Chlorine in PDB 5e8m: Crystal Structure of Human Heparanase

All present enzymatic activity of Crystal Structure of Human Heparanase:
3.2.1.166;

The structure of Crystal Structure of Human Heparanase, PDB code: 5e8m was solved by L.Wu, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.64 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.765, 70.972, 78.948, 90.00, 94.17, 90.00
R / Rfree (%)	16.4 / 20

The binding sites of Chlorine atom in the Crystal Structure of Human Heparanase (pdb code 5e8m). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Human Heparanase, PDB code: 5e8m:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Human Heparanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Heparanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl621 b:57.8 occ:1.00 OE1 A:GLN270 2.9 38.0 1.0 N A:GLN270 3.5 27.3 1.0 O A:HOH864 3.5 54.1 1.0 CD A:GLN270 3.7 36.9 1.0 O A:HIS296 3.7 24.0 1.0 CA A:GLY269 3.7 27.4 1.0 CG A:GLN270 3.8 34.3 1.0 C A:HIS296 4.1 23.8 1.0 C A:GLY269 4.1 28.3 1.0 CD1 A:TYR298 4.2 25.9 1.0 CB A:GLN270 4.2 36.2 1.0 CB A:HIS296 4.2 23.4 1.0 O1 A:EDO613 4.3 58.2 1.0 N A:HIS297 4.4 22.7 1.0 CA A:HIS297 4.4 21.6 1.0 OE2 A:GLU225 4.4 35.4 1.0 CA A:GLN270 4.4 29.3 1.0 N A:TYR298 4.5 22.1 1.0 C A:HIS297 4.7 23.8 1.0 CE1 A:TYR298 4.7 26.3 1.0 CA A:HIS296 4.8 20.6 1.0 C1 A:EDO613 4.9 55.7 1.0 NE2 A:GLN270 4.9 38.3 1.0 CD A:GLU225 5.0 43.0 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Human Heparanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Heparanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl622 b:33.9 occ:1.00 O B:HOH238 3.0 53.2 1.0 O B:HOH245 3.0 55.2 1.0 O A:HOH850 3.1 33.3 1.0 O A:HOH746 3.2 29.9 1.0 N A:ALA388 3.3 36.2 1.0 CA A:GLY387 3.7 30.3 1.0 CB B:ASP27 3.9 30.8 1.0 CD1 B:LEU30 4.0 33.1 1.0 CB B:LEU30 4.0 31.4 1.0 N B:LEU30 4.0 31.9 1.0 C A:GLY387 4.0 32.2 1.0 CB A:ALA388 4.0 41.5 1.0 CA B:LEU30 4.2 32.8 1.0 CA A:ALA388 4.3 38.6 1.0 CG B:LEU30 4.5 32.2 1.0 C B:ASN29 4.7 35.8 1.0 O B:ASP27 4.7 29.1 1.0 CB B:ASN29 4.7 35.7 1.0 CG B:ASP27 4.7 34.1 1.0 CA B:ASP27 4.9 28.1 1.0 O B:HOH213 5.0 47.5 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Human Heparanase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Heparanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl623 b:41.8 occ:1.00 N A:GLY239 3.4 35.5 1.0 CA A:MET278 3.6 32.6 1.0 CB A:MET278 3.7 33.3 1.0 CA A:ASN238 3.8 39.0 1.0 CB A:ASN238 3.8 39.7 1.0 OG A:SER281 4.0 46.8 1.0 N A:MET278 4.0 32.0 1.0 CE A:MET278 4.0 43.0 1.0 C A:ASN238 4.1 35.4 1.0 CG A:MET278 4.1 41.1 1.0 CZ A:PHE236 4.2 46.5 1.0 CA A:GLY239 4.3 39.1 1.0 O A:HOH823 4.4 39.7 1.0 C A:LYS277 4.5 32.1 1.0 O A:LYS277 4.5 32.5 1.0 CG A:LYS277 4.7 40.8 1.0 CD A:LYS277 4.9 51.6 1.0 C A:MET278 4.9 30.8 1.0 CE1 A:PHE236 4.9 49.4 1.0

L.Wu, C.M.Viola, A.M.Brzozowski, G.J.Davies. Structural Characterization of Human Heparanase Reveals Insights Into Substrate Recognition. Nat.Struct.Mol.Biol. V. 22 1016 2015.
ISSN: ESSN 1545-9985
PubMed: 26575439
DOI: 10.1038/NSMB.3136