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Calcium in PDB 3ts4: Human MMP12 in Complex with L-Glutamate Motif Inhibitor

Enzymatic activity of Human MMP12 in Complex with L-Glutamate Motif Inhibitor

All present enzymatic activity of Human MMP12 in Complex with L-Glutamate Motif Inhibitor:
3.4.24.65;

Protein crystallography data

The structure of Human MMP12 in Complex with L-Glutamate Motif Inhibitor, PDB code: 3ts4 was solved by E.A.Stura, V.Dive, L.Devel, B.Czarny, F.Beau, L.Vera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.98 / 1.59
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 70.090, 63.650, 37.370, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.3

Other elements in 3ts4:

The structure of Human MMP12 in Complex with L-Glutamate Motif Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human MMP12 in Complex with L-Glutamate Motif Inhibitor (pdb code 3ts4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human MMP12 in Complex with L-Glutamate Motif Inhibitor, PDB code: 3ts4:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3ts4

Go back to Calcium Binding Sites List in 3ts4
Calcium binding site 1 out of 3 in the Human MMP12 in Complex with L-Glutamate Motif Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human MMP12 in Complex with L-Glutamate Motif Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:21.2
occ:1.00
O A:GLY192 2.4 16.2 1.0
O A:GLY190 2.4 23.3 1.0
O A:HOH414 2.4 24.4 1.0
O A:ASP158 2.4 19.4 1.0
OD2 A:ASP194 2.5 16.4 1.0
O A:HOH421 2.5 25.4 1.0
CG A:ASP194 3.5 13.8 1.0
C A:GLY192 3.5 18.6 1.0
C A:ASP158 3.5 18.9 1.0
C A:GLY190 3.5 24.4 1.0
C A:ILE191 3.9 16.6 1.0
O A:HOH489 3.9 28.4 1.0
OD1 A:ASP194 4.0 16.0 1.0
N A:GLY192 4.0 19.9 1.0
O A:ILE191 4.1 17.6 1.0
N A:ASP194 4.2 14.4 1.0
CA A:ILE191 4.3 17.5 1.0
O A:ALA157 4.3 22.9 1.0
CA A:GLY192 4.3 18.4 1.0
N A:ILE191 4.4 21.0 1.0
CA A:ASP158 4.4 20.0 1.0
N A:ILE159 4.4 17.4 1.0
O A:GLY188 4.5 23.2 1.0
N A:GLY190 4.5 24.5 1.0
N A:GLY193 4.5 12.7 1.0
CA A:GLY190 4.5 28.9 1.0
CA A:ILE159 4.5 16.1 1.0
N A:LEU160 4.6 15.0 1.0
CA A:GLY193 4.6 15.8 1.0
CB A:ASP194 4.7 10.8 1.0
C A:GLY193 4.7 14.5 1.0
C A:SER189 4.8 23.6 1.0
CA A:ASP194 4.8 12.4 1.0
CH2 A:TRP109 4.9 24.4 1.0
O A:HOH406 4.9 32.2 1.0
O A:SER189 5.0 23.7 1.0

Calcium binding site 2 out of 3 in 3ts4

Go back to Calcium Binding Sites List in 3ts4
Calcium binding site 2 out of 3 in the Human MMP12 in Complex with L-Glutamate Motif Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human MMP12 in Complex with L-Glutamate Motif Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:23.1
occ:1.00
O A:GLU199 2.4 17.1 1.0
OD2 A:ASP124 2.5 23.4 1.0
O A:HOH434 2.5 23.6 1.0
O A:GLU201 2.5 21.0 1.0
OE2 A:GLU199 2.6 25.7 1.0
O A:HOH422 2.6 25.9 1.0
OD1 A:ASP124 2.7 29.3 1.0
CG A:ASP124 2.9 29.2 1.0
C A:GLU199 3.5 16.6 1.0
CD A:GLU199 3.6 26.6 1.0
C A:GLU201 3.7 20.4 1.0
CG A:GLU199 4.0 20.5 1.0
OG1 A:THR122 4.1 24.3 1.0
CA A:GLU199 4.2 15.4 1.0
CA A:PHE202 4.2 19.6 1.0
CB A:ASP124 4.4 25.0 1.0
N A:PHE202 4.4 25.2 1.0
CD1 A:TRP203 4.4 21.1 1.0
O A:HOH559 4.5 46.3 1.0
N A:GLU201 4.5 19.9 1.0
C A:ASP200 4.5 25.2 1.0
O A:HOH527 4.5 36.9 1.0
N A:ASP200 4.5 18.6 1.0
O A:HOH455 4.5 39.2 1.0
O A:HOH466 4.6 33.7 1.0
CB A:GLU199 4.7 17.0 1.0
CA A:ASP200 4.7 23.3 1.0
OE1 A:GLU199 4.7 24.0 1.0
CA A:GLU201 4.7 20.5 1.0
N A:TRP203 4.7 21.4 1.0
NE1 A:TRP203 4.9 18.5 1.0
CD1 A:PHE202 4.9 33.8 1.0
O A:ASP200 4.9 25.0 1.0
O A:HOH409 5.0 36.5 1.0

Calcium binding site 3 out of 3 in 3ts4

Go back to Calcium Binding Sites List in 3ts4
Calcium binding site 3 out of 3 in the Human MMP12 in Complex with L-Glutamate Motif Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human MMP12 in Complex with L-Glutamate Motif Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:18.9
occ:1.00
O A:GLY176 2.3 23.8 1.0
O A:ILE180 2.3 19.1 1.0
OE2 A:GLU201 2.4 26.5 1.0
OD1 A:ASP198 2.4 18.7 1.0
O A:GLY178 2.4 26.4 1.0
OD2 A:ASP175 2.4 21.1 1.0
C A:ILE180 3.5 18.6 1.0
C A:GLY178 3.5 25.9 1.0
C A:GLY176 3.5 24.0 1.0
CG A:ASP198 3.5 17.4 1.0
CG A:ASP175 3.5 20.6 1.0
CD A:GLU201 3.6 25.3 1.0
N A:ILE180 3.8 16.9 1.0
N A:GLY178 3.8 25.4 1.0
N A:GLY176 4.1 22.8 1.0
OD1 A:ASP175 4.1 22.6 1.0
CA A:ILE180 4.1 15.4 1.0
C A:GLY179 4.2 19.7 1.0
C A:LYS177 4.2 26.6 1.0
CB A:ASP198 4.2 14.0 1.0
C A:ASP175 4.2 20.5 1.0
N A:ASP175 4.3 20.3 1.0
CA A:GLY178 4.3 27.4 1.0
CG A:GLU201 4.3 18.9 1.0
CA A:GLY176 4.4 22.6 1.0
CA A:LYS177 4.4 27.0 1.0
N A:LYS177 4.4 24.4 1.0
CB A:ILE180 4.4 18.5 1.0
OD2 A:ASP198 4.5 17.8 1.0
N A:GLY179 4.5 26.4 1.0
OE1 A:GLU201 4.5 28.0 1.0
N A:LEU181 4.5 16.7 1.0
CA A:GLY179 4.6 21.0 1.0
CA A:ASP175 4.6 18.6 1.0
O A:GLY179 4.7 21.9 1.0
O A:ASP175 4.7 25.9 1.0
CB A:ASP175 4.7 17.2 1.0
CA A:LEU181 4.8 16.2 1.0
O A:LYS177 4.9 29.3 1.0

Reference:

L.Devel, F.Beau, M.Amoura, L.Vera, E.Cassar-Lajeunesse, S.Garcia, B.Czarny, E.A.Stura, V.Dive. Simple Pseudo-Dipeptides with A P2' Glutamate: A Novel Inhibitor Family of Matrix Metalloproteases and Other Metzincins. J.Biol.Chem. V. 287 26647 2012.
ISSN: ISSN 0021-9258
PubMed: 22689580
DOI: 10.1074/JBC.M112.380782
Page generated: Sat Dec 12 04:32:02 2020

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