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Calcium in PDB 3rts: Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide

Enzymatic activity of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide

All present enzymatic activity of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide:
3.4.24.65;

Protein crystallography data

The structure of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide, PDB code: 3rts was solved by I.Bertini, V.Calderone, M.Fragai, C.Luchinat, M.Mori, C.Nativi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.99 / 1.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.643, 60.475, 54.162, 90.00, 115.15, 90.00
R / Rfree (%) 17 / 23.6

Other elements in 3rts:

The structure of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide (pdb code 3rts). 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 Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide, PDB code: 3rts:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3rts

Go back to Calcium Binding Sites List in 3rts
Calcium binding site 1 out of 3 in the Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:13.8
occ:1.00
 O A:GLY190 2.4 8.1 1.0
O A:GLY192 2.4 5.1 1.0
O A:ASP158 2.5 5.6 1.0
OD2 A:ASP194 2.6 5.2 1.0
O A:HOH8 2.7 2.3 1.0
CG A:ASP194 3.5 5.7 1.0
C A:ASP158 3.5 4.8 1.0
C A:GLY190 3.6 8.5 1.0
C A:GLY192 3.6 4.4 1.0
OD1 A:ASP194 3.8 8.6 1.0
C A:ILE191 3.8 6.7 1.0
O A:ALA157 4.0 6.4 1.0
N A:GLY192 4.0 6.1 1.0
O A:ILE191 4.0 7.1 1.0
CA A:ILE191 4.1 8.0 1.0
O A:HOH58 4.2 13.0 1.0
N A:ILE191 4.3 7.2 1.0
CA A:ASP158 4.3 5.5 1.0
N A:ASP194 4.4 2.0 1.0
CA A:GLY192 4.4 5.2 1.0
N A:ILE159 4.4 4.3 1.0
N A:GLY193 4.5 4.8 1.0
O A:GLY188 4.5 8.2 1.0
O A:HOH270 4.5 26.6 1.0
CA A:ILE159 4.6 3.3 1.0
N A:LEU160 4.6 2.3 1.0
CA A:GLY193 4.6 2.9 1.0
CA A:GLY190 4.6 8.9 1.0
CB A:ASP194 4.7 3.0 1.0
C A:GLY193 4.7 2.8 1.0
N A:GLY190 4.7 8.2 1.0
O A:HOH53 4.7 4.5 1.0
CA A:ASP194 4.9 3.3 1.0
C A:ALA157 4.9 7.8 1.0

Calcium binding site 2 out of 3 in 3rts

Go back to Calcium Binding Sites List in 3rts
Calcium binding site 2 out of 3 in the Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:4.9
occ:1.00
 O A:GLU199 2.3 2.0 1.0
OD2 A:ASP124 2.3 3.2 1.0
OE2 A:GLU199 2.4 2.0 1.0
O A:GLU201 2.5 2.0 1.0
O A:HOH10 2.5 3.4 1.0
OD1 A:ASP124 2.5 2.0 1.0
O A:HOH32 2.6 5.7 1.0
CG A:ASP124 2.8 2.2 1.0
C A:GLU199 3.5 2.8 1.0
CD A:GLU199 3.5 2.6 1.0
C A:GLU201 3.7 2.2 1.0
CG A:GLU199 3.9 2.0 1.0
OG1 A:THR122 4.1 2.0 1.0
CA A:GLU199 4.1 2.3 1.0
CA A:PHE202 4.3 3.3 1.0
CB A:ASP124 4.3 2.5 1.0
CD1 A:TRP203 4.4 2.5 1.0
N A:PHE202 4.4 2.2 1.0
N A:GLU201 4.5 3.0 1.0
N A:ASP200 4.5 3.2 1.0
OE1 A:GLU199 4.6 4.5 1.0
C A:ASP200 4.6 3.9 1.0
CB A:GLU199 4.6 2.3 1.0
CD1 A:PHE202 4.7 2.0 1.0
CA A:GLU201 4.7 2.9 1.0
CA A:ASP200 4.7 3.6 1.0
O A:HOH13 4.8 6.3 1.0
N A:TRP203 4.8 3.9 1.0
NH2 A:ARG165 4.8 12.9 1.0
NE1 A:TRP203 4.9 2.0 1.0

Calcium binding site 3 out of 3 in 3rts

Go back to Calcium Binding Sites List in 3rts
Calcium binding site 3 out of 3 in the Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Mmp-12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2- Phenylethylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:8.4
occ:1.00
 OE2 A:GLU201 2.2 14.2 1.0
OD1 A:ASP198 2.3 5.8 1.0
O A:ILE180 2.3 9.2 1.0
O A:GLY176 2.3 8.7 1.0
O A:GLY178 2.4 8.7 1.0
OD2 A:ASP175 2.4 7.8 1.0
CD A:GLU201 3.4 8.4 1.0
CG A:ASP198 3.4 2.7 1.0
C A:ILE180 3.5 8.4 1.0
C A:GLY176 3.5 8.5 1.0
C A:GLY178 3.6 8.8 1.0
CG A:ASP175 3.6 9.7 1.0
N A:GLY178 3.7 9.1 1.0
N A:ILE180 4.0 8.9 1.0
CB A:ASP198 4.0 2.3 1.0
C A:LYS177 4.1 9.5 1.0
OD1 A:ASP175 4.2 10.7 1.0
OE1 A:GLU201 4.2 12.2 1.0
N A:GLY176 4.2 8.4 1.0
CA A:GLY178 4.3 8.9 1.0
CG A:GLU201 4.3 4.2 1.0
CA A:ILE180 4.3 9.0 1.0
N A:ASP175 4.3 7.3 1.0
CA A:LYS177 4.3 9.8 1.0
C A:GLY179 4.3 9.4 1.0
OD2 A:ASP198 4.4 4.1 1.0
N A:LYS177 4.4 8.1 1.0
C A:ASP175 4.4 8.3 1.0
N A:LEU181 4.4 7.5 1.0
CA A:GLY176 4.5 8.1 1.0
N A:GLY179 4.6 8.6 1.0
CA A:LEU181 4.6 6.4 1.0
O A:LYS177 4.7 9.5 1.0
CA A:ASP175 4.7 8.1 1.0
CB A:ILE180 4.7 9.4 1.0
CB A:ASP175 4.7 8.3 1.0
CA A:GLY179 4.8 9.4 1.0
O A:GLY179 4.8 9.8 1.0
O A:ASP175 4.9 9.6 1.0
CD2 A:LEU181 5.0 5.1 1.0

Reference:

A.Mordini, M.Mori, A.Massaro, V.Calderone, M.Fragai, C.Luchinat. Contribution of Ligand Free Energy of Solvation to Design New Potent Mmps Inhibitors. J.Med.Chem. 2012.
ISSN: ISSN 0022-2623
Page generated: Sat Jul 13 18:12:21 2024

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