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Calcium in PDB 4h49: 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: 4h49 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) 47.26 / 2.16
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.440, 106.490, 65.880, 90.00, 94.96, 90.00
R / Rfree (%) 16.7 / 24.1

Other elements in 4h49:

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) 8 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

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 4h49). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 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: 4h49:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 4h49

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Calcium binding site 1 out of 12 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:19.9
occ:1.00
 O A:HOH432 2.2 21.1 1.0
O A:GLY192 2.2 15.6 1.0
O A:ASP158 2.4 11.3 1.0
O A:GLY190 2.4 17.9 1.0
O A:HOH431 2.4 15.1 1.0
OD1 A:ASP194 2.6 12.3 1.0
C A:GLY192 3.4 14.9 1.0
C A:ASP158 3.4 14.7 1.0
CG A:ASP194 3.5 18.8 1.0
C A:GLY190 3.6 20.8 1.0
C A:ILE191 3.9 14.2 1.0
N A:GLY192 3.9 21.1 1.0
OD2 A:ASP194 3.9 16.8 1.0
O A:ILE191 4.2 17.8 1.0
N A:ASP194 4.2 9.9 1.0
CA A:GLY192 4.2 14.9 1.0
CA A:ILE191 4.2 18.5 1.0
CA A:ASP158 4.3 13.3 1.0
O A:ALA157 4.3 21.1 1.0
N A:ILE159 4.3 11.1 1.0
N A:ILE191 4.3 16.5 1.0
N A:GLY193 4.4 15.5 1.0
O A:GLY188 4.4 15.6 1.0
CA A:ILE159 4.5 10.2 1.0
CA A:GLY193 4.5 10.9 1.0
C A:GLY193 4.6 14.7 1.0
CA A:GLY190 4.6 22.4 1.0
N A:GLY190 4.6 18.5 1.0
CB A:ASP194 4.7 11.7 1.0
N A:LEU160 4.7 11.2 1.0
CA A:ASP194 4.9 14.9 1.0
C A:SER189 4.9 18.1 1.0
CH2 A:TRP109 4.9 18.4 1.0

Calcium binding site 2 out of 12 in 4h49

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Calcium binding site 2 out of 12 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:17.2
occ:1.00
 O A:GLU199 2.3 14.3 1.0
O A:GLU201 2.4 16.0 1.0
OD1 A:ASP124 2.4 12.9 1.0
O A:HOH408 2.4 21.3 1.0
O A:HOH409 2.5 21.8 1.0
OE2 A:GLU199 2.5 16.1 1.0
OD2 A:ASP124 2.7 20.8 1.0
CG A:ASP124 2.9 14.8 1.0
C A:GLU199 3.5 13.5 1.0
C A:GLU201 3.6 13.7 1.0
CD A:GLU199 3.6 22.3 1.0
CG A:GLU199 3.9 19.2 1.0
OG1 A:THR122 4.1 15.3 1.0
CA A:PHE202 4.2 12.3 1.0
CA A:GLU199 4.2 15.1 1.0
N A:PHE202 4.3 11.6 1.0
N A:GLU201 4.4 13.6 1.0
CD1 A:TRP203 4.4 12.7 1.0
CB A:ASP124 4.4 14.8 1.0
C A:ASP200 4.5 17.9 1.0
N A:ASP200 4.5 10.6 1.0
CA A:ASP200 4.6 16.2 1.0
CA A:GLU201 4.6 13.4 1.0
CB A:GLU199 4.7 17.5 1.0
OE1 A:GLU199 4.7 19.2 1.0
N A:TRP203 4.7 16.9 1.0
NE1 A:TRP203 4.9 11.5 1.0
O A:ASP200 4.9 18.4 1.0

Calcium binding site 3 out of 12 in 4h49

Go back to Calcium Binding Sites List in 4h49
Calcium binding site 3 out of 12 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:14.2
occ:1.00
 OE2 A:GLU201 2.2 20.8 1.0
OD2 A:ASP198 2.3 9.4 1.0
O A:GLY178 2.3 18.7 1.0
OD1 A:ASP175 2.3 15.8 1.0
O A:ILE180 2.4 17.1 1.0
O A:GLY176 2.5 16.8 1.0
CG A:ASP198 3.3 14.5 1.0
CD A:GLU201 3.4 18.3 1.0
C A:GLY178 3.5 21.7 1.0
C A:ILE180 3.5 17.9 1.0
CG A:ASP175 3.5 18.6 1.0
C A:GLY176 3.7 24.1 1.0
N A:GLY178 3.9 19.1 1.0
CB A:ASP198 3.9 11.7 1.0
N A:ILE180 4.1 17.8 1.0
N A:GLY176 4.2 18.8 1.0
OD2 A:ASP175 4.2 19.9 1.0
N A:ASP175 4.2 17.8 1.0
CG A:GLU201 4.2 16.2 1.0
C A:GLY179 4.2 19.5 1.0
C A:LYS177 4.2 24.5 1.0
CA A:GLY178 4.2 16.0 1.0
OD1 A:ASP198 4.3 12.3 1.0
C A:ASP175 4.3 17.9 1.0
OE1 A:GLU201 4.3 20.6 1.0
CA A:ILE180 4.3 15.1 1.0
N A:GLY179 4.4 17.2 1.0
N A:LEU181 4.5 10.0 1.0
CA A:LYS177 4.5 22.6 1.0
CA A:ASP175 4.5 17.9 1.0
O A:GLY179 4.5 16.1 1.0
CA A:LEU181 4.6 11.2 1.0
N A:LYS177 4.6 17.9 1.0
CA A:GLY179 4.6 18.2 1.0
CA A:GLY176 4.6 14.4 1.0
CB A:ASP175 4.6 19.1 1.0
O A:ASP175 4.7 19.7 1.0
CB A:ILE180 4.8 15.6 1.0
O A:LYS177 4.8 29.6 1.0

Calcium binding site 4 out of 12 in 4h49

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Calcium binding site 4 out of 12 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:Ca604

b:31.4
occ:1.00
 O B:ASP158 2.4 17.6 1.0
O B:HOH735 2.4 26.2 1.0
O B:GLY192 2.4 19.5 1.0
O B:GLY190 2.5 27.2 1.0
OD1 B:ASP194 2.6 22.2 1.0
C B:ASP158 3.4 20.9 1.0
C B:GLY192 3.6 24.4 1.0
CG B:ASP194 3.6 24.7 1.0
C B:GLY190 3.7 36.5 1.0
C B:ILE191 4.0 23.9 1.0
N B:GLY192 4.0 23.2 1.0
O B:ALA157 4.1 22.4 1.0
OD2 B:ASP194 4.1 29.4 1.0
O B:ILE191 4.2 26.2 1.0
CA B:ASP158 4.2 20.8 1.0
CA B:GLY192 4.3 25.9 1.0
N B:ASP194 4.4 17.4 1.0
N B:ILE159 4.4 15.4 1.0
O B:GLY188 4.4 37.5 1.0
CA B:ILE191 4.5 25.8 1.0
N B:ILE191 4.5 24.6 1.0
N B:GLY190 4.5 43.3 1.0
CA B:ILE159 4.5 17.4 1.0
N B:GLY193 4.6 23.5 1.0
CA B:GLY190 4.6 29.7 1.0
N B:LEU160 4.6 18.9 1.0
C B:SER189 4.8 35.6 1.0
CA B:GLY193 4.8 17.8 1.0
CB B:ASP194 4.8 21.5 1.0
C B:GLY193 4.8 20.4 1.0
CA B:ASP194 4.9 16.6 1.0
O B:HOH736 5.0 33.2 1.0
C B:ALA157 5.0 19.3 1.0

Calcium binding site 5 out of 12 in 4h49

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Calcium binding site 5 out of 12 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:Ca605

b:31.3
occ:1.00
 O B:GLU199 2.1 22.6 1.0
OD1 B:ASP124 2.4 28.7 1.0
O B:GLU201 2.4 24.7 1.0
O B:HOH708 2.7 23.3 1.0
OE2 B:GLU199 2.8 26.8 1.0
CG B:ASP124 3.2 26.6 1.0
OD2 B:ASP124 3.3 34.7 1.0
C B:GLU199 3.3 26.3 1.0
C B:GLU201 3.6 20.2 1.0
CD B:GLU199 3.8 34.2 1.0
CA B:GLU199 4.0 21.7 1.0
CG B:GLU199 4.0 28.0 1.0
OG1 B:THR122 4.1 29.7 1.0
C B:ASP200 4.2 26.3 1.0
N B:GLU201 4.2 20.0 1.0
CD1 B:TRP203 4.2 19.6 1.0
CA B:PHE202 4.3 22.2 1.0
N B:ASP200 4.3 26.4 1.0
N B:PHE202 4.4 18.8 1.0
CA B:ASP200 4.4 23.5 1.0
O B:ASP200 4.5 21.5 1.0
CA B:GLU201 4.6 15.0 1.0
CB B:ASP124 4.6 27.0 1.0
NE1 B:TRP203 4.6 15.1 1.0
CB B:GLU199 4.6 19.6 1.0
NH1 B:ARG165 4.6 34.0 1.0
N B:TRP203 4.8 23.5 1.0
O B:ASP198 5.0 16.0 1.0
OE1 B:GLU199 5.0 33.0 1.0

Calcium binding site 6 out of 12 in 4h49

Go back to Calcium Binding Sites List in 4h49
Calcium binding site 6 out of 12 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:Ca606

b:26.3
occ:1.00
 OE2 B:GLU201 2.2 20.9 1.0
O B:GLY176 2.3 30.7 1.0
OD2 B:ASP198 2.4 23.9 1.0
O B:GLY178 2.4 30.4 1.0
OD1 B:ASP175 2.4 27.1 1.0
O B:ILE180 2.4 24.9 1.0
CD B:GLU201 3.4 22.7 1.0
C B:GLY176 3.5 27.4 1.0
CG B:ASP198 3.5 31.8 1.0
C B:ILE180 3.6 24.1 1.0
C B:GLY178 3.6 20.6 1.0
CG B:ASP175 3.6 30.3 1.0
N B:GLY178 3.9 24.9 1.0
N B:ILE180 4.0 26.1 1.0
N B:GLY176 4.1 31.6 1.0
C B:LYS177 4.2 36.8 1.0
CB B:ASP198 4.2 23.8 1.0
CA B:ILE180 4.2 27.6 1.0
C B:GLY179 4.2 28.9 1.0
C B:ASP175 4.2 27.0 1.0
CG B:GLU201 4.3 20.6 1.0
N B:ASP175 4.3 26.0 1.0
OD2 B:ASP175 4.3 30.7 1.0
OE1 B:GLU201 4.3 20.9 1.0
CA B:GLY178 4.4 20.0 1.0
N B:LYS177 4.4 30.5 1.0
CA B:GLY176 4.4 24.0 1.0
CA B:LYS177 4.5 29.7 1.0
CB B:ILE180 4.5 25.1 1.0
OD1 B:ASP198 4.5 28.8 1.0
N B:GLY179 4.5 19.0 1.0
CA B:ASP175 4.6 25.9 1.0
O B:ASP175 4.6 34.0 1.0
CA B:GLY179 4.6 15.8 1.0
O B:LYS177 4.6 30.1 1.0
N B:LEU181 4.7 22.5 1.0
O B:GLY179 4.7 18.6 1.0
CB B:ASP175 4.7 32.4 1.0
O B:HOH722 4.9 29.7 1.0
CA B:LEU181 4.9 19.4 1.0

Calcium binding site 7 out of 12 in 4h49

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Calcium binding site 7 out of 12 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 7 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
C:Ca303

b:28.0
occ:1.00
 O C:HOH413 2.3 24.3 1.0
O C:GLY190 2.4 27.4 1.0
O C:ASP158 2.4 29.5 1.0
OD1 C:ASP194 2.5 18.5 1.0
O C:GLY192 2.5 19.7 1.0
CG C:ASP194 3.4 29.1 1.0
C C:ASP158 3.5 27.4 1.0
C C:GLY190 3.6 36.2 1.0
OD2 C:ASP194 3.7 21.7 1.0
C C:GLY192 3.7 24.7 1.0
C C:ILE191 4.0 25.5 1.0
N C:GLY192 4.1 26.9 1.0
O C:ALA157 4.2 25.8 1.0
O C:GLY188 4.3 29.9 1.0
O C:ILE191 4.3 25.4 1.0
CA C:ASP158 4.3 21.0 1.0
CA C:ILE191 4.3 34.9 1.0
N C:ASP194 4.3 20.4 1.0
N C:ILE191 4.4 33.5 1.0
CA C:GLY192 4.4 20.9 1.0
N C:ILE159 4.4 23.9 1.0
N C:GLY190 4.5 33.0 1.0
CA C:GLY190 4.6 25.4 1.0
N C:LEU160 4.6 19.6 1.0
CA C:ILE159 4.6 22.6 1.0
N C:GLY193 4.7 19.8 1.0
CB C:ASP194 4.7 24.2 1.0
C C:SER189 4.8 32.0 1.0
CA C:GLY193 4.8 18.3 1.0
C C:GLY193 4.8 24.2 1.0
CA C:ASP194 4.9 18.5 1.0
CH2 C:TRP109 4.9 25.1 1.0
O C:SER189 5.0 35.8 1.0

Calcium binding site 8 out of 12 in 4h49

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Calcium binding site 8 out of 12 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 8 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
C:Ca304

b:28.6
occ:1.00
 O C:GLU201 2.3 23.0 1.0
OD1 C:ASP124 2.4 23.1 1.0
O C:GLU199 2.4 18.9 1.0
OE2 C:GLU199 2.6 24.1 1.0
OD2 C:ASP124 2.8 27.2 1.0
CG C:ASP124 3.0 26.7 1.0
C C:GLU201 3.5 21.9 1.0
C C:GLU199 3.5 22.6 1.0
CD C:GLU199 3.7 28.7 1.0
CG C:GLU199 4.2 32.2 1.0
N C:GLU201 4.2 21.5 1.0
CA C:PHE202 4.3 24.4 1.0
CA C:GLU199 4.3 21.4 1.0
OG1 C:THR122 4.3 23.6 1.0
CD1 C:TRP203 4.3 20.5 1.0
C C:ASP200 4.3 25.3 1.0
N C:PHE202 4.3 20.2 1.0
CB C:ASP124 4.5 18.8 1.0
N C:ASP200 4.5 20.4 1.0
CA C:GLU201 4.5 14.7 1.0
CA C:ASP200 4.6 25.5 1.0
O C:ASP200 4.7 23.3 1.0
N C:TRP203 4.8 23.9 1.0
OE1 C:GLU199 4.8 31.8 1.0
NE1 C:TRP203 4.8 20.8 1.0
CB C:GLU199 4.9 24.4 1.0
NH1 C:ARG165 5.0 27.8 1.0

Calcium binding site 9 out of 12 in 4h49

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Calcium binding site 9 out of 12 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 9 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
C:Ca305

b:19.6
occ:1.00
 O C:GLY176 2.3 27.0 1.0
OE1 C:GLU201 2.3 24.9 1.0
OD2 C:ASP198 2.4 19.5 1.0
O C:GLY178 2.4 20.6 1.0
O C:ILE180 2.4 20.1 1.0
OD1 C:ASP175 2.4 21.6 1.0
C C:GLY178 3.4 27.3 1.0
CG C:ASP198 3.5 21.3 1.0
CG C:ASP175 3.5 28.4 1.0
C C:GLY176 3.5 25.3 1.0
C C:ILE180 3.5 17.5 1.0
CD C:GLU201 3.5 21.1 1.0
N C:ILE180 3.8 19.4 1.0
N C:GLY178 3.8 26.7 1.0
OD2 C:ASP175 4.0 25.0 1.0
N C:GLY176 4.1 23.5 1.0
CA C:ILE180 4.1 20.2 1.0
CB C:ASP198 4.1 17.1 1.0
C C:LYS177 4.1 25.8 0.5
C C:LYS177 4.2 25.8 0.5
C C:GLY179 4.2 23.5 1.0
CA C:GLY178 4.2 19.9 1.0
N C:ASP175 4.3 27.1 1.0
C C:ASP175 4.3 23.2 1.0
CG C:GLU201 4.4 18.0 1.0
N C:GLY179 4.4 21.3 1.0
OD1 C:ASP198 4.4 20.4 1.0
CA C:GLY176 4.4 23.3 1.0
OE2 C:GLU201 4.4 17.9 1.0
N C:LYS177 4.4 25.1 0.5
N C:LYS177 4.4 25.1 0.5
CB C:ILE180 4.5 20.5 1.0
CA C:LYS177 4.5 21.8 0.5
CA C:LYS177 4.5 21.8 0.5
CA C:GLY179 4.5 20.2 1.0
N C:LEU181 4.6 15.3 1.0
CA C:ASP175 4.6 21.6 1.0
CB C:ASP175 4.7 19.2 1.0
O C:LYS177 4.7 25.7 0.5
O C:LYS177 4.7 25.7 0.5
O C:ASP175 4.8 27.6 1.0
O C:GLY179 4.8 17.7 1.0
CA C:LEU181 4.9 14.2 1.0
O C:HOH405 5.0 18.4 1.0

Calcium binding site 10 out of 12 in 4h49

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Calcium binding site 10 out of 12 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 10 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
D:Ca303

b:26.0
occ:1.00
 O D:GLY190 2.2 29.2 1.0
O D:GLY192 2.3 15.5 1.0
O D:ASP158 2.4 26.0 1.0
OD1 D:ASP194 2.6 18.6 1.0
O D:HOH410 2.6 15.9 1.0
C D:GLY190 3.4 22.6 1.0
CG D:ASP194 3.4 22.1 1.0
C D:GLY192 3.5 15.8 1.0
C D:ASP158 3.6 23.6 1.0
OD2 D:ASP194 3.8 23.4 1.0
C D:ILE191 3.8 17.9 1.0
N D:GLY192 3.9 19.2 1.0
O D:ILE191 4.0 19.6 1.0
CA D:GLY192 4.2 19.0 1.0
N D:ASP194 4.2 14.9 1.0
O D:ALA157 4.3 35.7 1.0
CA D:ILE191 4.3 16.4 1.0
N D:ILE191 4.3 18.4 1.0
O D:GLY188 4.4 28.1 1.0
CA D:GLY190 4.4 19.9 1.0
N D:GLY190 4.4 25.2 1.0
CA D:ASP158 4.4 26.4 1.0
N D:GLY193 4.5 15.6 1.0
N D:ILE159 4.5 16.2 1.0
CA D:ILE159 4.6 20.0 1.0
N D:LEU160 4.6 19.2 1.0
CA D:GLY193 4.6 16.5 1.0
CB D:ASP194 4.7 19.6 1.0
C D:SER189 4.7 23.9 1.0
C D:GLY193 4.7 18.5 1.0
O D:HOH474 4.8 32.9 1.0
CA D:ASP194 4.8 20.4 1.0
O D:SER189 4.9 21.3 1.0
CH2 D:TRP109 4.9 25.2 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 07:38:04 2024

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