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Calcium in PDB 4h84: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor., PDB code: 4h84 was solved by E.A.Stura, C.Antoni, L.Vera, E.Cassar-Lajeunesse, E.Nuti, V.Dive, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.03 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.140, 62.790, 113.140, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.6

Other elements in 4h84:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor. also contains other interesting chemical elements:

Zinc (Zn) 4 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 Selective Carboxylate Based Inhibitor. (pdb code 4h84). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor., PDB code: 4h84:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4h84

Go back to Calcium Binding Sites List in 4h84
Calcium binding site 1 out of 6 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.


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 Selective Carboxylate Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:12.4
occ:1.00
 O A:HOH406 2.2 13.9 1.0
O A:GLY192 2.3 9.0 1.0
O A:ASP158 2.4 9.9 1.0
O A:GLY190 2.4 11.1 1.0
O A:HOH401 2.4 10.9 1.0
OD2 A:ASP194 2.7 10.5 1.0
C A:GLY192 3.5 8.0 1.0
C A:ASP158 3.5 13.1 1.0
C A:GLY190 3.6 11.0 1.0
CG A:ASP194 3.6 13.2 1.0
C A:ILE191 4.0 10.1 1.0
N A:GLY192 4.0 9.5 1.0
OD1 A:ASP194 4.0 14.4 1.0
O A:ILE191 4.2 11.0 1.0
N A:ASP194 4.3 9.4 1.0
CA A:GLY192 4.3 10.2 1.0
O A:HOH407 4.3 15.4 1.0
O A:ALA157 4.3 13.6 1.0
CA A:ASP158 4.3 12.3 1.0
O A:HOH498 4.4 27.2 1.0
CA A:ILE191 4.4 9.8 1.0
N A:GLY193 4.4 10.6 1.0
N A:ILE191 4.4 11.3 1.0
O A:GLY188 4.4 14.8 1.0
N A:ILE159 4.4 10.4 1.0
CA A:GLY193 4.5 9.5 1.0
CA A:GLY190 4.5 11.3 1.0
CA A:ILE159 4.6 7.7 1.0
N A:GLY190 4.6 12.6 1.0
C A:GLY193 4.7 10.3 1.0
CB A:ASP194 4.8 10.0 1.0
CH2 A:TRP109 4.8 14.1 1.0
N A:LEU160 4.9 8.8 1.0
CA A:ASP194 4.9 10.1 1.0
C A:SER189 4.9 10.4 0.9

Calcium binding site 2 out of 6 in 4h84

Go back to Calcium Binding Sites List in 4h84
Calcium binding site 2 out of 6 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.


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 Selective Carboxylate Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:10.8
occ:1.00
 O A:HOH471 2.3 16.1 1.0
O A:GLU199 2.4 11.0 1.0
O A:GLU201 2.4 11.3 1.0
O A:HOH402 2.4 14.0 1.0
OD2 A:ASP124 2.4 14.1 1.0
OE2 A:GLU199 2.4 14.6 1.0
OD1 A:ASP124 2.6 16.3 1.0
CG A:ASP124 2.8 12.8 1.0
C A:GLU199 3.5 8.0 1.0
CD A:GLU199 3.5 12.9 1.0
C A:GLU201 3.6 10.4 1.0
CG A:GLU199 4.0 13.6 1.0
CA A:GLU199 4.1 7.4 1.0
OG1 A:THR122 4.2 12.3 1.0
CA A:PHE202 4.2 8.3 1.0
N A:PHE202 4.3 9.2 1.0
CB A:ASP124 4.4 9.9 1.0
CD1 A:TRP203 4.4 6.9 1.0
N A:GLU201 4.4 7.8 1.0
C A:ASP200 4.5 12.2 1.0
N A:ASP200 4.5 8.2 1.0
O A:HOH522 4.6 26.4 1.0
O A:HOH452 4.6 25.6 1.0
OE1 A:GLU199 4.6 13.7 1.0
CA A:GLU201 4.7 6.7 1.0
CB A:GLU199 4.7 8.9 1.0
CA A:ASP200 4.7 11.5 1.0
N A:TRP203 4.8 8.4 1.0
CD1 A:PHE202 4.9 16.2 1.0
NE1 A:TRP203 4.9 7.7 1.0
O A:ASP200 5.0 13.5 1.0

Calcium binding site 3 out of 6 in 4h84

Go back to Calcium Binding Sites List in 4h84
Calcium binding site 3 out of 6 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.


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 Selective Carboxylate Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:10.1
occ:1.00
 OD1 A:ASP198 2.3 9.9 1.0
O A:GLY176 2.3 12.4 1.0
OE2 A:GLU201 2.3 20.8 1.0
O A:ILE180 2.3 10.7 0.5
O A:ILE180 2.3 10.7 0.5
O A:GLY178 2.4 14.6 1.0
OD2 A:ASP175 2.4 12.1 1.0
CG A:ASP198 3.4 9.0 1.0
C A:ILE180 3.5 9.6 0.5
C A:ILE180 3.5 9.6 0.5
C A:GLY178 3.5 15.8 1.0
CG A:ASP175 3.5 22.8 1.0
C A:GLY176 3.5 15.7 1.0
CD A:GLU201 3.5 21.5 1.0
N A:GLY178 3.8 13.8 1.0
N A:ILE180 3.9 8.3 0.5
N A:ILE180 4.0 8.3 0.5
OD1 A:ASP175 4.1 15.5 1.0
CB A:ASP198 4.1 6.7 1.0
N A:GLY176 4.1 12.4 1.0
C A:LYS177 4.2 13.5 1.0
CA A:ILE180 4.2 8.7 0.5
C A:GLY179 4.2 12.0 1.0
CA A:ILE180 4.3 8.7 0.5
CA A:GLY178 4.3 16.5 1.0
CG A:GLU201 4.3 11.4 1.0
N A:ASP175 4.4 13.9 1.0
C A:ASP175 4.4 18.7 1.0
OD2 A:ASP198 4.4 7.9 1.0
CA A:LYS177 4.4 15.1 1.0
N A:LYS177 4.4 15.7 1.0
CA A:GLY176 4.4 15.7 1.0
OE1 A:GLU201 4.5 16.5 1.0
N A:GLY179 4.5 13.9 1.0
N A:LEU181 4.5 7.7 1.0
CA A:GLY179 4.6 13.5 1.0
CB A:ILE180 4.7 9.9 0.5
O A:GLY179 4.7 13.7 1.0
CA A:ASP175 4.7 18.1 1.0
CB A:ASP175 4.7 16.7 1.0
CA A:LEU181 4.8 6.7 1.0
O A:ASP175 4.8 20.9 1.0
O A:LYS177 4.8 17.9 1.0
CB A:ILE180 4.8 9.7 0.5

Calcium binding site 4 out of 6 in 4h84

Go back to Calcium Binding Sites List in 4h84
Calcium binding site 4 out of 6 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:18.8
occ:1.00
 O B:GLY192 2.3 12.8 1.0
O B:ASP158 2.3 13.5 1.0
O B:HOH403 2.3 17.8 1.0
O B:GLY190 2.3 16.4 1.0
OD2 B:ASP194 2.7 12.3 1.0
C B:ASP158 3.4 12.5 1.0
C B:GLY192 3.4 13.0 1.0
C B:GLY190 3.5 15.1 1.0
CG B:ASP194 3.6 15.1 1.0
C B:ILE191 3.9 15.0 1.0
N B:GLY192 3.9 14.2 1.0
OD1 B:ASP194 4.0 13.7 1.0
O B:ILE191 4.1 14.3 1.0
CA B:GLY192 4.2 13.0 1.0
CA B:ASP158 4.3 10.9 1.0
N B:ASP194 4.3 12.7 1.0
N B:ILE159 4.3 13.0 1.0
CA B:ILE191 4.4 13.6 1.0
O B:ALA157 4.4 18.2 1.0
N B:ILE191 4.4 14.1 1.0
CA B:ILE159 4.4 11.4 1.0
N B:GLY193 4.4 10.5 1.0
O B:GLY188 4.5 20.2 1.0
CA B:GLY190 4.5 23.7 1.0
N B:GLY190 4.5 20.8 1.0
CA B:GLY193 4.6 11.2 1.0
C B:GLY193 4.7 13.9 1.0
CH2 B:TRP109 4.7 18.2 1.0
CB B:ASP194 4.8 11.9 1.0
N B:LEU160 4.8 10.3 1.0
C B:SER189 4.9 22.2 0.8
O B:HOH436 4.9 23.7 1.0
CA B:ASP194 4.9 10.3 1.0

Calcium binding site 5 out of 6 in 4h84

Go back to Calcium Binding Sites List in 4h84
Calcium binding site 5 out of 6 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:18.3
occ:1.00
 OD2 B:ASP124 2.3 19.7 1.0
O B:GLU199 2.3 17.7 1.0
OE2 B:GLU199 2.4 16.1 1.0
O B:HOH402 2.4 25.6 1.0
O B:GLU201 2.5 15.8 1.0
O B:HOH415 2.5 23.4 1.0
OD1 B:ASP124 2.7 19.6 1.0
CG B:ASP124 2.8 21.6 1.0
CD B:GLU199 3.5 19.7 1.0
C B:GLU199 3.5 17.2 1.0
C B:GLU201 3.7 16.6 1.0
CG B:GLU199 3.9 15.6 1.0
OG1 B:THR122 4.1 15.7 1.0
CA B:GLU199 4.2 15.5 1.0
CA B:PHE202 4.3 17.5 1.0
CB B:ASP124 4.3 18.1 1.0
O B:HOH467 4.4 36.4 1.0
N B:GLU201 4.4 15.1 1.0
CD1 B:TRP203 4.4 12.4 1.0
N B:PHE202 4.5 15.1 1.0
C B:ASP200 4.5 20.9 1.0
N B:ASP200 4.5 14.8 1.0
OE1 B:GLU199 4.6 19.9 1.0
CB B:GLU199 4.7 14.4 1.0
O B:HOH457 4.7 26.4 1.0
NH2 B:ARG165 4.7 22.7 1.0
CA B:ASP200 4.7 12.3 1.0
CA B:GLU201 4.7 13.0 1.0
O B:HOH422 4.8 31.2 1.0
N B:TRP203 4.8 13.5 1.0
NE1 B:TRP203 4.8 15.9 1.0
O B:ASP200 5.0 23.2 1.0

Calcium binding site 6 out of 6 in 4h84

Go back to Calcium Binding Sites List in 4h84
Calcium binding site 6 out of 6 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:14.9
occ:1.00
 O B:GLY176 2.3 16.3 1.0
OD1 B:ASP198 2.3 16.2 1.0
OE2 B:GLU201 2.3 24.0 1.0
O B:ILE180 2.3 15.7 1.0
O B:GLY178 2.3 19.9 1.0
OD2 B:ASP175 2.4 19.2 1.0
CG B:ASP198 3.5 19.3 1.0
C B:GLY176 3.5 25.6 1.0
CD B:GLU201 3.5 17.3 1.0
C B:ILE180 3.5 15.1 1.0
CG B:ASP175 3.5 24.1 1.0
C B:GLY178 3.5 23.3 1.0
N B:GLY178 3.8 22.0 1.0
N B:ILE180 3.9 15.3 1.0
OD1 B:ASP175 4.1 20.1 1.0
N B:GLY176 4.1 24.7 1.0
CB B:ASP198 4.1 12.2 1.0
C B:GLY179 4.2 13.3 1.0
C B:LYS177 4.2 24.6 0.5
CA B:ILE180 4.2 12.4 1.0
C B:LYS177 4.2 24.6 0.5
CG B:GLU201 4.3 17.9 1.0
CA B:GLY178 4.3 20.0 1.0
C B:ASP175 4.4 23.6 1.0
CA B:GLY176 4.4 15.6 1.0
N B:ASP175 4.4 18.2 1.0
N B:LYS177 4.4 22.9 0.5
N B:LYS177 4.4 22.9 0.5
CA B:LYS177 4.4 19.7 0.5
OD2 B:ASP198 4.4 14.7 1.0
OE1 B:GLU201 4.4 20.1 1.0
CA B:LYS177 4.5 19.7 0.5
N B:GLY179 4.5 18.5 1.0
N B:LEU181 4.6 11.7 1.0
CA B:GLY179 4.6 14.9 1.0
CA B:ASP175 4.7 27.9 1.0
CB B:ASP175 4.7 16.2 1.0
CB B:ILE180 4.7 11.9 0.8
O B:GLY179 4.7 21.5 1.0
O B:ASP175 4.8 24.5 1.0
CA B:LEU181 4.8 10.8 1.0
O B:LYS177 4.9 28.1 0.5
O B:LYS177 4.9 28.1 0.5

Reference:

C.Antoni, L.Vera, L.Devel, M.P.Catalani, B.Czarny, E.Cassar-Lajeunesse, E.Nuti, A.Rossello, V.Dive, E.A.Stura. Crystallization of Bi-Functional Ligand Protein Complexes. J.Struct.Biol. V. 182 246 2013.
ISSN: ISSN 1047-8477
PubMed: 23567804
DOI: 10.1016/J.JSB.2013.03.015
Page generated: Sun Jul 14 07:45:14 2024

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