Zinc in PDB 3e80: Structure of Heparinase II Complexed with Heparan Sulfate Degradation Disaccharide Product

The structure of Structure of Heparinase II Complexed with Heparan Sulfate Degradation Disaccharide Product, PDB code: 3e80 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)	37.57 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	201.280, 209.360, 59.220, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 26.7

The binding sites of Zinc atom in the Structure of Heparinase II Complexed with Heparan Sulfate Degradation Disaccharide Product (pdb code 3e80). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Heparinase II Complexed with Heparan Sulfate Degradation Disaccharide Product, PDB code: 3e80:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Heparinase II Complexed with Heparan Sulfate Degradation Disaccharide Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Heparinase II Complexed with Heparan Sulfate Degradation Disaccharide Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:27.9 occ:1.00 O A:HOH779 1.9 12.2 1.0 O A:HOH983 1.9 14.8 1.0 ND1 A:HIS408 2.2 25.4 1.0 NE2 A:HIS451 2.2 21.8 1.0 OD1 A:ASP425 2.2 21.0 1.0 O A:HOH778 2.4 27.4 1.0 CE1 A:HIS408 2.8 25.2 1.0 CG A:ASP425 3.0 22.2 1.0 CE1 A:HIS451 3.1 23.7 1.0 OD2 A:ASP425 3.1 19.2 1.0 CD2 A:HIS451 3.2 23.8 1.0 CG A:HIS408 3.4 24.8 1.0 NE2 A:HIS408 4.0 25.9 1.0 CB A:HIS408 4.0 23.7 1.0 N A:GLY306 4.1 21.3 1.0 O A:PHE445 4.1 22.6 1.0 ND1 A:HIS451 4.2 22.6 1.0 OD2 A:ASP410 4.3 21.9 1.0 O A:HOH792 4.3 8.3 1.0 CG A:HIS451 4.3 24.3 1.0 O A:GLY306 4.3 21.6 1.0 CD2 A:HIS408 4.3 25.7 1.0 CB A:ASP425 4.4 21.6 1.0 CE1 A:PHE445 4.5 21.6 1.0 CA A:GLY306 4.6 21.3 1.0 O A:ALA426 4.7 24.2 1.0 C A:GLY306 4.7 21.4 1.0 O A:ASP425 4.8 22.6 1.0 CD1 A:PHE445 4.9 21.1 1.0 C A:ASP425 4.9 22.7 1.0 CZ A:PHE445 4.9 21.8 1.0 C A:GLY305 4.9 20.8 1.0 O A:HOH845 5.0 7.4 1.0

Zinc binding site 2 out of 3 in the Structure of Heparinase II Complexed with Heparan Sulfate Degradation Disaccharide Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Heparinase II Complexed with Heparan Sulfate Degradation Disaccharide Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:26.4 occ:1.00 O B:HOH779 2.2 10.0 1.0 ND1 B:HIS408 2.2 23.6 1.0 O B:HOH778 2.2 14.5 1.0 O B:HOH927 2.3 19.8 1.0 OD1 B:ASP425 2.3 20.0 1.0 NE2 B:HIS451 2.3 25.9 1.0 CE1 B:HIS408 2.9 24.2 1.0 OD2 B:ASP425 2.9 20.6 1.0 CG B:ASP425 3.0 22.3 1.0 CD2 B:HIS451 3.0 25.2 1.0 CG B:HIS408 3.3 25.2 1.0 CE1 B:HIS451 3.4 25.3 1.0 CB B:HIS408 3.9 26.3 1.0 N B:GLY306 4.0 22.5 1.0 O B:HOH819 4.0 26.4 1.0 NE2 B:HIS408 4.1 23.6 1.0 O B:PHE445 4.1 24.6 1.0 CG B:HIS451 4.2 25.0 1.0 CA B:GLY306 4.3 22.6 1.0 ND1 B:HIS451 4.3 24.2 1.0 CD2 B:HIS408 4.3 24.2 1.0 CB B:ASP425 4.5 22.7 1.0 OD2 B:ASP410 4.6 30.6 1.0 O B:ALA426 4.7 24.2 1.0 O B:GLY306 4.7 22.6 1.0 CE1 B:PHE445 4.7 23.5 1.0 C B:GLY306 4.8 22.4 1.0 C B:GLY305 5.0 22.3 1.0 CD1 B:PHE445 5.0 24.2 1.0

Zinc binding site 3 out of 3 in the Structure of Heparinase II Complexed with Heparan Sulfate Degradation Disaccharide Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Heparinase II Complexed with Heparan Sulfate Degradation Disaccharide Product within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn3 b:25.0 occ:1.00 O C:HOH779 2.2 22.9 1.0 OD1 C:ASP425 2.2 21.6 1.0 ND1 C:HIS408 2.2 22.2 1.0 O C:HOH778 2.2 15.5 1.0 NE2 C:HIS451 2.3 25.9 1.0 CE1 C:HIS408 2.7 22.1 1.0 CG C:ASP425 3.0 23.2 1.0 CE1 C:HIS451 3.1 26.1 1.0 OD2 C:ASP425 3.1 22.7 1.0 CD2 C:HIS451 3.2 24.8 1.0 CG C:HIS408 3.5 24.0 1.0 O C:PHE445 3.9 24.2 1.0 NE2 C:HIS408 4.0 22.7 1.0 N C:GLY306 4.1 22.6 1.0 CB C:HIS408 4.1 24.7 1.0 ND1 C:HIS451 4.2 25.2 1.0 CG C:HIS451 4.2 24.7 1.0 O C:GLY306 4.3 22.0 1.0 CD2 C:HIS408 4.4 23.6 1.0 CB C:ASP425 4.5 23.8 1.0 O C:ALA426 4.5 23.2 1.0 CE1 C:PHE445 4.6 22.8 1.0 CA C:GLY306 4.6 22.4 1.0 C C:GLY306 4.8 22.4 1.0 O C:HOH832 4.9 7.7 1.0 CD1 C:PHE445 4.9 22.9 1.0 CZ C:PHE445 4.9 23.9 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