Calcium in PDB 4h76: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor, PDB code: 4h76 was solved by E.A.Stura, 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) 46.76 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.920, 62.890, 37.700, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.8

Other elements in 4h76:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor also contains other interesting chemical elements:

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 Broad Spectrum Hydroxamate Inhibitor (pdb code 4h76). 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 Broad Spectrum Hydroxamate Inhibitor, PDB code: 4h76:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4h76

Go back to Calcium Binding Sites List in 4h76
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate 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 Broad Spectrum Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:11.4
occ:1.00
 O A:HOH408 2.3 14.9 1.0
O A:GLY190 2.3 12.5 1.0
O A:GLY192 2.3 10.4 1.0
O A:ASP158 2.4 9.5 1.0
O A:HOH412 2.4 14.8 1.0
OD1 A:ASP194 2.4 10.4 1.0
CG A:ASP194 3.4 9.6 1.0
C A:GLY192 3.5 10.3 1.0
C A:GLY190 3.5 13.2 1.0
C A:ASP158 3.5 9.4 1.0
OD2 A:ASP194 3.8 11.1 1.0
C A:ILE191 4.0 12.7 1.0
O A:HOH502 4.0 25.3 1.0
N A:GLY192 4.1 11.8 1.0
O A:ILE191 4.2 10.2 1.0
O A:ALA157 4.2 13.3 1.0
N A:ASP194 4.2 9.7 1.0
CA A:ILE191 4.3 11.7 0.9
CA A:ASP158 4.4 7.4 1.0
CA A:GLY192 4.4 14.3 1.0
CA A:ILE191 4.4 11.9 0.1
O A:GLY188 4.4 15.3 1.0
N A:ILE191 4.4 12.2 1.0
N A:GLY193 4.5 10.7 1.0
N A:ILE159 4.5 9.9 1.0
CA A:GLY190 4.5 15.3 1.0
N A:GLY190 4.5 17.2 1.0
CA A:GLY193 4.6 11.2 1.0
CA A:ILE159 4.6 8.2 1.0
N A:LEU160 4.6 9.0 1.0
CB A:ASP194 4.6 8.6 1.0
C A:GLY193 4.6 10.5 1.0
CA A:ASP194 4.8 7.2 1.0
C A:SER189 4.8 13.8 1.0
O A:HOH531 4.9 20.9 1.0
CH2 A:TRP109 4.9 12.8 1.0

Calcium binding site 2 out of 3 in 4h76

Go back to Calcium Binding Sites List in 4h76
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate 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 Broad Spectrum Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:14.9
occ:1.00
 O A:GLU199 2.3 12.8 1.0
O A:HOH468 2.4 19.3 1.0
OD2 A:ASP124 2.4 15.4 1.0
O A:GLU201 2.4 13.3 1.0
OE2 A:GLU199 2.4 15.2 1.0
O A:HOH421 2.4 19.9 1.0
OD1 A:ASP124 2.7 16.4 1.0
CG A:ASP124 2.9 18.4 1.0
C A:GLU199 3.4 11.4 1.0
CD A:GLU199 3.5 14.2 1.0
C A:GLU201 3.6 12.7 1.0
CG A:GLU199 3.9 14.3 1.0
OG1 A:THR122 4.1 16.1 1.0
CA A:GLU199 4.1 13.1 1.0
CA A:PHE202 4.2 15.4 1.0
N A:PHE202 4.4 14.0 1.0
CD1 A:TRP203 4.4 10.0 1.0
CB A:ASP124 4.4 16.1 1.0
N A:GLU201 4.4 12.0 1.0
O A:HOH519 4.5 30.5 1.0
N A:ASP200 4.5 11.9 1.0
C A:ASP200 4.5 14.8 1.0
OE1 A:GLU199 4.6 15.2 1.0
CB A:GLU199 4.6 10.6 1.0
O A:HOH474 4.6 23.9 1.0
CA A:ASP200 4.7 12.3 1.0
CA A:GLU201 4.7 13.6 1.0
O A:HOH482 4.7 26.4 1.0
O A:HOH488 4.8 21.6 1.0
O A:HOH407 4.8 25.1 1.0
N A:TRP203 4.8 12.3 1.0
CD1 A:PHE202 4.8 20.5 1.0
NE1 A:TRP203 4.9 13.2 1.0

Calcium binding site 3 out of 3 in 4h76

Go back to Calcium Binding Sites List in 4h76
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate 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 Broad Spectrum Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:11.2
occ:1.00
 O A:GLY176 2.3 14.1 1.0
O A:ILE180 2.3 10.3 1.0
OD2 A:ASP198 2.3 12.6 1.0
O A:GLY178 2.3 14.2 1.0
OD1 A:ASP175 2.4 13.0 1.0
OE2 A:GLU201 2.4 20.1 1.0
C A:ILE180 3.5 9.2 1.0
CG A:ASP198 3.5 13.3 1.0
C A:GLY176 3.5 17.5 1.0
C A:GLY178 3.5 18.1 1.0
CG A:ASP175 3.5 12.2 1.0
CD A:GLU201 3.6 19.6 1.0
N A:ILE180 3.9 11.0 1.0
N A:GLY178 3.9 16.2 1.0
OD2 A:ASP175 4.1 12.7 1.0
N A:GLY176 4.1 11.8 1.0
CB A:ASP198 4.2 7.7 1.0
CA A:ILE180 4.2 8.6 1.0
C A:GLY179 4.2 11.8 1.0
C A:ASP175 4.3 11.9 1.0
C A:LYS177 4.3 15.4 1.0
CG A:GLU201 4.3 13.6 1.0
CA A:GLY178 4.3 18.6 1.0
N A:ASP175 4.3 13.1 1.0
CA A:GLY176 4.4 16.0 1.0
OD1 A:ASP198 4.4 9.3 1.0
N A:LYS177 4.4 16.8 1.0
N A:GLY179 4.5 12.9 1.0
CA A:LYS177 4.5 18.3 1.0
N A:LEU181 4.5 8.8 1.0
OE1 A:GLU201 4.6 19.6 1.0
CA A:GLY179 4.6 12.1 1.0
CA A:ASP175 4.6 11.0 1.0
CB A:ILE180 4.6 11.5 1.0
O A:ASP175 4.7 14.3 1.0
O A:GLY179 4.7 15.3 1.0
CB A:ASP175 4.7 11.0 1.0
CA A:LEU181 4.8 9.3 1.0
O A:LYS177 5.0 24.2 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: Sat Dec 12 04:49:57 2020

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