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Calcium in PDB 3lk8: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate, PDB code: 3lk8 was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.81 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.708, 60.251, 54.144, 90.00, 115.16, 90.00
R / Rfree (%) 16.8 / 20

Other elements in 3lk8:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate 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 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate (pdb code 3lk8). 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 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate, PDB code: 3lk8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3lk8

Go back to Calcium Binding Sites List in 3lk8
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate


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 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:14.6
occ:1.00
 O A:HOH305 2.2 20.7 1.0
O A:GLY192 2.3 6.5 1.0
O A:GLY190 2.4 10.6 1.0
O A:ASP158 2.5 6.6 1.0
O A:HOH5 2.6 3.8 1.0
OD2 A:ASP194 2.6 5.7 1.0
CG A:ASP194 3.5 6.2 1.0
C A:GLY192 3.5 6.0 1.0
C A:GLY190 3.5 9.9 1.0
C A:ASP158 3.6 6.2 1.0
OD1 A:ASP194 3.8 7.4 1.0
C A:ILE191 3.9 8.0 1.0
O A:ALA157 4.0 9.1 1.0
N A:GLY192 4.0 7.0 1.0
O A:ILE191 4.1 6.7 1.0
CA A:ILE191 4.3 9.2 1.0
O A:HOH70 4.3 15.8 1.0
N A:ILE191 4.3 9.2 1.0
CA A:GLY192 4.3 6.7 1.0
CA A:ASP158 4.4 6.3 1.0
N A:ASP194 4.4 4.7 1.0
O A:HOH311 4.4 28.3 1.0
N A:GLY193 4.5 5.6 1.0
N A:ILE159 4.5 5.2 1.0
O A:GLY188 4.5 10.8 1.0
CA A:GLY190 4.6 10.4 1.0
N A:GLY190 4.6 10.1 1.0
N A:LEU160 4.6 4.7 1.0
CA A:GLY193 4.6 5.3 1.0
CA A:ILE159 4.6 5.0 1.0
CB A:ASP194 4.7 4.3 1.0
C A:GLY193 4.7 5.1 1.0
C A:ALA157 4.9 8.2 1.0
O A:HOH46 4.9 7.7 1.0
CA A:ASP194 4.9 4.2 1.0
C A:SER189 4.9 10.8 1.0

Calcium binding site 2 out of 3 in 3lk8

Go back to Calcium Binding Sites List in 3lk8
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate


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 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:5.3
occ:1.00
 O A:GLU199 2.3 4.1 1.0
OE2 A:GLU199 2.4 6.0 1.0
OD2 A:ASP124 2.4 4.6 1.0
O A:HOH45 2.4 7.2 1.0
O A:GLU201 2.4 5.4 1.0
O A:HOH8 2.5 7.5 1.0
OD1 A:ASP124 2.6 4.6 1.0
CG A:ASP124 2.8 4.2 1.0
CD A:GLU199 3.4 5.3 1.0
C A:GLU199 3.4 5.0 1.0
C A:GLU201 3.7 5.2 1.0
CG A:GLU199 3.8 4.9 1.0
OG1 A:THR122 4.1 4.1 1.0
CA A:GLU199 4.1 4.9 1.0
CA A:PHE202 4.2 5.6 1.0
CB A:ASP124 4.3 5.3 1.0
CD1 A:TRP203 4.4 4.5 1.0
N A:PHE202 4.4 5.0 1.0
N A:GLU201 4.4 4.7 1.0
N A:ASP200 4.5 4.7 1.0
OE1 A:GLU199 4.5 4.2 1.0
CB A:GLU199 4.6 4.9 1.0
C A:ASP200 4.6 5.5 1.0
CA A:ASP200 4.7 5.3 1.0
CA A:GLU201 4.7 4.8 1.0
NH2 A:ARG165 4.7 12.4 1.0
CD1 A:PHE202 4.8 9.0 1.0
NE1 A:TRP203 4.8 3.7 1.0
N A:TRP203 4.9 5.1 1.0
O A:HOH22 4.9 7.2 1.0
O A:HOH48 5.0 9.9 1.0

Calcium binding site 3 out of 3 in 3lk8

Go back to Calcium Binding Sites List in 3lk8
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate


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 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:7.7
occ:1.00
 OE2 A:GLU201 2.2 11.7 1.0
OD1 A:ASP198 2.3 7.2 1.0
O A:GLY176 2.3 7.4 1.0
O A:ILE180 2.3 9.3 1.0
OD2 A:ASP175 2.3 10.5 1.0
O A:GLY178 2.4 9.4 1.0
CG A:ASP198 3.4 4.8 1.0
CD A:GLU201 3.4 8.7 1.0
C A:ILE180 3.5 9.2 1.0
C A:GLY176 3.5 9.0 1.0
C A:GLY178 3.6 9.9 1.0
CG A:ASP175 3.6 10.5 1.0
N A:GLY178 3.8 9.8 1.0
N A:ILE180 3.9 10.5 1.0
CB A:ASP198 4.0 3.6 1.0
OE1 A:GLU201 4.1 10.5 1.0
N A:GLY176 4.1 9.1 1.0
C A:LYS177 4.1 10.1 1.0
OD1 A:ASP175 4.2 11.7 1.0
CA A:ILE180 4.2 10.0 1.0
N A:ASP175 4.3 8.9 1.0
CA A:GLY178 4.3 10.1 1.0
OD2 A:ASP198 4.3 5.6 1.0
C A:ASP175 4.3 8.8 1.0
C A:GLY179 4.3 10.2 1.0
CA A:LYS177 4.4 10.2 1.0
N A:LYS177 4.4 8.5 1.0
CA A:GLY176 4.4 8.7 1.0
CG A:GLU201 4.4 4.2 1.0
N A:LEU181 4.5 7.7 1.0
N A:GLY179 4.6 10.1 1.0
CA A:ASP175 4.6 9.0 1.0
CA A:LEU181 4.6 6.9 1.0
CB A:ILE180 4.7 9.8 1.0
CB A:ASP175 4.7 9.3 1.0
O A:LYS177 4.7 10.5 1.0
CA A:GLY179 4.7 10.7 1.0
O A:ASP175 4.8 9.8 1.0
O A:GLY179 4.9 10.8 1.0
CD2 A:LEU181 5.0 2.8 1.0

Reference:

I.Bertini, V.Calderone, M.Fragai, A.Giachetti, M.Loconte, C.Luchinat, M.Maletta, C.Nativi, K.J.Yeo. Exploring the Subtleties of Drug-Receptor Interactions: the Case of Matrix Metalloproteinases J.Am.Chem.Soc. V. 129 2466 2007.
ISSN: ISSN 0002-7863
PubMed: 17269766
Page generated: Sat Jul 13 13:08:58 2024

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