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Calcium in PDB 4guy: Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide

Enzymatic activity of Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide

All present enzymatic activity of Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide:
3.4.24.65;

Protein crystallography data

The structure of Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide, PDB code: 4guy was solved by V.Calderone, M.Fragai, C.Luchinat, A.Massaro, A.Mordini, M.Mori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.56 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 50.989, 61.107, 54.213, 90.00, 114.50, 90.00
R / Rfree (%) 22.7 / 29.3

Other elements in 4guy:

The structure of Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide (pdb code 4guy). 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 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide, PDB code: 4guy:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4guy

Go back to Calcium Binding Sites List in 4guy
Calcium binding site 1 out of 3 in the Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:8.8
occ:1.00
 O A:GLY190 2.2 12.4 1.0
O A:ASP158 2.3 11.5 1.0
O A:GLY192 2.3 9.9 1.0
OD2 A:ASP194 2.3 11.2 1.0
O A:HOH433 2.5 10.5 1.0
CG A:ASP194 3.3 11.4 1.0
C A:GLY190 3.5 13.5 1.0
C A:ASP158 3.5 11.8 1.0
C A:GLY192 3.5 10.3 1.0
OD1 A:ASP194 3.7 12.1 1.0
C A:ILE191 3.9 12.2 1.0
O A:ALA157 4.0 14.2 1.0
N A:GLY192 4.0 11.4 1.0
O A:ILE191 4.1 11.9 1.0
CA A:ILE191 4.2 13.2 1.0
N A:ILE191 4.3 13.0 1.0
N A:ASP194 4.3 10.7 1.0
CA A:ASP158 4.3 12.2 1.0
CA A:GLY192 4.3 10.5 1.0
N A:ILE159 4.4 11.6 1.0
O A:GLY188 4.4 11.2 1.0
O A:HOH429 4.5 9.2 1.0
CB A:ASP194 4.5 11.3 1.0
N A:GLY193 4.5 10.2 1.0
CA A:GLY190 4.5 12.8 1.0
N A:GLY190 4.5 13.6 1.0
CA A:ILE159 4.6 11.3 1.0
C A:GLY193 4.6 10.6 1.0
N A:LEU160 4.6 10.8 1.0
CA A:GLY193 4.6 10.6 1.0
CA A:ASP194 4.8 10.9 1.0
C A:SER189 4.8 13.5 1.0
CH2 A:TRP109 4.9 10.4 1.0
C A:ALA157 5.0 15.0 1.0

Calcium binding site 2 out of 3 in 4guy

Go back to Calcium Binding Sites List in 4guy
Calcium binding site 2 out of 3 in the Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:14.2
occ:1.00
 OD2 A:ASP124 2.2 13.8 1.0
OE2 A:GLU199 2.3 9.6 1.0
O A:GLU201 2.3 11.8 1.0
O A:GLU199 2.4 10.8 1.0
OD1 A:ASP124 2.6 12.3 1.0
CG A:ASP124 2.7 12.4 1.0
O A:HOH412 2.9 15.7 1.0
CD A:GLU199 3.5 9.6 1.0
C A:GLU199 3.5 11.3 1.0
C A:GLU201 3.5 11.4 1.0
CG A:GLU199 4.0 9.7 1.0
CA A:PHE202 4.1 11.5 1.0
CA A:GLU199 4.1 10.2 1.0
OG1 A:THR122 4.2 9.6 1.0
CD1 A:TRP203 4.2 13.4 1.0
CB A:ASP124 4.3 10.8 1.0
N A:PHE202 4.3 11.2 1.0
N A:GLU201 4.4 11.7 1.0
OE1 A:GLU199 4.5 9.0 1.0
N A:ASP200 4.6 11.8 1.0
C A:ASP200 4.6 12.3 1.0
CA A:GLU201 4.6 11.8 1.0
N A:TRP203 4.6 12.1 1.0
NE1 A:TRP203 4.7 13.0 1.0
CB A:GLU199 4.7 10.1 1.0
CA A:ASP200 4.8 12.4 1.0
CB A:PHE202 4.9 11.1 1.0
CD1 A:PHE202 4.9 9.9 1.0
C A:PHE202 5.0 11.8 1.0

Calcium binding site 3 out of 3 in 4guy

Go back to Calcium Binding Sites List in 4guy
Calcium binding site 3 out of 3 in the Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human MMP12 Catalytic Domain in Complex with*N*-Hydroxy-2-(2-(4- Methoxyphenyl)Ethylsulfonamido)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:13.5
occ:1.00
 O A:GLY178 2.1 13.2 1.0
OD1 A:ASP198 2.3 8.2 1.0
OE2 A:GLU201 2.3 14.1 1.0
OD2 A:ASP175 2.4 14.9 1.0
O A:GLY176 2.4 12.8 1.0
O A:ILE180 2.7 13.2 1.0
C A:GLY178 3.4 13.1 1.0
CD A:GLU201 3.5 13.3 1.0
CG A:ASP175 3.5 14.5 1.0
C A:ILE180 3.5 14.1 1.0
CG A:ASP198 3.5 8.0 1.0
C A:GLY176 3.6 12.2 1.0
N A:GLY178 3.8 12.6 1.0
N A:ILE180 3.8 14.8 1.0
OD1 A:ASP175 3.9 14.3 1.0
C A:LYS177 4.0 13.2 1.0
OE1 A:GLU201 4.1 13.3 1.0
CA A:ILE180 4.1 14.6 1.0
CA A:LYS177 4.2 12.5 1.0
C A:GLY179 4.2 14.3 1.0
CA A:GLY178 4.2 13.4 1.0
CB A:ASP198 4.3 8.3 1.0
C A:ASP175 4.3 12.3 1.0
N A:LYS177 4.3 11.6 1.0
N A:GLY179 4.3 13.7 1.0
O A:ASP175 4.4 11.6 1.0
N A:ASP175 4.4 12.7 1.0
N A:GLY176 4.4 12.2 1.0
N A:LEU181 4.4 14.0 1.0
OD2 A:ASP198 4.4 8.2 1.0
CA A:GLY179 4.4 14.6 1.0
CG A:GLU201 4.5 12.6 1.0
CA A:GLY176 4.6 11.9 1.0
O A:LYS177 4.6 13.2 1.0
CB A:ILE180 4.6 15.0 1.0
CA A:ASP175 4.7 12.9 1.0
CB A:ASP175 4.7 13.4 1.0
CA A:LEU181 4.8 13.8 1.0
O A:GLY179 4.8 14.9 1.0

Reference:

M.Mori, A.Massaro, V.Calderone, M.Fragai, C.Luchinat, A.Mordini. Contribution of Free Energy of Solvation to Ligand Affinity in New Potent Mmps Inhibitors. To Be Published.
Page generated: Sat Dec 12 04:48:56 2020

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