Zinc in PDB 3e7j: Heparinaseii H202A/Y257A Double Mutant Complexed with A Heparan Sulfate Tetrasaccharide Substrate

The structure of Heparinaseii H202A/Y257A Double Mutant Complexed with A Heparan Sulfate Tetrasaccharide Substrate, PDB code: 3e7j was solved by D.Shaya, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.52 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.951, 162.210, 93.838, 90.00, 105.97, 90.00
R / Rfree (%)	19.9 / 23.5

The binding sites of Zinc atom in the Heparinaseii H202A/Y257A Double Mutant Complexed with A Heparan Sulfate Tetrasaccharide Substrate (pdb code 3e7j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Heparinaseii H202A/Y257A Double Mutant Complexed with A Heparan Sulfate Tetrasaccharide Substrate, PDB code: 3e7j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Heparinaseii H202A/Y257A Double Mutant Complexed with A Heparan Sulfate Tetrasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Heparinaseii H202A/Y257A Double Mutant Complexed with A Heparan Sulfate Tetrasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:42.3 occ:1.00 O A:HOH1162 2.0 37.9 1.0 NE2 A:HIS451 2.2 49.8 1.0 OD1 A:ASP425 2.2 50.3 1.0 O A:HOH780 2.2 46.4 1.0 O A:HOH1189 2.3 43.7 1.0 ND1 A:HIS408 2.3 49.5 1.0 CG A:ASP425 3.0 50.3 1.0 CD2 A:HIS451 3.0 49.6 1.0 CE1 A:HIS408 3.0 49.3 1.0 OD2 A:ASP425 3.1 49.9 1.0 CE1 A:HIS451 3.2 49.5 1.0 CG A:HIS408 3.4 49.7 1.0 CB A:HIS408 3.9 49.6 1.0 O A:PHE445 4.1 49.4 1.0 O A:HOH1141 4.1 36.0 1.0 N A:GLY306 4.1 49.5 1.0 CG A:HIS451 4.1 49.9 1.0 ND1 A:HIS451 4.2 49.5 1.0 NE2 A:HIS408 4.2 49.3 1.0 O A:GLY306 4.4 49.3 1.0 CB A:ASP425 4.4 50.2 1.0 CD2 A:HIS408 4.4 49.8 1.0 OD2 A:ASP410 4.5 49.5 1.0 CE1 A:PHE445 4.6 50.0 1.0 CA A:GLY306 4.6 49.4 1.0 O A:ALA426 4.7 50.0 1.0 C A:GLY306 4.8 49.4 1.0 O A:HOH836 4.9 28.9 1.0 C A:ASP425 4.9 50.1 1.0 C A:GLY305 5.0 49.6 1.0 CA A:ASP425 5.0 50.0 1.0

Zinc binding site 2 out of 2 in the Heparinaseii H202A/Y257A Double Mutant Complexed with A Heparan Sulfate Tetrasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Heparinaseii H202A/Y257A Double Mutant Complexed with A Heparan Sulfate Tetrasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:55.3 occ:1.00 NE2 B:HIS451 2.2 49.9 1.0 O B:HOH1347 2.2 72.0 1.0 O B:HOH1287 2.2 42.6 1.0 ND1 B:HIS408 2.2 49.5 1.0 OD1 B:ASP425 2.2 50.2 1.0 O B:HOH1249 2.3 57.7 1.0 CE1 B:HIS408 2.9 49.3 1.0 CD2 B:HIS451 3.0 49.7 1.0 CG B:ASP425 3.1 50.2 1.0 CE1 B:HIS451 3.1 49.6 1.0 OD2 B:ASP425 3.2 49.9 1.0 CG B:HIS408 3.3 49.7 1.0 CB B:HIS408 3.9 49.6 1.0 O B:PHE445 3.9 49.6 1.0 O B:HOH1265 4.0 42.0 1.0 NE2 B:HIS408 4.1 49.3 1.0 CG B:HIS451 4.2 49.8 1.0 ND1 B:HIS451 4.2 49.6 1.0 N B:GLY306 4.2 49.6 1.0 CD2 B:HIS408 4.3 49.8 1.0 O B:GLY306 4.5 49.4 1.0 CB B:ASP425 4.5 50.1 1.0 CE1 B:PHE445 4.5 50.0 1.0 OD2 B:ASP410 4.6 49.6 1.0 O B:ALA426 4.6 49.9 1.0 CA B:GLY306 4.7 49.5 1.0 CD1 B:PHE445 4.8 49.9 1.0 C B:GLY306 4.9 49.4 1.0 CZ B:PHE445 5.0 50.0 1.0 C B:ASP425 5.0 50.0 1.0

D.Shaya, W.Zhao, M.L.Garron, Z.Xiao, Q.Cui, Z.Zhang, T.Sulea, R.J.Linhardt, M.Cygler. Catalytic Mechanism of Heparinase II Investigated By Site-Directed Mutagenesis and the Crystal Structure with Its Substrate. J.Biol.Chem. V. 285 20051 2010.
ISSN: ISSN 0021-9258
PubMed: 20404324
DOI: 10.1074/JBC.M110.101071