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Calcium in PDB 5i0l: Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27)., PDB code: 5i0l was solved by E.A.Stura, L.Rosalia, D.Cuffaro, L.Tepshi, L.Ciccone, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.22 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.090, 62.860, 63.750, 90.00, 102.54, 90.00
R / Rfree (%) 17.5 / 25.3

Other elements in 5i0l:

The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). (pdb code 5i0l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27)., PDB code: 5i0l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5i0l

Go back to Calcium Binding Sites List in 5i0l
Calcium binding site 1 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).


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 Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:23.0
occ:1.00
 O A:ASP158 2.3 26.4 1.0
O A:HOH450 2.3 20.9 1.0
O A:HOH422 2.3 25.5 1.0
O A:GLY192 2.3 13.3 1.0
O A:GLY190 2.4 32.2 1.0
OD1 A:ASP194 2.4 19.9 1.0
CG A:ASP194 3.3 21.3 1.0
C A:ASP158 3.5 30.9 1.0
C A:GLY192 3.5 24.6 1.0
C A:GLY190 3.6 29.4 1.0
OD2 A:ASP194 3.7 19.7 1.0
C A:ILE191 3.9 25.1 1.0
O A:ALA157 4.0 28.5 1.0
O A:ILE191 4.0 34.7 1.0
N A:ASP194 4.1 27.2 1.0
N A:GLY192 4.1 20.8 1.0
CA A:GLY192 4.3 19.4 1.0
CA A:ASP158 4.4 27.0 1.0
CA A:ILE191 4.4 29.8 1.0
N A:ILE159 4.4 20.6 1.0
N A:ILE191 4.4 30.0 1.0
CA A:ILE159 4.5 19.6 1.0
O A:GLY188 4.5 25.3 1.0
CB A:ASP194 4.5 17.1 1.0
N A:GLY193 4.6 28.1 1.0
CA A:GLY190 4.6 26.4 1.0
N A:GLY190 4.6 30.2 1.0
CA A:ASP194 4.7 21.5 1.0
C A:GLY193 4.7 28.3 1.0
N A:LEU160 4.7 19.2 1.0
CA A:GLY193 4.8 20.1 1.0
O A:HOH453 4.8 35.9 1.0
CH2 A:TRP109 4.8 33.8 1.0
C A:SER189 4.9 31.1 1.0
C A:ALA157 4.9 20.9 1.0
O A:SER189 5.0 25.6 1.0

Calcium binding site 2 out of 6 in 5i0l

Go back to Calcium Binding Sites List in 5i0l
Calcium binding site 2 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).


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 Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:37.1
occ:1.00
 O A:GLU199 2.3 29.0 1.0
OD2 A:ASP124 2.4 27.6 1.0
OE2 A:GLU199 2.4 38.1 1.0
O A:GLU201 2.5 19.9 1.0
O A:HOH462 2.5 38.2 1.0
OD1 A:ASP124 2.7 26.7 1.0
O A:HOH522 2.9 27.1 1.0
CG A:ASP124 2.9 23.9 1.0
C A:GLU199 3.4 19.7 1.0
CD A:GLU199 3.5 33.0 1.0
C A:GLU201 3.7 37.1 1.0
CG A:GLU199 4.0 25.4 1.0
OG1 A:THR122 4.1 16.2 1.0
CA A:GLU199 4.2 17.0 1.0
CA A:PHE202 4.3 17.0 1.0
CD1 A:TRP203 4.4 15.6 1.0
CB A:ASP124 4.4 21.1 1.0
N A:ASP200 4.5 17.7 1.0
N A:GLU201 4.5 17.4 1.0
N A:PHE202 4.5 16.5 1.0
C A:ASP200 4.5 24.1 1.0
CA A:ASP200 4.6 22.4 1.0
NH1 A:ARG165 4.6 28.0 1.0
OE1 A:GLU199 4.6 24.5 1.0
N A:TRP203 4.6 15.2 1.0
CB A:GLU199 4.7 17.9 1.0
CA A:GLU201 4.8 25.8 1.0
NE1 A:TRP203 4.9 14.3 1.0

Calcium binding site 3 out of 6 in 5i0l

Go back to Calcium Binding Sites List in 5i0l
Calcium binding site 3 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).


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 Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:28.2
occ:1.00
 O A:ILE180 2.2 32.0 1.0
OE2 A:GLU201 2.2 33.0 1.0
O A:GLY176 2.3 26.6 1.0
OD2 A:ASP198 2.4 21.5 1.0
O A:GLY178 2.4 19.5 1.0
OD1 A:ASP175 2.4 27.0 1.0
C A:ILE180 3.3 28.5 1.0
CG A:ASP198 3.3 27.2 1.0
CD A:GLU201 3.4 29.5 1.0
C A:GLY176 3.5 23.5 1.0
C A:GLY178 3.5 31.1 1.0
CG A:ASP175 3.6 30.3 1.0
N A:ILE180 3.8 29.4 1.0
N A:GLY178 3.8 22.9 1.0
CB A:ASP198 4.0 16.4 1.0
CA A:ILE180 4.1 26.3 1.0
C A:LYS177 4.1 31.0 1.0
OD2 A:ASP175 4.2 24.5 1.0
OE1 A:GLU201 4.2 30.1 1.0
C A:ASP175 4.2 35.7 1.0
N A:ASP175 4.2 32.0 1.0
N A:GLY176 4.2 35.8 1.0
OD1 A:ASP198 4.2 23.5 1.0
CA A:GLY178 4.3 26.5 1.0
N A:LEU181 4.3 28.9 1.0
N A:LYS177 4.3 22.1 1.0
CA A:LYS177 4.4 30.2 1.0
CA A:GLY176 4.4 24.4 1.0
CG A:GLU201 4.4 19.8 1.0
C A:GLY179 4.4 38.9 1.0
O A:ASP175 4.5 36.0 1.0
CB A:ILE180 4.5 30.4 1.0
CA A:LEU181 4.5 26.6 1.0
CA A:ASP175 4.6 29.3 1.0
N A:GLY179 4.6 37.6 1.0
CB A:ASP175 4.7 23.7 1.0
O A:LYS177 4.7 48.8 1.0
CA A:GLY179 4.8 37.5 1.0

Calcium binding site 4 out of 6 in 5i0l

Go back to Calcium Binding Sites List in 5i0l
Calcium binding site 4 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:25.1
occ:1.00
 O B:ASP158 2.2 36.6 1.0
O B:GLY190 2.4 25.9 1.0
O B:GLY192 2.4 15.1 1.0
O B:HOH417 2.4 23.5 1.0
O B:HOH430 2.4 21.7 1.0
OD1 B:ASP194 2.5 13.1 1.0
C B:ASP158 3.4 26.8 1.0
CG B:ASP194 3.5 15.7 1.0
C B:GLY192 3.6 26.4 1.0
C B:GLY190 3.6 28.9 1.0
C B:ILE191 3.9 29.4 1.0
O B:ILE191 3.9 24.0 1.0
OD2 B:ASP194 4.0 25.9 1.0
O B:ALA157 4.0 16.1 1.0
N B:ASP194 4.1 18.1 1.0
N B:GLY192 4.2 32.5 1.0
CA B:ASP158 4.2 25.7 1.0
N B:ILE159 4.4 24.0 1.0
CA B:ILE191 4.4 26.6 1.0
CA B:GLY192 4.4 20.1 1.0
O B:GLY188 4.4 33.1 1.0
N B:ILE191 4.4 27.9 1.0
N B:GLY193 4.5 23.0 1.0
CA B:GLY190 4.5 27.1 1.0
CA B:ILE159 4.5 22.1 1.0
N B:GLY190 4.5 26.0 1.0
CB B:ASP194 4.6 23.1 1.0
C B:GLY193 4.6 28.9 1.0
CA B:GLY193 4.6 19.4 1.0
CA B:ASP194 4.7 17.3 1.0
N B:LEU160 4.7 16.4 1.0
CH2 B:TRP109 4.8 24.4 1.0
C B:SER189 4.8 40.0 1.0
O B:HOH414 4.9 22.5 1.0
C B:ALA157 5.0 18.1 1.0
O B:SER189 5.0 39.6 1.0

Calcium binding site 5 out of 6 in 5i0l

Go back to Calcium Binding Sites List in 5i0l
Calcium binding site 5 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:38.3
occ:1.00
 O B:GLU199 2.2 21.9 1.0
O B:HOH463 2.2 44.3 1.0
OD2 B:ASP124 2.3 31.2 1.0
OE2 B:GLU199 2.3 30.8 1.0
O B:GLU201 2.5 15.1 1.0
OD1 B:ASP124 2.9 37.8 1.0
CG B:ASP124 3.0 28.6 1.0
C B:GLU199 3.3 20.7 1.0
CD B:GLU199 3.4 26.1 1.0
C B:GLU201 3.7 24.2 1.0
O B:HOH451 3.7 29.1 1.0
CG B:GLU199 3.8 16.4 1.0
CA B:GLU199 3.9 20.8 1.0
OG1 B:THR122 4.0 24.4 1.0
CD1 B:TRP203 4.1 19.9 1.0
N B:GLU201 4.2 20.9 1.0
N B:ASP200 4.3 26.0 1.0
C B:ASP200 4.4 24.3 1.0
CB B:ASP124 4.4 17.5 1.0
CA B:PHE202 4.4 22.5 1.0
CB B:GLU199 4.5 16.4 1.0
CA B:ASP200 4.5 19.4 1.0
OE1 B:GLU199 4.5 28.3 1.0
N B:PHE202 4.5 16.2 1.0
N B:TRP203 4.6 19.1 1.0
NE1 B:TRP203 4.6 19.5 1.0
CA B:GLU201 4.7 26.6 1.0
NH1 B:ARG165 4.9 39.4 1.0
O B:ASP200 5.0 21.8 1.0
O B:HOH519 5.0 46.7 1.0

Calcium binding site 6 out of 6 in 5i0l

Go back to Calcium Binding Sites List in 5i0l
Calcium binding site 6 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:23.9
occ:1.00
 OD1 B:ASP175 2.2 17.8 1.0
OE2 B:GLU201 2.2 25.4 1.0
O B:ILE180 2.2 37.6 1.0
O B:GLY176 2.2 20.6 1.0
OD2 B:ASP198 2.3 18.2 1.0
O B:GLY178 2.4 21.4 1.0
C B:ILE180 3.4 36.0 1.0
CG B:ASP175 3.4 26.0 1.0
C B:GLY176 3.4 20.4 1.0
CG B:ASP198 3.4 27.0 1.0
CD B:GLU201 3.4 22.8 1.0
C B:GLY178 3.6 31.4 1.0
N B:GLY178 3.9 28.2 1.0
C B:ASP175 4.0 32.8 1.0
N B:ILE180 4.0 29.9 1.0
N B:GLY176 4.0 29.0 1.0
OD2 B:ASP175 4.1 16.8 1.0
CB B:ASP198 4.1 17.9 1.0
N B:ASP175 4.1 27.9 1.0
OE1 B:GLU201 4.2 22.5 1.0
CA B:ILE180 4.2 30.7 1.0
C B:GLY179 4.2 29.5 1.0
O B:ASP175 4.2 31.5 1.0
CA B:GLY176 4.3 22.1 1.0
C B:LYS177 4.3 29.5 1.0
CG B:GLU201 4.3 17.3 1.0
N B:LYS177 4.3 20.7 1.0
OD1 B:ASP198 4.3 19.9 1.0
N B:LEU181 4.4 32.3 1.0
CA B:ASP175 4.4 26.4 1.0
CA B:GLY178 4.4 31.6 1.0
CA B:LYS177 4.5 25.4 1.0
CB B:ASP175 4.5 23.3 1.0
N B:GLY179 4.5 37.3 1.0
CA B:LEU181 4.6 17.9 1.0
O B:GLY179 4.6 31.2 1.0
CB B:ILE180 4.6 37.6 1.0
CA B:GLY179 4.7 35.6 1.0
O B:HOH454 4.9 32.3 1.0
O B:LYS177 4.9 28.1 1.0

Reference:

E.Nuti, D.Cuffaro, F.D'andrea, L.Rosalia, L.Tepshi, M.Fabbi, G.Carbotti, S.Ferrini, S.Santamaria, C.Camodeca, L.Ciccone, E.Orlandini, S.Nencetti, E.A.Stura, V.Dive, A.Rossello. Sugar-Based Arylsulfonamide Carboxylates As Selective and Water-Soluble Matrix Metalloproteinase-12 Inhibitors. Chemmedchem V. 11 1626 2016.
ISSN: ESSN 1860-7187
PubMed: 27356908
DOI: 10.1002/CMDC.201600235
Page generated: Sun Jul 14 20:16:45 2024

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