Zinc in PDB 2fuq: Crystal Structure of Heparinase II

The structure of Crystal Structure of Heparinase II, PDB code: 2fuq 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)	102.60 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.046, 119.339, 200.700, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.5

The binding sites of Zinc atom in the Crystal Structure of Heparinase II (pdb code 2fuq). 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 Heparinase II, PDB code: 2fuq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Heparinase II


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 Heparinase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:23.7 occ:1.00 OD1 A:ASP425 2.1 30.8 1.0 NE2 A:HIS451 2.1 27.8 1.0 O A:HOH1320 2.2 14.7 1.0 ND1 A:HIS408 2.2 23.9 1.0 O A:HOH1339 2.3 18.9 1.0 O A:HOH1319 2.3 12.2 1.0 CG A:ASP425 2.9 29.3 1.0 CE1 A:HIS408 3.0 24.5 1.0 CE1 A:HIS451 3.1 26.8 1.0 CD2 A:HIS451 3.1 27.1 1.0 OD2 A:ASP425 3.1 30.0 1.0 CG A:HIS408 3.4 26.9 1.0 CB A:HIS408 3.8 27.3 1.0 O A:PHE445 4.0 28.0 1.0 O A:HOH980 4.1 16.0 1.0 ND1 A:HIS451 4.1 27.4 1.0 CG A:HIS451 4.2 27.9 1.0 NE2 A:HIS408 4.2 25.2 1.0 N A:GLY306 4.2 25.9 1.0 O A:GLY306 4.3 24.7 1.0 CB A:ASP425 4.4 28.7 1.0 CD2 A:HIS408 4.4 25.4 1.0 OD2 A:ASP410 4.5 29.2 1.0 CE1 A:PHE445 4.5 26.9 1.0 O A:ALA426 4.7 27.4 1.0 CA A:GLY306 4.7 25.4 1.0 CD1 A:PHE445 4.9 26.9 1.0 C A:GLY306 4.9 25.0 1.0 CZ A:PHE445 5.0 26.2 1.0 C A:ASP425 5.0 28.1 1.0 CA A:ASP425 5.0 28.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Heparinase II


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 Heparinase II within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:29.1 occ:1.00 OD1 B:ASP425 2.0 26.2 1.0 ND1 B:HIS408 2.1 23.9 1.0 NE2 B:HIS451 2.2 28.2 1.0 O B:HOH1328 2.3 21.8 1.0 O B:HOH1327 2.3 16.4 1.0 O B:HOH1306 2.3 23.1 1.0 CE1 B:HIS408 2.8 23.9 1.0 CG B:ASP425 3.0 28.5 1.0 CD2 B:HIS451 3.1 28.6 1.0 CE1 B:HIS451 3.2 29.6 1.0 OD2 B:ASP425 3.2 29.4 1.0 CG B:HIS408 3.3 25.2 1.0 CB B:HIS408 3.9 26.3 1.0 O B:PHE445 3.9 27.3 1.0 NE2 B:HIS408 4.0 23.3 1.0 O B:HOH972 4.2 22.5 1.0 N B:GLY306 4.2 26.1 1.0 ND1 B:HIS451 4.2 30.4 1.0 CG B:HIS451 4.2 29.6 1.0 CD2 B:HIS408 4.3 23.8 1.0 O B:GLY306 4.4 25.8 1.0 CB B:ASP425 4.4 28.1 1.0 OD2 B:ASP410 4.5 29.8 1.0 CE1 B:PHE445 4.5 26.1 1.0 O B:ALA426 4.7 27.2 1.0 CA B:GLY306 4.7 25.6 1.0 CD1 B:PHE445 4.9 25.9 1.0 C B:GLY306 4.9 25.5 1.0 C B:ASP425 5.0 28.2 1.0 CA B:ASP425 5.0 28.2 1.0 CZ B:PHE445 5.0 25.3 1.0

D.Shaya, A.Tocilj, Y.Li, J.Myette, G.Venkataraman, R.Sasisekharan, M.Cygler. Crystal Structure of Heparinase II From Pedobacter Heparinus and Its Complex with A Disaccharide Product. J.Biol.Chem. V. 281 15525 2006.
ISSN: ISSN 0021-9258
PubMed: 16565082
DOI: 10.1074/JBC.M512055200