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Calcium in PDB 4gr8: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470C

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470C

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470C:
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 RXP470C, PDB code: 4gr8 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) 30.01 / 1.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.830, 61.470, 33.460, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.3

Other elements in 4gr8:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470C 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 RXP470C (pdb code 4gr8). 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 RXP470C, PDB code: 4gr8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4gr8

Go back to Calcium Binding Sites List in 4gr8
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470C


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 RXP470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:13.0
occ:1.00
 O A:HOH408 2.3 18.1 1.0
O A:HOH432 2.3 17.7 1.0
O A:GLY190 2.3 14.8 1.0
O A:GLY192 2.3 12.3 1.0
OD1 A:ASP194 2.3 13.0 1.0
O A:ASP158 2.4 13.9 1.0
CG A:ASP194 3.3 12.6 1.0
C A:ASP158 3.5 13.2 1.0
C A:GLY192 3.5 12.1 1.0
C A:GLY190 3.5 14.8 1.0
OD2 A:ASP194 3.7 13.0 1.0
C A:ILE191 4.1 14.2 1.0
N A:GLY192 4.1 13.8 1.0
O A:ALA157 4.1 17.6 1.0
N A:ASP194 4.2 11.5 1.0
O A:GLY188 4.3 16.9 1.0
CA A:ASP158 4.3 16.2 1.0
O A:HOH436 4.3 18.7 1.0
CA A:GLY192 4.3 13.4 1.0
O A:ILE191 4.4 13.9 1.0
CA A:ILE191 4.4 15.8 1.0
N A:ILE159 4.4 12.0 1.0
N A:ILE191 4.4 15.9 1.0
CA A:GLY190 4.4 15.1 1.0
N A:GLY190 4.4 13.9 1.0
N A:GLY193 4.5 13.2 1.0
CB A:ASP194 4.5 11.5 1.0
CA A:ILE159 4.5 12.9 1.0
O A:HOH416 4.6 18.2 1.0
N A:LEU160 4.6 12.5 1.0
O A:HOH500 4.6 20.6 1.0
C A:GLY193 4.6 12.4 1.0
CA A:GLY193 4.6 15.6 1.0
CA A:ASP194 4.7 12.1 1.0
C A:SER189 4.8 15.0 1.0
CG A:LEU160 4.8 12.7 1.0
O A:SER189 5.0 15.6 1.0

Calcium binding site 2 out of 3 in 4gr8

Go back to Calcium Binding Sites List in 4gr8
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470C


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 RXP470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:14.8
occ:1.00
 O A:GLU199 2.4 14.5 1.0
O A:GLU201 2.4 15.2 1.0
O A:HOH426 2.4 19.7 1.0
O A:HOH420 2.4 19.2 1.0
OE2 A:GLU199 2.4 15.4 1.0
OD2 A:ASP124 2.4 16.0 1.0
OD1 A:ASP124 2.6 16.6 1.0
CG A:ASP124 2.9 17.3 1.0
C A:GLU199 3.5 15.1 1.0
CD A:GLU199 3.5 14.4 1.0
C A:GLU201 3.6 15.5 1.0
CG A:GLU199 3.9 16.3 1.0
CA A:GLU199 4.1 13.7 1.0
OG1 A:THR122 4.2 15.6 1.0
CA A:PHE202 4.2 14.7 1.0
N A:PHE202 4.3 14.6 1.0
CD1 A:TRP203 4.4 12.6 1.0
CB A:ASP124 4.4 15.7 1.0
N A:GLU201 4.4 14.2 1.0
C A:ASP200 4.5 16.8 1.0
N A:ASP200 4.5 13.2 1.0
OE1 A:GLU199 4.6 15.9 1.0
O A:HOH515 4.6 32.4 1.0
O A:HOH504 4.6 27.2 1.0
CB A:GLU199 4.6 13.9 1.0
CA A:GLU201 4.7 14.8 1.0
O A:HOH514 4.7 24.6 1.0
CA A:ASP200 4.7 17.4 1.0
N A:TRP203 4.8 15.5 1.0
O A:HOH551 4.8 31.0 1.0
NE1 A:TRP203 4.9 13.3 1.0
CD1 A:PHE202 4.9 21.1 1.0
O A:ASP200 4.9 17.3 1.0
NH1 A:ARG165 4.9 22.5 0.6

Calcium binding site 3 out of 3 in 4gr8

Go back to Calcium Binding Sites List in 4gr8
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470C


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 RXP470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:13.9
occ:1.00
 OE2 A:GLU201 2.3 19.2 1.0
OD2 A:ASP198 2.3 13.7 1.0
O A:ILE180 2.3 14.1 1.0
O A:GLY176 2.3 17.1 1.0
OD1 A:ASP175 2.3 15.4 1.0
O A:GLY178 2.4 17.8 1.0
CG A:ASP198 3.4 13.8 1.0
C A:ILE180 3.4 12.8 1.0
CD A:GLU201 3.5 16.4 1.0
CG A:ASP175 3.5 18.8 1.0
C A:GLY176 3.5 17.2 1.0
C A:GLY178 3.6 17.5 1.0
N A:ILE180 3.9 14.5 1.0
N A:GLY178 3.9 17.4 1.0
N A:GLY176 4.0 15.8 1.0
CB A:ASP198 4.0 12.8 1.0
OD2 A:ASP175 4.1 17.3 1.0
N A:ASP175 4.2 14.8 1.0
CA A:ILE180 4.2 15.2 1.0
C A:ASP175 4.2 17.9 1.0
OE1 A:GLU201 4.2 18.7 1.0
C A:LYS177 4.3 19.3 1.0
C A:GLY179 4.3 18.1 1.0
CA A:GLY176 4.4 16.9 1.0
N A:LEU181 4.4 14.2 1.0
OD1 A:ASP198 4.4 13.3 1.0
CA A:GLY178 4.4 19.3 1.0
N A:LYS177 4.5 18.6 1.0
CA A:LYS177 4.5 18.0 1.0
CA A:LEU181 4.5 13.9 1.0
CG A:GLU201 4.5 15.6 1.0
CA A:ASP175 4.6 15.6 1.0
N A:GLY179 4.6 17.6 1.0
CB A:ASP175 4.7 17.0 1.0
CA A:GLY179 4.7 18.0 1.0
O A:ASP175 4.7 17.5 1.0
O A:GLY179 4.8 18.4 1.0
CB A:ILE180 4.8 14.8 1.0
O A:LYS177 4.9 21.2 1.0

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: Sun Jul 14 07:22:47 2024

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