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Calcium in PDB 3ehx: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid

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

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic 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-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid, PDB code: 3ehx was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.27 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.181, 60.554, 54.428, 90.00, 115.90, 90.00
R / Rfree (%) 16.3 / 20.1

Other elements in 3ehx:

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

Calcium binding site 1 out of 3 in 3ehx

Go back to Calcium Binding Sites List in 3ehx
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic 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-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:12.1
occ:1.00
 O A:ASP158 2.3 6.2 1.0
O A:GLY192 2.3 5.2 1.0
O A:GLY190 2.4 8.9 1.0
O A:HOH287 2.5 2.2 1.0
OD2 A:ASP194 2.5 3.1 1.0
CG A:ASP194 3.4 3.4 1.0
C A:GLY192 3.5 4.3 1.0
C A:ASP158 3.5 5.3 1.0
C A:GLY190 3.5 9.1 1.0
C A:ILE191 3.8 7.7 1.0
OD1 A:ASP194 3.8 4.5 1.0
N A:GLY192 3.9 7.3 1.0
O A:ILE191 4.0 6.5 1.0
O A:ALA157 4.1 8.8 1.0
CA A:ILE191 4.2 8.4 1.0
CA A:GLY192 4.3 5.4 1.0
CA A:ASP158 4.3 5.3 1.0
N A:ILE191 4.3 8.7 1.0
N A:ASP194 4.3 2.0 1.0
O A:HOH305 4.3 9.2 1.0
N A:GLY193 4.4 2.6 1.0
N A:ILE159 4.5 3.3 1.0
O A:GLY188 4.5 9.4 1.0
CA A:GLY193 4.6 2.0 1.0
CA A:GLY190 4.6 8.2 1.0
CA A:ILE159 4.6 3.5 1.0
N A:LEU160 4.6 2.8 1.0
CB A:ASP194 4.6 2.0 1.0
N A:GLY190 4.6 9.3 1.0
C A:GLY193 4.7 2.0 1.0
O A:HOH277 4.8 6.3 1.0
CA A:ASP194 4.8 2.5 1.0
C A:SER189 5.0 9.2 1.0

Calcium binding site 2 out of 3 in 3ehx

Go back to Calcium Binding Sites List in 3ehx
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic 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-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:4.6
occ:1.00
 OD2 A:ASP124 2.2 3.3 1.0
OE2 A:GLU199 2.3 2.0 1.0
O A:GLU199 2.4 2.7 1.0
O A:GLU201 2.5 3.2 1.0
OD1 A:ASP124 2.6 2.0 1.0
O A:HOH310 2.6 6.3 1.0
O A:HOH296 2.6 4.8 1.0
CG A:ASP124 2.7 4.2 1.0
CD A:GLU199 3.4 2.7 1.0
C A:GLU199 3.4 2.9 1.0
C A:GLU201 3.7 2.0 1.0
CG A:GLU199 3.9 2.9 1.0
OG1 A:THR122 4.1 2.0 1.0
CA A:GLU199 4.1 2.0 1.0
CB A:ASP124 4.2 3.6 1.0
CA A:PHE202 4.2 2.9 1.0
CD1 A:TRP203 4.4 2.4 1.0
N A:PHE202 4.4 2.0 1.0
N A:GLU201 4.4 2.0 1.0
N A:ASP200 4.5 3.4 1.0
OE1 A:GLU199 4.5 4.3 1.0
C A:ASP200 4.6 2.7 1.0
CB A:GLU199 4.6 3.2 1.0
CA A:ASP200 4.7 2.4 1.0
CA A:GLU201 4.7 2.5 1.0
O A:HOH301 4.7 8.8 1.0
N A:TRP203 4.8 2.0 1.0
NE1 A:TRP203 4.8 4.1 1.0
CD1 A:PHE202 4.9 3.0 1.0
NH2 A:ARG165 4.9 6.5 1.0

Calcium binding site 3 out of 3 in 3ehx

Go back to Calcium Binding Sites List in 3ehx
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (R)-2-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic 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-(Biphenyl-4- Ylsulfonamido)-4-Methylpentanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:8.6
occ:1.00
 OE2 A:GLU201 2.2 16.1 1.0
O A:GLY176 2.3 7.8 1.0
O A:ILE180 2.3 8.8 1.0
OD1 A:ASP198 2.3 6.3 1.0
O A:GLY178 2.4 12.2 1.0
OD2 A:ASP175 2.4 6.7 1.0
CD A:GLU201 3.4 9.4 1.0
CG A:ASP198 3.4 6.5 1.0
C A:ILE180 3.5 9.0 1.0
C A:GLY176 3.5 8.7 1.0
C A:GLY178 3.5 12.7 1.0
CG A:ASP175 3.6 8.3 1.0
N A:GLY178 3.8 12.2 1.0
N A:ILE180 3.9 11.0 1.0
CB A:ASP198 4.1 2.0 1.0
C A:LYS177 4.1 11.9 1.0
OD1 A:ASP175 4.1 9.2 1.0
N A:GLY176 4.2 6.6 1.0
OE1 A:GLU201 4.2 11.7 1.0
CA A:ILE180 4.2 10.3 1.0
CA A:GLY178 4.2 12.8 1.0
CG A:GLU201 4.3 3.9 1.0
C A:ASP175 4.3 5.9 1.0
OD2 A:ASP198 4.3 5.8 1.0
N A:ASP175 4.4 5.6 1.0
CA A:LYS177 4.4 10.9 1.0
C A:GLY179 4.4 12.4 1.0
N A:LYS177 4.4 9.6 1.0
N A:LEU181 4.5 6.7 1.0
CA A:GLY176 4.5 6.7 1.0
O A:ASP175 4.6 6.4 1.0
CA A:LEU181 4.6 6.6 1.0
N A:GLY179 4.6 12.2 1.0
CB A:ILE180 4.6 11.0 1.0
CA A:ASP175 4.7 6.3 1.0
CB A:ASP175 4.7 6.1 1.0
O A:LYS177 4.7 13.8 1.0
CA A:GLY179 4.8 12.6 1.0
O A:GLY179 4.9 13.3 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 Jul 13 09:26:07 2024

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