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Calcium in PDB 3rtt: Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide

Enzymatic activity of Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide

All present enzymatic activity of Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide:
3.4.24.65;

Protein crystallography data

The structure of Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide, PDB code: 3rtt 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) 30.20 / 1.82
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.487, 60.431, 54.207, 90.00, 115.21, 90.00
R / Rfree (%) 23.4 / 31.7

Other elements in 3rtt:

The structure of Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide 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*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide (pdb code 3rtt). 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*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide, PDB code: 3rtt:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3rtt

Go back to Calcium Binding Sites List in 3rtt
Calcium binding site 1 out of 3 in the Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide


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*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:11.0
occ:1.00
 O A:GLY190 2.3 3.1 1.0
OD2 A:ASP194 2.4 3.8 1.0
O A:ASP158 2.4 5.9 1.0
O A:GLY192 2.6 3.1 1.0
O A:HOH13 2.8 2.0 1.0
CG A:ASP194 3.4 2.4 1.0
C A:GLY190 3.5 5.8 1.0
C A:ASP158 3.5 5.0 1.0
OD1 A:ASP194 3.7 5.0 1.0
C A:GLY192 3.7 3.6 1.0
C A:ILE191 3.9 6.3 1.0
N A:GLY192 4.1 4.4 1.0
CA A:ILE191 4.1 5.7 1.0
O A:ILE191 4.1 7.7 1.0
O A:ALA157 4.2 7.8 1.0
N A:ILE191 4.2 5.5 1.0
O A:HOH22 4.3 11.4 1.0
CA A:ASP158 4.4 5.3 1.0
N A:ASP194 4.4 2.0 1.0
N A:ILE159 4.5 2.6 1.0
CA A:GLY192 4.5 3.8 1.0
N A:LEU160 4.6 2.0 1.0
CA A:GLY190 4.6 6.4 1.0
N A:GLY193 4.6 3.4 1.0
CB A:ASP194 4.6 2.0 1.0
CA A:ILE159 4.6 2.0 1.0
O A:HOH46 4.6 8.7 1.0
CA A:GLY193 4.7 3.2 1.0
N A:GLY190 4.7 6.2 1.0
C A:GLY193 4.7 2.0 1.0
O A:HOH99 4.8 17.2 1.0
O A:GLY188 4.8 7.6 1.0
CA A:ASP194 4.8 2.0 1.0
O A:SER189 5.0 8.5 1.0
C A:ALA157 5.0 8.3 1.0
C A:SER189 5.0 7.6 1.0

Calcium binding site 2 out of 3 in 3rtt

Go back to Calcium Binding Sites List in 3rtt
Calcium binding site 2 out of 3 in the Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide


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*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:5.9
occ:1.00
 OD2 A:ASP124 2.2 7.1 1.0
OE2 A:GLU199 2.3 6.3 1.0
O A:GLU199 2.3 3.6 1.0
O A:GLU201 2.5 3.7 1.0
OD1 A:ASP124 2.5 2.0 1.0
CG A:ASP124 2.7 4.7 1.0
O A:HOH17 2.8 6.5 1.0
CD A:GLU199 3.4 5.2 1.0
C A:GLU199 3.4 2.6 1.0
C A:GLU201 3.7 3.0 1.0
OG1 A:THR122 4.0 2.5 1.0
CG A:GLU199 4.0 2.0 1.0
CA A:GLU199 4.0 2.0 1.0
CB A:ASP124 4.2 3.3 1.0
CA A:PHE202 4.2 3.9 1.0
CD1 A:TRP203 4.3 3.3 1.0
N A:PHE202 4.4 3.0 1.0
OE1 A:GLU199 4.5 7.4 1.0
N A:GLU201 4.5 3.1 1.0
N A:ASP200 4.5 3.6 1.0
C A:ASP200 4.6 4.1 1.0
CB A:GLU199 4.6 2.5 1.0
CA A:ASP200 4.8 3.3 1.0
CA A:GLU201 4.8 3.5 1.0
N A:TRP203 4.8 2.2 1.0
NE1 A:TRP203 4.8 3.5 1.0
CD1 A:PHE202 4.8 2.0 1.0
NH2 A:ARG165 4.8 12.1 1.0
O A:HOH73 4.9 10.8 1.0

Calcium binding site 3 out of 3 in 3rtt

Go back to Calcium Binding Sites List in 3rtt
Calcium binding site 3 out of 3 in the Human Mmp-12 Catalytic Domain in Complex with*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide


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*(R)-N*-Hydroxy-1- (Phenethylsulfonyl)Pyrrolidine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:9.7
occ:1.00
 OE2 A:GLU201 2.0 9.6 1.0
O A:GLY176 2.2 8.7 1.0
OD1 A:ASP198 2.4 3.9 1.0
O A:GLY178 2.4 5.3 1.0
OD2 A:ASP175 2.4 12.2 1.0
O A:ILE180 2.6 5.7 1.0
CD A:GLU201 3.2 3.4 1.0
C A:GLY176 3.4 8.3 1.0
CG A:ASP198 3.4 3.8 1.0
C A:GLY178 3.6 5.0 1.0
C A:ILE180 3.6 5.3 1.0
CG A:ASP175 3.6 12.4 1.0
OE1 A:GLU201 3.7 5.2 1.0
N A:GLY178 3.8 5.9 1.0
CB A:ASP198 4.0 2.0 1.0
C A:LYS177 4.1 5.9 1.0
N A:GLY176 4.1 9.3 1.0
N A:ILE180 4.1 5.8 1.0
CA A:LYS177 4.2 6.5 1.0
OD1 A:ASP175 4.2 15.2 1.0
N A:LYS177 4.2 6.8 1.0
CA A:GLY178 4.3 5.8 1.0
C A:GLY179 4.3 5.4 1.0
CA A:GLY176 4.3 8.3 1.0
OD2 A:ASP198 4.4 2.0 1.0
N A:ASP175 4.4 7.0 1.0
N A:LEU181 4.4 3.2 1.0
CG A:GLU201 4.4 2.4 1.0
C A:ASP175 4.4 8.9 1.0
CA A:ILE180 4.4 5.3 1.0
CA A:LEU181 4.6 4.0 1.0
N A:GLY179 4.6 4.6 1.0
CA A:GLY179 4.7 5.5 1.0
O A:LYS177 4.7 5.6 1.0
O A:GLY179 4.8 6.9 1.0
CA A:ASP175 4.8 8.7 1.0
CB A:ASP175 4.8 9.8 1.0
O A:ASP175 5.0 9.8 1.0
CB A:ILE180 5.0 5.8 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: Tue Jul 8 16:25:35 2025

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