 1.0
O A:HOH659 4.7 37.5 1.0
CA A:ASP194 4.8 5.9 1.0
C A:SER189 4.8 16.2 1.0
O A:HOH594 4.9 22.2 1.0
O A:HOH409 4.9 13.0 1.0

Calcium binding site 2 out of 3 in 4gr3

Go back to Calcium Binding Sites List in 4gr3
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A


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 the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:12.0
occ:1.00
OD2 A:ASP124 2.4 13.8 1.0
O A:GLU199 2.4 10.5 1.0
O A:HOH437 2.4 14.1 1.0
OE2 A:GLU199 2.4 10.8 1.0
O A:GLU201 2.4 12.9 1.0
O A:HOH425 2.4 15.9 1.0
OD1 A:ASP124 2.7 13.7 1.0
CG A:ASP124 2.9 15.6 1.0
CD A:GLU199 3.5 12.4 1.0
C A:GLU199 3.5 10.2 1.0
C A:GLU201 3.6 16.4 1.0
CG A:GLU199 3.9 13.8 1.0
OG1 A:THR122 4.1 12.0 1.0
CA A:PHE202 4.2 14.7 1.0
CA A:GLU199 4.2 9.3 1.0
O A:HOH452 4.2 27.8 1.0
CD1 A:TRP203 4.3 11.1 1.0
N A:PHE202 4.3 13.1 1.0
CB A:ASP124 4.4 13.5 1.0
N A:GLU201 4.4 11.1 1.0
C A:ASP200 4.5 12.9 1.0
N A:ASP200 4.5 10.8 1.0
OE1 A:GLU199 4.6 11.3 1.0
O A:HOH468 4.6 22.6 1.0
O A:HOH558 4.6 29.1 1.0
O A:HOH495 4.6 23.5 1.0
CA A:GLU201 4.7 13.7 1.0
CB A:GLU199 4.7 8.6 1.0
CA A:ASP200 4.7 9.7 1.0
N A:TRP203 4.7 12.4 1.0
NE1 A:TRP203 4.8 10.6 1.0
O A:HOH412 4.9 20.2 1.0
CD1 A:PHE202 5.0 20.3 1.0
O A:ASP200 5.0 13.2 1.0

Calcium binding site 3 out of 3 in 4gr3

Go back to Calcium Binding Sites List in 4gr3
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A


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 the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:9.9
occ:1.00
OE2 A:GLU201 2.2 16.2 1.0
O A:GLY176 2.3 11.8 1.0
OD1 A:ASP198 2.3 9.2 1.0
O A:ILE180 2.3 9.7 1.0
O A:GLY178 2.3 10.7 1.0
OD2 A:ASP175 2.4 11.5 1.0
CG A:ASP198 3.4 10.1 1.0
C A:ILE180 3.4 13.2 1.0
CD A:GLU201 3.5 12.9 1.0
C A:GLY176 3.5 13.8 1.0
C A:GLY178 3.5 14.5 1.0
CG A:ASP175 3.6 15.0 1.0
N A:GLY178 3.9 14.7 1.0
N A:ILE180 3.9 11.7 1.0
CB A:ASP198 4.1 10.5 1.0
N A:GLY176 4.1 9.9 1.0
C A:LYS177 4.2 14.9 1.0
OD1 A:ASP175 4.2 12.4 1.0
OE1 A:GLU201 4.2 14.4 1.0
N A:ASP175 4.2 10.9 1.0
CA A:ILE180 4.2 11.1 0.3
CA A:ILE180 4.3 11.0 0.7
C A:GLY179 4.3 13.7 1.0
CA A:GLY178 4.3 13.1 1.0
C A:ASP175 4.3 14.0 1.0
CG2 A:ILE180 4.3 12.2 0.7
OD2 A:ASP198 4.3 9.0 1.0
CA A:GLY176 4.4 13.6 1.0
N A:LYS177 4.4 16.6 1.0
CA A:LYS177 4.4 14.7 1.0
N A:LEU181 4.4 9.9 1.0
CG A:GLU201 4.4 12.0 1.0
N A:GLY179 4.5 14.2 1.0
CA A:LEU181 4.6 9.4 1.0
CB A:ILE180 4.6 12.7 0.3
CA A:ASP175 4.6 11.1 1.0
CA A:GLY179 4.6 10.3 1.0
CB A:ASP175 4.7 9.7 1.0
O A:HOH591 4.7 23.1 1.0
O A:LYS177 4.7 16.5 1.0
O A:ASP175 4.8 13.8 1.0
O A:GLY179 4.8 12.8 1.0
CB A:ILE180 4.9 11.7 0.7

Reference:

B.Czarny, E.A.Stura, L.Devel, L.Vera, E.Cassar-Lajeunesse, F.Beau, V.Calderone, M.Fragai, C.Luchinat, V.Dive. Molecular Determinants of A Selective Matrix Metalloprotease-12 Inhibitor: Insights From Crystallography and Thermodynamic Studies. J.Med.Chem. V. 56 1149 2013.
ISSN: ISSN 0022-2623
PubMed: 23343195
DOI: 10.1021/JM301574D
Page generated: Sat Dec 12 04:48:43 2020

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