Chlorine in PDB 5zja: Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid

All present enzymatic activity of Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid:
1.4.3.3;

The structure of Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid, PDB code: 5zja was solved by Y.Kato, N.Hin, N.Maita, A.G.Thomas, S.Kurosawa, C.Rojas, K.Yorita, B.S.Slusher, K.Fukui, T.Tsukamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.23 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	150.294, 182.641, 51.121, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 26

The binding sites of Chlorine atom in the Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid (pdb code 5zja). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid, PDB code: 5zja:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:66.8 occ:1.00 CL1 A:9E9402 0.0 66.8 1.0 C5 A:9E9402 1.7 61.4 1.0 C6 A:9E9402 2.7 55.2 1.0 S1 A:9E9402 3.0 65.0 1.0 H6 A:9E9402 3.0 66.3 1.0 O4 A:FAD401 3.4 44.8 1.0 O A:LEU51 3.4 59.7 1.0 C4 A:FAD401 3.5 50.2 1.0 N3 A:FAD401 3.5 45.8 1.0 OH A:TYR224 3.8 57.9 1.0 O A:GLN53 3.8 38.5 1.0 O A:HOH507 3.8 47.1 1.0 C7 A:9E9402 3.9 57.7 1.0 C2 A:9E9402 4.1 59.2 1.0 CB A:LEU51 4.1 49.7 1.0 C A:LEU51 4.1 50.1 1.0 N A:GLN53 4.2 47.5 1.0 CG A:LEU51 4.2 44.4 1.0 CB A:GLN53 4.2 46.5 1.0 CD2 A:LEU51 4.3 34.1 1.0 CZ A:TYR224 4.4 60.5 1.0 C4X A:FAD401 4.4 48.1 1.0 C2 A:FAD401 4.4 43.3 1.0 O A:GLY313 4.5 59.7 1.0 CA A:GLN53 4.6 45.7 1.0 CA A:LEU51 4.6 45.7 1.0 C A:GLN53 4.6 43.8 1.0 H7 A:9E9402 4.9 69.2 1.0 CE1 A:TYR224 4.9 49.6 1.0 C A:TRP52 4.9 46.1 1.0 N A:LEU51 4.9 44.4 1.0 O2 A:FAD401 4.9 45.3 1.0 N A:TRP52 5.0 44.5 1.0 N5 A:FAD401 5.0 45.1 1.0

Chlorine binding site 2 out of 4 in the Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:62.9 occ:1.00 CL1 B:9E9402 0.0 62.9 1.0 C5 B:9E9402 1.7 73.8 1.0 C6 B:9E9402 2.7 68.7 1.0 S1 B:9E9402 3.0 88.6 1.0 H6 B:9E9402 3.0 82.5 1.0 O B:LEU51 3.5 34.8 1.0 O B:GLN53 3.5 53.6 1.0 OH B:TYR224 3.6 68.7 1.0 N3 B:FAD401 3.6 29.8 1.0 O4 B:FAD401 3.7 36.4 1.0 C4 B:FAD401 3.8 37.9 1.0 C7 B:9E9402 3.9 71.8 1.0 N B:GLN53 4.0 50.7 1.0 CB B:GLN53 4.0 37.4 1.0 C2 B:9E9402 4.1 79.4 1.0 C B:LEU51 4.2 40.8 1.0 CZ B:TYR224 4.2 70.2 1.0 CB B:LEU51 4.2 43.4 1.0 O B:GLY313 4.3 49.6 1.0 CA B:GLN53 4.4 45.6 1.0 C B:GLN53 4.4 46.3 1.0 C2 B:FAD401 4.4 33.2 1.0 CD2 B:LEU51 4.5 24.7 1.0 CG B:LEU51 4.5 42.5 1.0 C4X B:FAD401 4.6 47.1 1.0 CA B:LEU51 4.7 46.2 1.0 CE2 B:TYR224 4.7 68.2 1.0 CE1 B:TYR224 4.8 63.0 1.0 C B:TRP52 4.8 37.5 1.0 O2 B:FAD401 4.9 41.8 1.0 H7 B:9E9402 4.9 86.1 1.0 CD2 B:LEU215 4.9 57.1 1.0 OG1 B:THR317 4.9 34.5 1.0

Chlorine binding site 3 out of 4 in the Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl402 b:59.1 occ:1.00 CL1 C:9E9402 0.0 59.1 1.0 C5 C:9E9402 1.7 57.6 1.0 C6 C:9E9402 2.7 50.9 1.0 S1 C:9E9402 3.0 60.5 1.0 H6 C:9E9402 3.0 61.0 1.0 O C:LEU51 3.3 37.4 1.0 O4 C:FAD401 3.5 41.3 1.0 O C:GLN53 3.6 30.1 1.0 N3 C:FAD401 3.6 34.4 1.0 OH C:TYR224 3.7 53.7 1.0 C4 C:FAD401 3.7 39.4 1.0 C7 C:9E9402 3.9 50.5 1.0 N C:GLN53 3.9 33.7 1.0 CB C:LEU51 3.9 17.3 1.0 CB C:GLN53 3.9 46.6 1.0 C C:LEU51 4.0 36.5 1.0 C2 C:9E9402 4.1 50.1 1.0 CD2 C:LEU51 4.2 30.4 1.0 CG C:LEU51 4.2 31.1 1.0 CA C:GLN53 4.3 44.3 1.0 C C:GLN53 4.4 26.5 1.0 CZ C:TYR224 4.4 52.9 1.0 C2 C:FAD401 4.4 32.9 1.0 CA C:LEU51 4.5 26.2 1.0 O C:GLY313 4.5 46.6 1.0 C4X C:FAD401 4.6 32.0 1.0 C C:TRP52 4.7 37.8 1.0 H7 C:9E9402 4.8 60.6 1.0 OG1 C:THR317 4.9 29.7 1.0 CG C:GLN53 4.9 41.1 1.0 O2 C:FAD401 4.9 38.9 1.0 N C:LEU51 4.9 26.2 1.0 N C:TRP52 4.9 39.5 1.0 CE1 C:TYR224 5.0 48.0 1.0

Chlorine binding site 4 out of 4 in the Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-2- Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl402 b:58.5 occ:1.00 CL1 D:9E9402 0.0 58.5 1.0 C5 D:9E9402 1.7 62.6 1.0 C6 D:9E9402 2.7 50.6 1.0 S1 D:9E9402 3.0 57.6 1.0 H6 D:9E9402 3.0 60.7 1.0 O D:LEU51 3.3 28.1 1.0 O D:HOH505 3.5 45.7 1.0 O D:GLN53 3.5 38.5 1.0 OH D:TYR224 3.6 39.6 1.0 O4 D:FAD401 3.7 39.4 1.0 N3 D:FAD401 3.7 29.1 1.0 C4 D:FAD401 3.8 47.5 1.0 CB D:GLN53 3.9 43.7 1.0 C7 D:9E9402 3.9 58.4 1.0 N D:GLN53 4.0 32.1 1.0 CB D:LEU51 4.0 39.2 1.0 C D:LEU51 4.0 36.1 1.0 C2 D:9E9402 4.1 64.7 1.0 CD2 D:LEU51 4.2 29.3 1.0 CZ D:TYR224 4.2 42.5 1.0 CG D:LEU51 4.2 43.8 1.0 CA D:GLN53 4.3 33.0 1.0 C D:GLN53 4.4 40.8 1.0 C2 D:FAD401 4.5 30.5 1.0 CA D:LEU51 4.5 36.4 1.0 O D:GLY313 4.6 41.6 1.0 C4X D:FAD401 4.7 46.6 1.0 C D:TRP52 4.7 29.7 1.0 CE2 D:TYR224 4.8 41.2 1.0 H7 D:9E9402 4.9 70.0 1.0 OG1 D:THR317 4.9 41.0 1.0 N D:LEU51 4.9 31.8 1.0 CE1 D:TYR224 4.9 43.3 1.0 N D:TRP52 5.0 29.9 1.0 CG D:GLN53 5.0 47.0 1.0 O2 D:FAD401 5.0 38.6 1.0 CD2 D:LEU215 5.0 30.9 1.0

Y.Kato, N.Hin, N.Maita, A.G.Thomas, S.Kurosawa, C.Rojas, K.Yorita, B.S.Slusher, K.Fukui, T.Tsukamoto. Structural Basis For Potent Inhibition of D-Amino Acid Oxidase By Thiophene Carboxylic Acids Eur J Med Chem V. 159 23 2018.
ISSN: ISSN 1768-3254
PubMed: 30265959
DOI: 10.1016/J.EJMECH.2018.09.040