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Zinc 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:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5i0l

Go back to Zinc Binding Sites List in 5i0l
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn302

b:25.9
occ:1.00
 O98 A:H27301 1.8 26.5 1.0
NE2 A:HIS222 2.1 19.1 1.0
CE1 A:HIS228 2.2 27.4 1.0
NE2 A:HIS218 2.2 25.2 1.0
C A:H27301 2.6 28.6 1.0
NE2 A:HIS228 2.7 19.2 1.0
OZ2 A:H27301 2.7 30.8 1.0
CE1 A:HIS222 3.1 18.4 1.0
CD2 A:HIS222 3.1 21.4 1.0
CD2 A:HIS218 3.1 20.0 1.0
CE1 A:HIS218 3.2 23.2 1.0
ND1 A:HIS228 3.3 29.9 1.0
CZA A:H27301 3.9 27.1 1.0
CD2 A:HIS228 4.0 18.4 1.0
ND1 A:HIS222 4.2 25.0 1.0
CG A:HIS222 4.2 27.2 1.0
CG A:HIS228 4.2 19.3 1.0
ND1 A:HIS218 4.3 21.0 1.0
CG A:HIS218 4.3 27.4 1.0
NA A:H27301 4.4 28.1 1.0
C24 A:H27301 4.5 28.4 1.0
C17 A:H27301 4.7 31.1 1.0
CZ1 A:H27301 4.7 23.0 1.0
O A:HOH519 4.7 37.0 1.0
CE A:MET236 4.7 16.6 1.0
OE2 A:GLU219 4.7 30.3 1.0
C16 A:H27301 4.8 26.5 1.0
CC2 A:H27301 4.8 25.0 1.0
C12 A:H27301 4.9 37.2 1.0
C15 A:H27301 5.0 24.6 1.0

Zinc binding site 2 out of 4 in 5i0l

Go back to Zinc Binding Sites List in 5i0l
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn303

b:21.9
occ:1.00
 OD2 A:ASP170 1.8 23.3 1.0
NE2 A:HIS168 2.0 15.8 1.0
NE2 A:HIS183 2.1 11.0 1.0
ND1 A:HIS196 2.2 22.2 1.0
CG A:ASP170 2.6 27.8 1.0
CD2 A:HIS168 2.7 25.9 1.0
OD1 A:ASP170 3.0 31.8 1.0
CE1 A:HIS183 3.0 12.3 1.0
CE1 A:HIS196 3.1 32.0 1.0
CE1 A:HIS168 3.1 19.6 1.0
CG A:HIS196 3.2 21.8 1.0
CD2 A:HIS183 3.2 20.2 1.0
CB A:HIS196 3.6 30.8 1.0
CB A:ASP170 3.9 26.6 1.0
CG A:HIS168 3.9 31.4 1.0
O A:HIS172 4.1 30.2 1.0
ND1 A:HIS168 4.1 27.1 1.0
CE1 A:PHE185 4.1 18.9 1.0
ND1 A:HIS183 4.2 20.3 1.0
NE2 A:HIS196 4.2 35.2 1.0
CG A:HIS183 4.3 33.8 1.0
CD2 A:HIS196 4.3 23.1 1.0
CZ A:PHE185 4.5 21.1 1.0
CZ A:PHE174 4.7 16.5 1.0
CE2 A:PHE174 4.7 15.3 1.0
O A:HOH413 4.9 17.0 1.0
CB A:HIS172 5.0 19.7 1.0

Zinc binding site 3 out of 4 in 5i0l

Go back to Zinc Binding Sites List in 5i0l
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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
B:Zn302

b:30.7
occ:1.00
 NE2 B:HIS222 1.9 15.7 1.0
OZ2 B:H27301 2.0 30.6 1.0
NE2 B:HIS218 2.1 20.6 1.0
NE2 B:HIS228 2.2 40.8 1.0
C B:H27301 2.6 29.1 1.0
O98 B:H27301 2.8 21.4 1.0
CD2 B:HIS222 2.9 13.2 1.0
CE1 B:HIS222 2.9 17.8 1.0
CE1 B:HIS218 3.0 23.1 1.0
CD2 B:HIS228 3.1 40.5 1.0
CD2 B:HIS218 3.2 20.8 1.0
CE1 B:HIS228 3.2 29.8 1.0
CZA B:H27301 4.0 30.7 1.0
ND1 B:HIS222 4.0 17.8 1.0
CG B:HIS222 4.0 15.4 1.0
ND1 B:HIS218 4.2 24.9 1.0
CG B:HIS228 4.2 33.8 1.0
ND1 B:HIS228 4.2 29.2 1.0
CG B:HIS218 4.3 28.8 1.0
OE2 B:GLU219 4.5 14.9 1.0
CC2 B:H27301 4.6 43.2 1.0
CZ1 B:H27301 4.6 38.7 1.0
NA B:H27301 4.6 30.6 1.0
C24 B:H27301 4.7 42.6 1.0
CE B:MET236 4.7 22.7 1.0

Zinc binding site 4 out of 4 in 5i0l

Go back to Zinc Binding Sites List in 5i0l
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn 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:Zn303

b:20.7
occ:1.00
 OD2 B:ASP170 1.7 23.8 1.0
NE2 B:HIS168 2.1 14.1 1.0
NE2 B:HIS183 2.1 12.3 1.0
ND1 B:HIS196 2.2 32.3 1.0
CG B:ASP170 2.7 19.5 1.0
CD2 B:HIS168 2.8 28.2 1.0
CE1 B:HIS183 2.9 13.2 1.0
CE1 B:HIS196 3.1 22.9 1.0
OD1 B:ASP170 3.1 16.9 1.0
CD2 B:HIS183 3.2 21.3 1.0
CE1 B:HIS168 3.2 16.0 1.0
CG B:HIS196 3.2 23.6 1.0
CB B:HIS196 3.6 23.4 1.0
O B:HIS172 4.0 17.5 1.0
CG B:HIS168 4.0 26.4 1.0
CB B:ASP170 4.1 26.6 1.0
ND1 B:HIS183 4.1 20.3 1.0
CE1 B:PHE185 4.2 14.9 1.0
ND1 B:HIS168 4.2 30.0 1.0
CG B:HIS183 4.3 31.6 1.0
NE2 B:HIS196 4.3 24.5 1.0
CD2 B:HIS196 4.4 16.9 1.0
CE2 B:PHE174 4.5 26.1 1.0
CZ B:PHE174 4.6 21.6 1.0
CZ B:PHE185 4.7 15.1 1.0
O B:HOH416 4.9 20.9 1.0
CB B:HIS172 4.9 16.2 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 Oct 27 17:44:56 2024

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