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Chlorine in PDB 5l9z: Crystal Structure of Human Heparanase Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355

Enzymatic activity of Crystal Structure of Human Heparanase Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355

All present enzymatic activity of Crystal Structure of Human Heparanase Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355:
3.2.1.166;

Protein crystallography data

The structure of Crystal Structure of Human Heparanase Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355, PDB code: 5l9z was solved by L.Wu, Y.Jin, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.00 / 1.57
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 46.190, 71.050, 78.690, 90.00, 95.20, 90.00
R / Rfree (%) 16.6 / 19.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Heparanase Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355 (pdb code 5l9z). 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 Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355, PDB code: 5l9z:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5l9z

Go back to Chlorine Binding Sites List in 5l9z
Chlorine binding site 1 out of 3 in the Crystal Structure of Human Heparanase Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355


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 Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl611

b:57.0
occ:1.00
 O A:HOH989 3.0 55.2 1.0
NZ A:LYS337 3.4 28.8 1.0
NH1 A:ARG334 3.8 33.3 1.0
CD A:ARG334 3.9 27.9 1.0
CE A:LYS337 3.9 29.6 1.0
CA A:GLU288 4.1 30.1 1.0
O A:GLY287 4.1 27.6 1.0
CG A:GLU288 4.3 40.1 1.0
O A:HOH1010 4.5 54.1 1.0
C A:GLY287 4.6 26.0 1.0
N A:GLU288 4.6 25.8 1.0
O A:HOH804 4.6 39.3 1.0
CB A:GLU288 4.7 33.5 1.0
CZ A:ARG334 4.7 32.6 1.0
NE A:ARG334 4.7 29.9 1.0
O A:GLU288 4.8 32.0 1.0
C A:GLU288 4.9 29.2 1.0
CG A:ARG334 4.9 27.7 1.0
CB A:ARG334 4.9 26.1 1.0

Chlorine binding site 2 out of 3 in 5l9z

Go back to Chlorine Binding Sites List in 5l9z
Chlorine binding site 2 out of 3 in the Crystal Structure of Human Heparanase Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355


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 Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl612

b:32.4
occ:1.00
 O A:HOH726 3.0 37.8 1.0
O A:HOH896 3.1 34.9 1.0
N A:GLY239 3.3 26.3 1.0
CA A:MET278 3.5 23.8 1.0
CB A:MET278 3.7 23.7 1.0
OG A:SER281 3.8 24.8 0.5
CA A:ASN238 3.8 28.4 1.0
CB A:ASN238 3.9 30.1 1.0
CG A:MET278 4.0 26.4 1.0
N A:MET278 4.1 24.0 1.0
CE A:MET278 4.1 28.0 1.0
C A:ASN238 4.1 24.2 1.0
CZ A:PHE236 4.1 38.1 1.0
CA A:GLY239 4.2 25.8 1.0
C A:LYS277 4.5 26.4 1.0
O A:HOH902 4.5 26.4 1.0
O A:LYS277 4.6 25.9 1.0
CG A:LYS277 4.7 34.1 1.0
CE A:LYS277 4.8 48.3 1.0
C A:MET278 4.8 23.3 1.0
OG A:SER281 4.8 27.2 0.5
CE1 A:PHE236 4.8 37.8 1.0
CB A:SER281 4.9 25.6 0.5
CE2 A:PHE236 4.9 38.5 1.0
SD A:MET278 5.0 28.6 1.0
CD A:LYS277 5.0 40.8 1.0

Chlorine binding site 3 out of 3 in 5l9z

Go back to Chlorine Binding Sites List in 5l9z
Chlorine binding site 3 out of 3 in the Crystal Structure of Human Heparanase Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355


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 Nucleophile Mutant (E343Q), in Complex with Unreacted Glucuronic Acid Configured Aziridine Probe JJB355 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl613

b:26.8
occ:1.00
 O B:HOH346 3.1 44.6 1.0
O B:HOH360 3.1 38.6 1.0
O A:HOH915 3.2 23.9 1.0
O A:HOH783 3.3 24.9 1.0
N A:ALA388 3.3 24.2 1.0
CA A:GLY387 3.7 23.6 1.0
CB B:LEU65 3.9 26.4 1.0
CD1 B:LEU65 4.0 26.6 1.0
C A:GLY387 4.0 24.4 1.0
CB B:ASP62 4.0 23.3 1.0
CB A:ALA388 4.1 27.3 1.0
N B:LEU65 4.1 25.5 1.0
CA B:LEU65 4.1 25.9 1.0
CA A:ALA388 4.3 25.8 1.0
CG B:LEU65 4.5 27.5 1.0
C B:ASN64 4.7 26.9 1.0
CB B:ASN64 4.7 30.8 1.0
O B:ASP62 4.7 24.7 1.0
CG B:ASP62 4.9 29.9 1.0
N A:GLY389 4.9 24.6 1.0
CA B:ASP62 5.0 21.1 1.0
O A:PHE386 5.0 21.1 1.0

Reference:

L.Wu, J.Jiang, Y.Jin, W.W.Kallemeijn, C.L.Kuo, M.Artola, W.Dai, C.Van Elk, M.Van Eijk, G.A.Van Der Marel, J.D.C.Codee, B.I.Florea, J.M.F.G.Aerts, H.S.Overkleeft, G.J.Davies. Activity-Based Probes For Functional Interrogation of Retaining Beta-Glucuronidases. Nat. Chem. Biol. V. 13 867 2017.
ISSN: ESSN 1552-4469
PubMed: 28581485
DOI: 10.1038/NCHEMBIO.2395
Page generated: Sat Jul 12 04:28:13 2025

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