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Calcium in PDB 4h30: Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor., PDB code: 4h30 was solved by C.Antoni, E.A.Stura, L.Vera, E.Nuti, L.Carafa, E.Cassar-Lajeunesse, V.Dive, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.31 / 1.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.910, 61.750, 112.560, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.7

Other elements in 4h30:

The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. (pdb code 4h30). 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 Mmp-12 in Complex with A Twin Inhibitor., PDB code: 4h30:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4h30

Go back to Calcium Binding Sites List in 4h30
Calcium binding site 1 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:11.8
occ:1.00
 O A:GLY192 2.3 11.6 1.0
O A:GLY190 2.3 13.0 1.0
O A:ASP158 2.3 12.3 1.0
O A:HOH424 2.4 17.8 1.0
O A:HOH416 2.4 14.9 1.0
OD1 A:ASP194 2.4 11.0 1.0
CG A:ASP194 3.4 11.9 1.0
C A:GLY192 3.5 12.2 1.0
C A:ASP158 3.5 10.9 1.0
C A:GLY190 3.5 14.1 1.0
OD2 A:ASP194 3.8 13.4 1.0
C A:ILE191 3.9 11.9 1.0
N A:GLY192 4.0 13.5 1.0
O A:HOH605 4.1 29.2 1.0
O A:ILE191 4.1 12.3 1.0
N A:ASP194 4.3 10.5 1.0
O A:ALA157 4.3 15.7 1.0
CA A:GLY192 4.3 12.7 1.0
CA A:ASP158 4.3 11.7 1.0
CA A:ILE191 4.3 13.9 1.0
N A:ILE191 4.4 12.8 1.0
O A:GLY188 4.4 15.6 1.0
N A:GLY190 4.4 16.4 1.0
CA A:GLY190 4.4 16.0 1.0
N A:ILE159 4.5 10.7 1.0
N A:GLY193 4.5 10.7 1.0
O A:HOH402 4.5 33.7 1.0
CA A:ILE159 4.6 10.3 1.0
CA A:GLY193 4.6 11.7 1.0
CB A:ASP194 4.6 13.7 1.0
N A:LEU160 4.6 11.1 1.0
C A:GLY193 4.7 11.1 1.0
C A:SER189 4.7 16.9 1.0
O A:HOH444 4.8 17.3 1.0
CA A:ASP194 4.8 11.0 1.0
O A:SER189 4.9 16.6 1.0
CH2 A:TRP109 4.9 14.3 1.0

Calcium binding site 2 out of 6 in 4h30

Go back to Calcium Binding Sites List in 4h30
Calcium binding site 2 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:17.0
occ:1.00
 O A:GLU199 2.3 15.2 1.0
OD2 A:ASP124 2.4 14.4 1.0
O A:HOH405 2.4 22.1 1.0
OE2 A:GLU199 2.4 17.8 1.0
O A:GLU201 2.4 15.3 1.0
O A:HOH404 2.5 18.8 1.0
OD1 A:ASP124 2.7 19.4 1.0
CG A:ASP124 2.9 18.1 1.0
C A:GLU199 3.4 13.6 1.0
CD A:GLU199 3.5 17.9 1.0
C A:GLU201 3.6 14.1 1.0
CG A:GLU199 3.9 17.3 1.0
OG1 A:THR122 4.1 16.6 1.0
CA A:GLU199 4.1 14.7 1.0
CA A:PHE202 4.3 14.1 1.0
CD1 A:TRP203 4.3 12.2 1.0
O A:HOH616 4.4 36.2 1.0
CB A:ASP124 4.4 14.9 1.0
N A:PHE202 4.4 15.4 1.0
N A:GLU201 4.4 13.7 1.0
C A:ASP200 4.5 16.9 1.0
N A:ASP200 4.5 13.0 1.0
O A:HOH548 4.5 28.5 1.0
OE1 A:GLU199 4.6 18.6 1.0
O A:HOH452 4.6 28.5 1.0
CA A:ASP200 4.6 14.3 1.0
CB A:GLU199 4.7 14.8 1.0
CA A:GLU201 4.7 12.9 1.0
N A:TRP203 4.8 13.2 1.0
O A:HOH617 4.8 43.2 1.0
NE1 A:TRP203 4.8 12.4 1.0
NH2 A:ARG165 4.8 31.1 1.0
O A:HOH472 4.9 30.3 1.0
O A:ASP200 4.9 16.9 1.0
CD1 A:PHE202 4.9 21.3 1.0

Calcium binding site 3 out of 6 in 4h30

Go back to Calcium Binding Sites List in 4h30
Calcium binding site 3 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:12.1
occ:1.00
 OE2 A:GLU201 2.3 20.1 1.0
O A:ILE180 2.3 12.8 1.0
OD2 A:ASP198 2.3 13.0 1.0
O A:GLY176 2.3 15.0 1.0
O A:GLY178 2.3 16.0 1.0
OD1 A:ASP175 2.4 14.2 1.0
CG A:ASP198 3.4 13.1 1.0
C A:ILE180 3.5 12.2 1.0
CD A:GLU201 3.5 17.4 1.0
C A:GLY178 3.5 17.6 1.0
CG A:ASP175 3.5 15.1 1.0
C A:GLY176 3.5 16.2 1.0
N A:GLY178 3.8 16.7 1.0
N A:ILE180 3.9 12.8 1.0
OD2 A:ASP175 4.1 15.5 1.0
CB A:ASP198 4.1 12.3 1.0
N A:GLY176 4.1 15.7 1.0
C A:GLY179 4.2 12.2 1.0
CA A:ILE180 4.2 10.7 1.0
C A:LYS177 4.2 18.5 1.0
CG A:GLU201 4.2 15.2 1.0
C A:ASP175 4.3 15.8 1.0
CA A:GLY178 4.3 18.3 1.0
N A:ASP175 4.3 13.5 1.0
OD1 A:ASP198 4.4 13.0 1.0
CA A:LYS177 4.4 15.5 1.0
CA A:GLY176 4.4 14.9 1.0
N A:LYS177 4.4 17.3 1.0
OE1 A:GLU201 4.4 16.8 1.0
N A:GLY179 4.5 14.9 1.0
N A:LEU181 4.5 11.1 1.0
CA A:GLY179 4.6 13.4 1.0
O A:GLY179 4.6 13.9 1.0
CB A:ILE180 4.6 12.9 1.0
CA A:ASP175 4.6 15.3 1.0
CB A:ASP175 4.7 14.9 1.0
CA A:LEU181 4.7 11.1 1.0
O A:ASP175 4.7 18.8 1.0
O A:LYS177 4.9 20.3 1.0

Calcium binding site 4 out of 6 in 4h30

Go back to Calcium Binding Sites List in 4h30
Calcium binding site 4 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:13.0
occ:0.43
 O B:GLY192 2.3 17.4 1.0
O B:ASP158 2.3 13.0 1.0
O B:GLY190 2.4 18.6 1.0
O B:HOH442 2.5 23.1 1.0
OD1 B:ASP194 2.7 11.1 1.0
C B:GLY192 3.4 16.1 1.0
C B:ASP158 3.4 11.7 1.0
C B:GLY190 3.6 19.1 1.0
CG B:ASP194 3.7 10.9 1.0
C B:ILE191 3.8 20.1 1.0
N B:GLY192 3.9 16.5 1.0
O B:ALA157 4.0 16.1 1.0
O B:ILE191 4.1 16.7 1.0
OD2 B:ASP194 4.1 12.3 1.0
N B:ASP194 4.1 10.8 1.0
CA B:GLY192 4.2 14.5 1.0
CA B:ILE191 4.2 14.2 0.8
CA B:ASP158 4.2 10.6 1.0
N B:ILE191 4.3 21.1 1.0
N B:ILE159 4.3 10.8 1.0
N B:GLY193 4.4 15.5 1.0
O B:GLY188 4.4 21.3 1.0
O B:HOH616 4.5 35.2 1.0
CA B:ILE159 4.5 11.8 1.0
CA B:GLY193 4.5 14.6 1.0
C B:GLY193 4.6 10.3 1.0
CA B:GLY190 4.6 22.0 1.0
N B:GLY190 4.7 20.9 1.0
N B:LEU160 4.7 10.1 1.0
CB B:ASP194 4.7 11.7 1.0
CH2 B:TRP109 4.8 16.8 1.0
CA B:ASP194 4.8 10.6 1.0
C B:SER189 4.9 23.0 1.0
O B:HOH441 4.9 25.5 1.0
C B:ALA157 5.0 13.4 1.0
O B:SER189 5.0 21.6 1.0

Calcium binding site 5 out of 6 in 4h30

Go back to Calcium Binding Sites List in 4h30
Calcium binding site 5 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:15.8
occ:1.00
 O B:GLU199 2.3 15.9 1.0
O B:HOH408 2.3 17.2 1.0
O B:HOH407 2.4 18.7 1.0
OE2 B:GLU199 2.4 16.5 1.0
O B:GLU201 2.4 14.2 1.0
OD2 B:ASP124 2.4 14.5 1.0
OD1 B:ASP124 2.7 16.3 1.0
CG B:ASP124 2.9 15.9 1.0
C B:GLU199 3.4 13.8 1.0
CD B:GLU199 3.5 19.1 1.0
C B:GLU201 3.6 12.6 1.0
CG B:GLU199 3.9 17.1 1.0
OG1 B:THR122 4.1 13.9 1.0
CA B:GLU199 4.1 14.6 1.0
CA B:PHE202 4.2 11.2 1.0
CD1 B:TRP203 4.3 11.4 1.0
N B:GLU201 4.4 13.7 1.0
N B:PHE202 4.4 12.4 1.0
C B:ASP200 4.4 16.9 1.0
CB B:ASP124 4.4 14.4 1.0
O B:HOH462 4.4 24.6 1.0
N B:ASP200 4.4 13.3 1.0
O B:HOH504 4.5 26.2 1.0
OE1 B:GLU199 4.6 18.5 1.0
CA B:ASP200 4.6 14.4 1.0
CA B:GLU201 4.6 11.8 1.0
O B:HOH409 4.6 18.9 1.0
CB B:GLU199 4.7 15.3 1.0
N B:TRP203 4.8 12.6 1.0
NE1 B:TRP203 4.8 12.2 1.0
CD1 B:PHE202 4.8 15.9 1.0
O B:ASP200 4.9 16.4 1.0
O B:HOH505 4.9 26.1 1.0
O B:HOH503 5.0 44.7 1.0

Calcium binding site 6 out of 6 in 4h30

Go back to Calcium Binding Sites List in 4h30
Calcium binding site 6 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:13.2
occ:1.00
 OD2 B:ASP198 2.2 13.3 1.0
O B:ILE180 2.3 12.5 1.0
O B:GLY176 2.3 15.0 1.0
O B:GLY178 2.4 14.5 1.0
OE2 B:GLU201 2.4 16.3 1.0
OD1 B:ASP175 2.4 14.2 1.0
CG B:ASP198 3.4 14.1 1.0
C B:ILE180 3.4 12.3 1.0
CD B:GLU201 3.5 15.0 1.0
C B:GLY176 3.5 19.0 1.0
C B:GLY178 3.5 15.8 1.0
CG B:ASP175 3.6 15.6 1.0
N B:GLY178 3.8 15.4 1.0
N B:ILE180 3.9 12.4 1.0
OD2 B:ASP175 4.1 16.8 1.0
CA B:ILE180 4.1 12.2 1.0
CG B:GLU201 4.1 13.1 1.0
CB B:ASP198 4.2 11.7 1.0
N B:GLY176 4.2 16.1 1.0
C B:GLY179 4.2 12.6 1.0
C B:LYS177 4.2 16.7 1.0
C B:ASP175 4.3 18.0 1.0
CA B:GLY178 4.3 19.1 1.0
OD1 B:ASP198 4.3 13.8 1.0
N B:ASP175 4.3 15.3 1.0
CA B:LYS177 4.3 16.3 1.0
N B:LYS177 4.4 19.8 1.0
CA B:GLY176 4.5 15.3 1.0
N B:LEU181 4.5 10.9 1.0
OE1 B:GLU201 4.5 15.2 1.0
N B:GLY179 4.5 16.4 1.0
CB B:ILE180 4.6 13.9 1.0
O B:GLY179 4.6 15.9 1.0
CA B:ASP175 4.6 17.7 1.0
CA B:GLY179 4.7 16.1 1.0
O B:ASP175 4.7 19.7 1.0
CB B:ASP175 4.7 18.5 1.0
CA B:LEU181 4.8 10.6 1.0

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 07:36:56 2024

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