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Calcium in PDB 5cxa: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470, PDB code: 5cxa was solved by C.Rouanet-Mehouas, L.Devel, V.Dive, E.A.Stura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.62 / 1.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.230, 63.700, 36.620, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 18.1

Other elements in 5cxa:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
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 A Carboxylate Inhibitor Related to RXP470 (pdb code 5cxa). 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 A Carboxylate Inhibitor Related to RXP470, PDB code: 5cxa:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5cxa

Go back to Calcium Binding Sites List in 5cxa
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470


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 A Carboxylate Inhibitor Related to RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:11.3
occ:1.00
 O A:GLY190 2.3 14.0 1.0
O A:GLY192 2.3 12.2 1.0
O A:ASP158 2.3 10.3 1.0
O A:HOH420 2.4 14.6 1.0
OD1 A:ASP194 2.4 10.7 1.0
O A:HOH423 2.4 12.8 1.0
CG A:ASP194 3.4 10.0 1.0
C A:ASP158 3.5 9.4 1.0
C A:GLY190 3.5 13.7 1.0
C A:GLY192 3.5 11.8 1.0
OD2 A:ASP194 3.8 11.3 1.0
C A:ILE191 4.0 12.6 1.0
N A:GLY192 4.1 12.9 1.0
O A:ILE191 4.2 11.9 1.0
N A:ASP194 4.2 9.9 1.0
O A:ALA157 4.3 13.5 1.0
CA A:GLY192 4.3 13.0 1.0
CA A:ASP158 4.4 10.2 1.0
CA A:ILE191 4.4 15.3 1.0
O A:GLY188 4.4 14.8 1.0
N A:ILE191 4.4 14.0 1.0
N A:ILE159 4.4 8.9 1.0
CA A:GLY190 4.4 14.1 1.0
N A:GLY190 4.4 14.6 1.0
N A:GLY193 4.5 11.3 1.0
O A:HOH634 4.5 41.3 1.0
CA A:ILE159 4.5 9.3 1.0
CA A:GLY193 4.5 10.0 1.0
O A:HOH417 4.6 31.1 1.0
C A:GLY193 4.6 10.3 1.0
CB A:ASP194 4.6 10.5 1.0
N A:LEU160 4.6 8.8 1.0
CA A:ASP194 4.8 9.4 1.0
C A:SER189 4.8 16.0 1.0
CH2 A:TRP109 4.9 11.4 1.0
O A:HOH443 4.9 14.0 1.0

Calcium binding site 2 out of 3 in 5cxa

Go back to Calcium Binding Sites List in 5cxa
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470


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 A Carboxylate Inhibitor Related to RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:12.1
occ:1.00
 OD2 A:ASP124 2.4 11.3 1.0
OE2 A:GLU199 2.4 11.7 1.0
O A:HOH555 2.4 16.4 1.0
O A:GLU201 2.4 12.2 1.0
O A:GLU199 2.4 10.9 1.0
O A:HOH586 2.4 15.5 1.0
OD1 A:ASP124 2.6 13.5 1.0
CG A:ASP124 2.8 11.6 1.0
CD A:GLU199 3.5 11.4 1.0
C A:GLU199 3.6 10.1 1.0
C A:GLU201 3.6 11.2 1.0
CG A:GLU199 3.9 12.5 1.0
OG1 A:THR122 4.1 11.4 1.0
CA A:GLU199 4.2 10.1 1.0
CA A:PHE202 4.3 11.9 1.0
CD1 A:TRP203 4.3 12.4 1.0
CB A:ASP124 4.4 13.2 1.0
N A:PHE202 4.4 11.8 1.0
O A:HOH635 4.5 29.9 1.0
N A:GLU201 4.5 10.3 1.0
OE1 A:GLU199 4.6 11.9 1.0
C A:ASP200 4.6 11.8 1.0
N A:ASP200 4.6 10.4 1.0
O A:HOH419 4.6 21.6 1.0
CB A:GLU199 4.6 11.5 1.0
O A:HOH518 4.7 27.9 1.0
CA A:GLU201 4.7 11.6 1.0
O A:HOH449 4.7 36.6 1.0
CA A:ASP200 4.7 11.3 1.0
N A:TRP203 4.8 11.4 1.0
NE1 A:TRP203 4.8 10.6 1.0
O A:HOH670 4.9 19.6 1.0
CD1 A:PHE202 4.9 16.4 1.0

Calcium binding site 3 out of 3 in 5cxa

Go back to Calcium Binding Sites List in 5cxa
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470


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 A Carboxylate Inhibitor Related to RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:10.3
occ:1.00
 O A:GLY176 2.3 13.0 1.0
O A:ILE180 2.3 12.4 1.0
O A:GLY178 2.3 12.8 1.0
OE2 A:GLU201 2.3 17.4 1.0
OD2 A:ASP198 2.3 10.7 1.0
OD1 A:ASP175 2.4 11.8 1.0
C A:ILE180 3.4 11.3 1.0
CG A:ASP198 3.4 9.6 1.0
C A:GLY178 3.5 12.6 1.0
C A:GLY176 3.5 12.2 1.0
CG A:ASP175 3.5 10.6 1.0
CD A:GLU201 3.6 14.9 1.0
N A:GLY178 3.8 12.7 1.0
N A:ILE180 3.9 10.9 1.0
N A:GLY176 4.1 11.5 1.0
OD2 A:ASP175 4.1 12.8 1.0
CA A:ILE180 4.1 11.0 1.0
CB A:ASP198 4.1 9.2 1.0
C A:LYS177 4.2 13.4 1.0
C A:GLY179 4.2 11.3 1.0
CA A:GLY178 4.2 13.5 1.0
N A:ASP175 4.3 11.3 1.0
C A:ASP175 4.3 11.1 1.0
OD1 A:ASP198 4.4 10.3 1.0
CG A:GLU201 4.4 11.9 1.0
CA A:LYS177 4.4 13.3 1.0
OE1 A:GLU201 4.4 16.0 1.0
N A:LYS177 4.4 12.7 1.0
CA A:GLY176 4.4 12.3 1.0
CB A:ILE180 4.5 12.3 1.0
N A:LEU181 4.5 10.4 1.0
N A:GLY179 4.5 12.6 1.0
CA A:ASP175 4.6 10.5 1.0
CA A:GLY179 4.6 11.8 1.0
CB A:ASP175 4.7 10.8 1.0
CA A:LEU181 4.7 11.1 1.0
O A:ASP175 4.7 13.2 1.0
O A:HOH500 4.8 38.2 1.0
O A:GLY179 4.8 12.0 1.0
O A:LYS177 4.9 16.7 1.0

Reference:

C.Rouanet-Mehouas, B.Czarny, F.Beau, E.Cassar-Lajeunesse, E.A.Stura, V.Dive, L.Devel. Zinc-Metalloproteinase Inhibitors: Evaluation of the Complex Role Played By the Zinc-Binding Group on Potency and Selectivity. J. Med. Chem. V. 60 403 2017.
ISSN: ISSN 1520-4804
PubMed: 27996256
DOI: 10.1021/ACS.JMEDCHEM.6B01420
Page generated: Wed Jul 9 04:49:14 2025

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