Atomistry » Calcium » PDB 4gzt-4h82 » 4h30
Atomistry »
  Calcium »
    PDB 4gzt-4h82 »
      4h30 »

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: Sat Dec 12 04:49:46 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy