Chlorine in PDB 5dfi: Human APE1 Phosphorothioate Substrate Complex

All present enzymatic activity of Human APE1 Phosphorothioate Substrate Complex:
4.2.99.18;

The structure of Human APE1 Phosphorothioate Substrate Complex, PDB code: 5dfi was solved by B.D.Freudenthal, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.19 / 1.63
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.418, 60.828, 73.212, 83.00, 80.53, 89.12
R / Rfree (%)	16.7 / 19.5

The binding sites of Chlorine atom in the Human APE1 Phosphorothioate Substrate Complex (pdb code 5dfi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Human APE1 Phosphorothioate Substrate Complex, PDB code: 5dfi:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Human APE1 Phosphorothioate Substrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human APE1 Phosphorothioate Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:31.5 occ:1.00 O A:HOH545 2.9 20.3 1.0 NE2 B:HIS116 2.9 15.4 1.0 OE2 A:GLU101 2.9 16.1 1.0 N A:TRP119 2.9 12.6 1.0 O A:TRP119 3.4 13.6 1.0 O B:ARG136 3.4 14.6 1.0 CD A:GLU101 3.7 19.5 1.0 CA A:TYR118 3.7 11.1 1.0 CD2 B:HIS116 3.7 14.0 1.0 OE1 A:GLU101 3.7 24.7 1.0 OH A:TYR144 3.7 12.0 1.0 C A:TYR118 3.8 11.8 1.0 CA A:TRP119 3.8 11.5 1.0 O A:HOH566 3.8 20.9 1.0 CE1 B:HIS116 4.0 10.3 1.0 CB A:TRP119 4.0 14.6 1.0 C A:TRP119 4.0 12.3 1.0 N B:CYS138 4.1 13.6 1.0 CD1 A:TRP119 4.2 11.8 1.0 O A:GLN117 4.3 16.2 1.0 CA B:GLN137 4.3 16.2 1.0 CG A:TRP119 4.5 13.3 1.0 C B:ARG136 4.5 15.1 1.0 CB A:TYR118 4.5 12.5 1.0 C B:GLN137 4.5 15.6 1.0 O B:HOH518 4.6 15.8 1.0 CZ A:TYR144 4.7 13.0 1.0 N A:TYR118 4.7 10.8 1.0 OG B:SER115 4.8 13.4 1.0 CB B:CYS138 4.9 12.5 1.0 N B:GLN137 4.9 12.7 1.0 C A:GLN117 4.9 12.7 1.0 CG B:HIS116 4.9 11.3 1.0 CD2 A:TYR118 5.0 12.4 1.0 O A:TYR118 5.0 12.4 1.0 CA B:CYS138 5.0 14.7 1.0

Chlorine binding site 2 out of 2 in the Human APE1 Phosphorothioate Substrate Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human APE1 Phosphorothioate Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:29.9 occ:1.00 N B:ARG156 3.1 16.3 1.0 O B:HOH503 3.3 26.9 1.0 N B:VAL157 3.5 11.3 1.0 CA B:GLY145 3.6 15.8 1.0 CB B:ARG156 3.8 15.3 1.0 CA B:ARG156 3.8 15.2 1.0 N B:GLY155 3.9 28.2 1.0 C B:ARG156 4.1 11.4 1.0 C B:GLY155 4.1 16.4 1.0 CB B:VAL157 4.2 12.0 1.0 CA B:GLY155 4.2 20.4 1.0 N B:GLY145 4.3 17.4 1.0 N B:GLU154 4.3 37.1 1.0 CA B:VAL157 4.4 11.9 1.0 O B:VAL157 4.5 13.9 1.0 CG2 B:VAL157 4.5 15.8 1.0 C B:GLY145 4.5 19.6 1.0 CG B:ARG156 4.6 16.9 1.0 C B:GLU154 4.7 23.7 1.0 N B:ILE146 4.7 20.4 1.0 C B:VAL157 4.9 14.9 1.0

B.D.Freudenthal, W.A.Beard, M.J.Cuneo, N.S.Dyrkheeva, S.H.Wilson. Capturing Snapshots of APE1 Processing Dna Damage. Nat.Struct.Mol.Biol. V. 22 924 2015.
ISSN: ESSN 1545-9985
PubMed: 26458045
DOI: 10.1038/NSMB.3105