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Calcium in PDB 3ehy: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid, PDB code: 3ehy was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.23 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.256, 60.479, 54.598, 90.00, 116.17, 90.00
R / Rfree (%) 15.5 / 20.4

Other elements in 3ehy:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid 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 (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid (pdb code 3ehy). 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 (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid, PDB code: 3ehy:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3ehy

Go back to Calcium Binding Sites List in 3ehy
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid


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 (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:6.8
occ:1.00
 O A:HOH334 2.2 13.2 1.0
O A:GLY192 2.2 5.4 1.0
O A:GLY190 2.3 8.5 1.0
O A:ASP158 2.3 6.5 1.0
O A:HOH276 2.4 2.9 1.0
OD2 A:ASP194 2.6 2.0 1.0
C A:GLY190 3.4 8.8 1.0
C A:GLY192 3.4 4.2 1.0
C A:ASP158 3.5 5.7 1.0
CG A:ASP194 3.5 2.5 1.0
C A:ILE191 3.9 8.0 1.0
N A:GLY192 4.0 7.9 1.0
OD1 A:ASP194 4.0 2.0 1.0
O A:ILE191 4.1 8.2 1.0
O A:ALA157 4.2 7.2 1.0
CA A:ILE191 4.2 8.5 1.0
CA A:GLY192 4.3 5.7 1.0
N A:ILE191 4.3 8.6 1.0
N A:ASP194 4.3 2.0 1.0
O A:HOH337 4.3 8.9 1.0
CA A:ASP158 4.3 5.5 1.0
N A:GLY190 4.4 7.1 1.0
CA A:GLY190 4.4 7.6 1.0
N A:GLY193 4.4 2.9 1.0
O A:GLY188 4.4 7.4 1.0
N A:ILE159 4.5 4.7 1.0
CA A:GLY193 4.5 2.0 1.0
O A:HOH402 4.6 15.1 1.0
CA A:ILE159 4.6 3.9 1.0
C A:GLY193 4.7 2.0 1.0
N A:LEU160 4.7 3.8 1.0
CB A:ASP194 4.7 2.0 1.0
O A:HOH301 4.8 7.8 1.0
C A:SER189 4.8 7.9 1.0
CA A:ASP194 4.8 2.0 1.0

Calcium binding site 2 out of 3 in 3ehy

Go back to Calcium Binding Sites List in 3ehy
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid


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 (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:4.2
occ:1.00
 OE2 A:GLU199 2.3 2.0 1.0
OD2 A:ASP124 2.3 2.0 1.0
O A:GLU199 2.3 2.3 1.0
O A:HOH320 2.4 4.7 1.0
O A:HOH291 2.4 5.2 1.0
O A:GLU201 2.5 2.0 1.0
OD1 A:ASP124 2.6 2.0 1.0
CG A:ASP124 2.8 3.5 1.0
CD A:GLU199 3.4 3.0 1.0
C A:GLU199 3.5 3.8 1.0
C A:GLU201 3.7 2.0 1.0
CG A:GLU199 3.9 2.3 1.0
OG1 A:THR122 4.1 3.3 1.0
CA A:GLU199 4.2 2.9 1.0
CA A:PHE202 4.2 2.1 1.0
CB A:ASP124 4.3 2.7 1.0
N A:PHE202 4.4 2.0 1.0
CD1 A:TRP203 4.4 3.7 1.0
OE1 A:GLU199 4.5 4.2 1.0
N A:GLU201 4.5 2.0 1.0
N A:ASP200 4.5 4.2 1.0
C A:ASP200 4.6 2.9 1.0
CB A:GLU199 4.7 2.4 1.0
CA A:ASP200 4.7 2.9 1.0
NH2 A:ARG165 4.8 12.3 1.0
CA A:GLU201 4.8 2.0 1.0
O A:HOH284 4.8 5.0 1.0
CD1 A:PHE202 4.9 2.0 1.0
N A:TRP203 4.9 3.8 1.0
NE1 A:TRP203 4.9 3.1 1.0

Calcium binding site 3 out of 3 in 3ehy

Go back to Calcium Binding Sites List in 3ehy
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid


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 (R)-2-(4- Methoxyphenylsulfonamido)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:4.8
occ:1.00
 O A:GLY176 2.2 2.6 1.0
OE2 A:GLU201 2.3 10.1 1.0
O A:ILE180 2.3 7.1 1.0
O A:GLY178 2.3 3.7 1.0
OD1 A:ASP198 2.4 2.0 1.0
OD2 A:ASP175 2.4 3.0 1.0
C A:ILE180 3.4 7.0 1.0
C A:GLY176 3.5 3.6 1.0
CD A:GLU201 3.5 5.7 1.0
CG A:ASP198 3.5 3.1 1.0
C A:GLY178 3.5 4.9 1.0
CG A:ASP175 3.5 4.9 1.0
N A:GLY178 3.8 5.7 1.0
N A:ILE180 3.9 7.1 1.0
C A:LYS177 4.1 6.4 1.0
CB A:ASP198 4.1 2.0 1.0
OD1 A:ASP175 4.1 2.0 1.0
CA A:ILE180 4.2 7.9 1.0
CA A:GLY178 4.2 5.8 1.0
N A:GLY176 4.2 2.5 1.0
C A:GLY179 4.2 6.3 1.0
CG A:GLU201 4.3 2.0 1.0
C A:ASP175 4.3 2.8 1.0
N A:ASP175 4.3 3.3 1.0
N A:LYS177 4.3 4.8 1.0
CA A:LYS177 4.4 6.0 1.0
OE1 A:GLU201 4.4 7.3 1.0
N A:LEU181 4.4 4.7 1.0
CA A:GLY176 4.4 2.6 1.0
OD2 A:ASP198 4.5 2.0 1.0
N A:GLY179 4.5 4.8 1.0
O A:ASP175 4.6 3.8 1.0
CB A:ILE180 4.6 8.7 1.0
CA A:LEU181 4.6 3.8 1.0
O A:LYS177 4.6 7.1 1.0
CA A:ASP175 4.6 2.7 1.0
CA A:GLY179 4.7 6.5 1.0
CB A:ASP175 4.7 2.8 1.0
O A:GLY179 4.7 6.6 1.0

Reference:

E.Dragoni, V.Calderone, M.Fragai, R.Jaiswal, C.Luchinat, C.Nativi. Biotin-Tagged Probes For Mmp Expression and Activation: Design, Synthesis, and Binding Properties Bioconjug.Chem. V. 20 719 2009.
ISSN: ISSN 1043-1802
PubMed: 19275207
DOI: 10.1021/BC8003827
Page generated: Sat Dec 12 04:10:10 2020

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