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Zinc 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:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 5i12

Go back to Zinc Binding Sites List in 5i12
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn301

b:27.4
occ:1.00
O98 A:H27306 1.9 29.9 1.0
NE2 A:HIS226 2.0 22.2 1.0
NE2 A:HIS230 2.0 27.1 1.0
NE2 A:HIS236 2.1 28.3 1.0
C A:H27306 2.6 33.1 1.0
OZ2 A:H27306 2.8 27.9 1.0
CE1 A:HIS226 2.9 23.3 1.0
CE1 A:HIS230 3.0 30.7 1.0
CD2 A:HIS236 3.0 28.9 1.0
CD2 A:HIS226 3.0 23.5 1.0
CD2 A:HIS230 3.0 22.4 1.0
CE1 A:HIS236 3.2 38.1 1.0
ND1 A:HIS226 4.0 27.7 1.0
CZA A:H27306 4.1 24.8 1.0
ND1 A:HIS230 4.1 27.5 1.0
CG A:HIS226 4.1 22.3 1.0
CG A:HIS230 4.2 26.5 1.0
CG A:HIS236 4.2 32.5 1.0
ND1 A:HIS236 4.2 31.4 1.0
NA A:H27306 4.6 30.2 1.0
C24 A:H27306 4.7 33.1 1.0
OE2 A:GLU227 4.7 23.5 1.0
CC2 A:H27306 4.7 45.0 1.0
C14 A:H27306 4.7 25.5 1.0
C13 A:H27306 4.7 29.2 1.0
CZ1 A:H27306 4.8 36.1 1.0
C12 A:H27306 4.9 25.2 1.0
C15 A:H27306 4.9 22.1 1.0
CE A:MET244 4.9 29.2 1.0
O A:HOH402 4.9 38.6 0.5
C17 A:H27306 4.9 25.9 1.0
C16 A:H27306 5.0 30.9 1.0

Zinc binding site 2 out of 2 in 5i12

Go back to Zinc Binding Sites List in 5i12
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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:Zn302

b:25.4
occ:1.00
OD2 A:ASP177 2.0 25.3 1.0
ND1 A:HIS203 2.0 22.3 1.0
NE2 A:HIS190 2.1 25.7 1.0
NE2 A:HIS175 2.1 20.8 1.0
CG A:ASP177 2.9 23.5 1.0
CE1 A:HIS190 2.9 28.2 1.0
CD2 A:HIS175 2.9 21.0 1.0
CE1 A:HIS203 3.0 23.6 1.0
CG A:HIS203 3.1 22.5 1.0
CE1 A:HIS175 3.1 27.1 1.0
CD2 A:HIS190 3.2 22.1 1.0
OD1 A:ASP177 3.2 28.3 1.0
CB A:HIS203 3.4 19.5 1.0
ND1 A:HIS190 4.1 25.4 1.0
NE2 A:HIS203 4.1 24.3 1.0
CG A:HIS175 4.1 23.8 1.0
CD2 A:HIS203 4.2 21.9 1.0
ND1 A:HIS175 4.2 22.5 1.0
CG A:HIS190 4.2 26.9 1.0
CB A:ASP177 4.3 23.4 1.0
O A:TYR179 4.4 30.0 1.0
CE1 A:PHE192 4.5 31.9 1.0
CZ A:PHE181 4.6 22.2 1.0
O A:HOH457 4.7 43.3 1.0
O A:HOH432 4.7 28.3 1.0
CZ A:PHE192 4.7 42.2 1.0
CE2 A:PHE181 4.9 18.7 1.0
CA A:HIS203 4.9 20.0 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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