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Calcium in PDB 5i12: Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-9 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-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27).:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27)., PDB code: 5i12 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) 34.26 / 1.59
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 39.560, 39.560, 163.550, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 22.8

Other elements in 5i12:

The structure of Crystal Structure of the Catalytic Domain of Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). 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 Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27). (pdb code 5i12). 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 Mmp-9 in Complex with A Selective Sugar-Conjugated Arylsulfonamide Carboxylate Water-Soluble Inhibitor (DC27)., PDB code: 5i12:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5i12

Go back to Calcium Binding Sites List in 5i12
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Mmp-9 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-9 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:Ca303

b:25.0
occ:1.00
 O A:LEU187 2.3 26.2 1.0
O A:GLY183 2.3 23.7 1.0
OE2 A:GLU208 2.3 31.4 1.0
O A:ASP185 2.3 30.4 1.0
OD2 A:ASP205 2.4 23.3 1.0
OD1 A:ASP182 2.4 24.8 1.0
CG A:ASP205 3.4 22.6 1.0
C A:ASP185 3.4 30.8 1.0
C A:LEU187 3.4 24.3 1.0
CG A:ASP182 3.5 30.1 1.0
C A:GLY183 3.5 27.9 1.0
CD A:GLU208 3.5 26.2 1.0
N A:ASP185 3.8 30.0 1.0
N A:LEU187 3.9 26.0 1.0
C A:LYS184 4.1 28.9 1.0
N A:GLY183 4.1 31.1 1.0
OD2 A:ASP182 4.1 28.2 1.0
CB A:ASP205 4.1 19.2 1.0
CA A:LEU187 4.1 24.6 1.0
CA A:ASP185 4.1 26.9 1.0
C A:GLY186 4.2 27.2 1.0
N A:ASP182 4.3 25.8 1.0
C A:ASP182 4.3 30.2 1.0
OD1 A:ASP205 4.3 22.1 1.0
CG A:GLU208 4.4 24.2 1.0
OE1 A:GLU208 4.4 31.0 1.0
CA A:GLY183 4.4 27.0 1.0
N A:LYS184 4.4 25.6 1.0
CA A:LYS184 4.5 26.4 1.0
N A:GLY186 4.5 31.8 1.0
O A:LYS184 4.5 31.0 1.0
N A:LEU188 4.5 19.6 1.0
CB A:LEU187 4.5 31.0 1.0
CA A:GLY186 4.6 33.8 1.0
CA A:ASP182 4.6 27.8 1.0
CB A:ASP182 4.7 29.4 1.0
CA A:LEU188 4.7 19.7 1.0
O A:GLY186 4.7 28.5 1.0
O A:ASP182 4.8 35.1 1.0

Calcium binding site 2 out of 3 in 5i12

Go back to Calcium Binding Sites List in 5i12
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Mmp-9 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-9 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:29.0
occ:1.00
 O A:GLY197 2.3 34.1 1.0
O A:HOH424 2.3 32.9 1.0
OD1 A:ASP201 2.3 27.2 1.0
O A:GLN199 2.4 30.3 1.0
O A:ASP165 2.4 28.2 1.0
O A:HOH420 2.4 31.0 1.0
CG A:ASP201 3.4 23.6 1.0
C A:GLN199 3.5 29.1 1.0
C A:GLY197 3.5 37.3 1.0
C A:ASP165 3.6 25.2 1.0
OD2 A:ASP201 3.9 27.6 1.0
N A:ASP201 4.0 25.6 1.0
O A:ALA164 4.0 33.8 1.0
C A:ILE198 4.1 29.9 1.0
O A:ILE198 4.1 30.9 1.0
N A:GLN199 4.2 28.3 1.0
C A:GLY200 4.3 26.1 1.0
CA A:GLY200 4.3 27.7 1.0
N A:GLY197 4.3 43.2 1.0
O A:HOH416 4.3 38.0 1.0
CA A:ASP165 4.3 27.5 1.0
N A:GLY200 4.3 26.5 1.0
O A:GLY195 4.4 38.0 1.0
CA A:GLY197 4.4 38.1 1.0
CA A:GLN199 4.5 28.1 1.0
N A:ILE198 4.5 35.2 1.0
CB A:ASP201 4.5 21.7 1.0
N A:ILE166 4.5 26.4 1.0
CA A:ILE198 4.6 30.1 1.0
N A:VAL167 4.6 24.0 1.0
CA A:ASP201 4.6 25.9 1.0
CA A:ILE166 4.7 23.7 1.0
C A:PRO196 4.7 35.6 1.0
CH2 A:TRP116 4.8 28.9 1.0
CG2 A:VAL167 4.8 28.6 1.0
O A:HOH413 4.9 44.0 1.0
O A:PRO196 5.0 35.6 1.0
O A:GLY200 5.0 25.0 1.0

Calcium binding site 3 out of 3 in 5i12

Go back to Calcium Binding Sites List in 5i12
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Mmp-9 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-9 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:32.3
occ:1.00
 O A:HOH451 2.3 41.0 1.0
O A:GLU208 2.3 23.7 1.0
O A:ASP206 2.4 20.8 1.0
OD2 A:ASP131 2.4 21.7 1.0
OD1 A:ASP206 2.4 22.4 1.0
O A:HOH476 3.1 77.5 1.0
CG A:ASP131 3.1 28.3 1.0
OD1 A:ASP131 3.2 29.4 1.0
C A:ASP206 3.3 22.7 1.0
CG A:ASP206 3.4 21.6 1.0
C A:GLU208 3.5 19.8 1.0
CA A:ASP206 3.7 16.8 1.0
OG A:SER129 3.9 22.8 1.0
CD1 A:TRP210 4.1 17.9 1.0
CB A:ASP206 4.1 18.2 1.0
O A:HOH446 4.1 42.9 1.0
O A:HOH510 4.2 55.0 1.0
OD2 A:ASP206 4.2 26.9 1.0
N A:GLU208 4.2 20.6 1.0
CA A:LEU209 4.3 21.7 1.0
O A:HOH508 4.3 26.2 1.0
N A:LEU209 4.3 20.9 1.0
N A:ASP207 4.4 20.1 1.0
C A:ASP207 4.5 22.6 1.0
CB A:ASP131 4.5 24.9 1.0
CA A:GLU208 4.5 22.4 1.0
O A:HOH487 4.6 45.2 1.0
N A:TRP210 4.6 20.8 1.0
CA A:ASP207 4.6 19.9 1.0
O A:HOH426 4.6 29.2 1.0
NE1 A:TRP210 4.6 20.0 1.0
CB A:SER129 5.0 22.3 1.0
C A:LEU209 5.0 24.2 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 20:18:18 2024

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