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Chlorine in PDB 5zj9: Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-3- Carboxylic Acid

Enzymatic activity of Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-3- Carboxylic Acid

All present enzymatic activity of Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-3- Carboxylic Acid:
1.4.3.3;

Protein crystallography data

The structure of Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-3- Carboxylic Acid, PDB code: 5zj9 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) 39.15 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 150.140, 182.730, 51.100, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 25.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-3- Carboxylic Acid (pdb code 5zj9). 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-3- Carboxylic Acid, PDB code: 5zj9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5zj9

Go back to Chlorine Binding Sites List in 5zj9
Chlorine binding site 1 out of 4 in the Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-3- 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-3- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:33.3
occ:1.00
 CL1 A:9E6402 0.0 33.3 1.0
C5 A:9E6402 1.8 33.6 1.0
C4 A:9E6402 2.9 33.2 1.0
S1 A:9E6402 3.1 33.1 1.0
O A:LEU51 3.2 37.8 1.0
N3 A:FAD401 3.3 34.7 1.0
O A:GLN53 3.3 40.8 1.0
O A:HOH503 3.4 37.7 1.0
C4 A:FAD401 3.5 36.0 1.0
O4 A:FAD401 3.5 36.3 1.0
OH A:TYR224 3.7 37.6 1.0
N A:GLN53 3.9 34.7 1.0
CB A:GLN53 3.9 34.9 1.0
O A:GLY313 4.0 38.9 1.0
C2 A:FAD401 4.0 36.2 1.0
C A:LEU51 4.1 34.8 1.0
C2 A:9E6402 4.1 36.0 1.0
OG1 A:THR317 4.2 36.3 1.0
C A:GLN53 4.2 41.2 1.0
CA A:GLN53 4.2 40.6 1.0
CB A:LEU51 4.2 27.8 1.0
C7 A:9E6402 4.3 33.0 1.0
CZ A:TYR224 4.4 39.0 1.0
C4X A:FAD401 4.4 35.3 1.0
O2 A:FAD401 4.4 30.6 1.0
CG A:LEU51 4.4 30.2 1.0
CD2 A:LEU51 4.5 31.4 1.0
CA A:LEU51 4.6 31.8 1.0
C A:TRP52 4.7 31.4 1.0
N1 A:FAD401 4.8 37.9 1.0
N A:LEU51 4.9 25.4 1.0
N A:TRP52 5.0 33.0 1.0
CE2 A:TYR224 5.0 35.7 1.0

Chlorine binding site 2 out of 4 in 5zj9

Go back to Chlorine Binding Sites List in 5zj9
Chlorine binding site 2 out of 4 in the Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-3- 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-3- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:30.2
occ:1.00
 CL1 B:9E6402 0.0 30.2 1.0
C5 B:9E6402 1.8 29.8 1.0
C4 B:9E6402 2.9 28.5 1.0
O B:LEU51 3.1 31.1 1.0
S1 B:9E6402 3.1 26.8 1.0
N3 B:FAD401 3.2 25.0 1.0
O4 B:FAD401 3.3 29.9 1.0
C4 B:FAD401 3.3 28.3 1.0
O B:HOH514 3.5 31.3 1.0
O B:GLN53 3.5 30.8 1.0
OH B:TYR224 3.6 37.2 1.0
N B:GLN53 3.9 37.6 1.0
C2 B:FAD401 4.0 25.8 1.0
C B:LEU51 4.0 31.4 1.0
O B:GLY313 4.0 28.5 1.0
C2 B:9E6402 4.1 30.1 1.0
CB B:GLN53 4.1 29.5 1.0
OG1 B:THR317 4.2 31.4 1.0
C4X B:FAD401 4.2 30.0 1.0
CB B:LEU51 4.2 27.6 1.0
C B:GLN53 4.3 37.9 1.0
C7 B:9E6402 4.3 30.2 1.0
CA B:GLN53 4.3 32.5 1.0
CZ B:TYR224 4.4 32.9 1.0
O2 B:FAD401 4.4 26.6 1.0
CD2 B:LEU51 4.5 27.0 1.0
CG B:LEU51 4.5 28.1 1.0
CA B:LEU51 4.6 30.3 1.0
C B:TRP52 4.7 34.7 1.0
N1 B:FAD401 4.7 24.8 1.0
N B:LEU51 4.8 31.5 1.0
C10 B:FAD401 4.8 24.8 1.0
N B:TRP52 4.9 33.1 1.0
CE2 B:TYR224 4.9 34.7 1.0
N5 B:FAD401 4.9 26.8 1.0

Chlorine binding site 3 out of 4 in 5zj9

Go back to Chlorine Binding Sites List in 5zj9
Chlorine binding site 3 out of 4 in the Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-3- 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-3- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl402

b:21.1
occ:1.00
 CL1 C:9E6402 0.0 21.1 1.0
C5 C:9E6402 1.8 25.5 1.0
C4 C:9E6402 2.9 24.3 1.0
O C:LEU51 3.1 25.1 1.0
S1 C:9E6402 3.1 26.9 1.0
N3 C:FAD401 3.3 22.3 1.0
O4 C:FAD401 3.4 25.0 1.0
O C:GLN53 3.4 25.2 1.0
OH C:TYR224 3.5 31.0 1.0
C4 C:FAD401 3.5 23.1 1.0
N C:GLN53 3.8 25.7 1.0
C C:LEU51 3.9 25.7 1.0
CB C:GLN53 4.0 26.6 1.0
CB C:LEU51 4.0 18.9 1.0
C2 C:9E6402 4.1 27.4 1.0
C2 C:FAD401 4.1 23.4 1.0
O C:GLY313 4.1 26.5 1.0
CD2 C:LEU51 4.2 23.9 1.0
OG1 C:THR317 4.2 27.6 1.0
CA C:GLN53 4.2 28.4 1.0
C C:GLN53 4.3 28.1 1.0
CZ C:TYR224 4.3 21.9 1.0
C7 C:9E6402 4.3 27.0 1.0
C4X C:FAD401 4.4 23.1 1.0
CA C:LEU51 4.5 23.0 1.0
CG C:LEU51 4.5 23.9 1.0
O2 C:FAD401 4.5 23.7 1.0
C C:TRP52 4.6 25.5 1.0
N C:TRP52 4.8 24.9 1.0
N C:LEU51 4.8 18.2 1.0
CE2 C:TYR224 4.8 24.1 1.0
N1 C:FAD401 4.9 27.4 1.0

Chlorine binding site 4 out of 4 in 5zj9

Go back to Chlorine Binding Sites List in 5zj9
Chlorine binding site 4 out of 4 in the Human D-Amino Acid Oxidase Complexed with 5-Chlorothiophene-3- 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-3- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:25.1
occ:1.00
 CL1 D:9E6402 0.0 25.1 1.0
C5 D:9E6402 1.8 27.9 1.0
C4 D:9E6402 2.9 27.5 1.0
O D:LEU51 3.1 34.5 1.0
S1 D:9E6402 3.1 28.7 1.0
O D:GLN53 3.2 35.1 1.0
N3 D:FAD401 3.3 26.0 1.0
O4 D:FAD401 3.4 27.1 1.0
O D:HOH507 3.4 33.6 1.0
C4 D:FAD401 3.4 31.7 1.0
OH D:TYR224 3.5 34.4 1.0
N D:GLN53 3.8 33.4 1.0
CB D:GLN53 4.0 26.8 1.0
C D:LEU51 4.0 30.8 1.0
O D:GLY313 4.0 31.6 1.0
C2 D:9E6402 4.1 29.5 1.0
C2 D:FAD401 4.1 26.3 1.0
C D:GLN53 4.1 32.1 1.0
CA D:GLN53 4.2 28.3 1.0
OG1 D:THR317 4.2 32.9 1.0
CB D:LEU51 4.2 23.1 1.0
CZ D:TYR224 4.3 28.7 1.0
C7 D:9E6402 4.3 34.3 1.0
C4X D:FAD401 4.4 30.4 1.0
CD2 D:LEU51 4.4 29.0 1.0
CG D:LEU51 4.4 27.3 1.0
O2 D:FAD401 4.6 26.8 1.0
CA D:LEU51 4.6 30.0 1.0
C D:TRP52 4.7 29.3 1.0
CE2 D:TYR224 4.9 30.2 1.0
N D:LEU51 4.9 27.4 1.0
N D:TRP52 4.9 26.1 1.0
N1 D:FAD401 4.9 28.1 1.0

Reference:

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
Page generated: Sat Jul 12 11:10:28 2025

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