Chlorine in PDB 5xu8: Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine

Enzymatic activity of Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine

All present enzymatic activity of Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine:
3.4.19.12;

Protein crystallography data

The structure of Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine, PDB code: 5xu8 was solved by C.Y.Chou, S.J.Chuang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.953, 54.650, 72.687, 90.00, 107.54, 90.00
R / Rfree (%) 17.9 / 23.8

Other elements in 5xu8:

The structure of Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine (pdb code 5xu8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine, PDB code: 5xu8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5xu8

Go back to Chlorine Binding Sites List in 5xu8
Chlorine binding site 1 out of 5 in the Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine


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 USP2 in Complex with Ubiquitin and 6- Thioguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl703

b:61.1
occ:1.00
 N A:LYS514 3.0 35.0 1.0
CB A:THR552 3.4 34.3 1.0
CB A:SER513 3.5 39.7 1.0
CA A:SER513 3.5 38.7 1.0
CA A:THR552 3.6 35.0 1.0
N A:THR553 3.6 39.3 1.0
CB A:LYS514 3.7 30.0 1.0
C A:SER513 3.8 35.2 1.0
CA A:LYS514 4.0 29.8 1.0
CG2 A:THR552 4.0 37.7 1.0
C A:THR552 4.1 37.1 1.0
CG2 A:THR553 4.4 38.0 1.0
OG1 A:THR553 4.5 44.8 1.0
OG1 A:THR552 4.6 34.9 1.0
O A:LYS514 4.6 33.2 1.0
OG A:SER513 4.7 44.7 1.0
O A:THR512 4.8 43.8 1.0
CA A:THR553 4.8 42.9 1.0
CB A:THR553 4.8 44.4 1.0
C A:LYS514 4.8 32.4 1.0
N A:SER513 4.9 39.8 1.0
N A:THR552 5.0 32.8 1.0

Chlorine binding site 2 out of 5 in 5xu8

Go back to Chlorine Binding Sites List in 5xu8
Chlorine binding site 2 out of 5 in the Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine


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 USP2 in Complex with Ubiquitin and 6- Thioguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl704

b:80.4
occ:1.00
 O A:HOH891 2.9 56.1 1.0
O A:HOH947 3.1 90.8 1.0
CA A:SER308 3.7 64.9 1.0
O A:GLY307 3.9 65.1 1.0
N A:SER308 4.0 56.1 1.0
C A:GLY307 4.0 57.7 1.0
CB A:SER308 4.1 64.5 1.0
N A:GLY307 4.8 49.3 1.0
C A:SER308 4.9 73.2 1.0
CA A:GLY307 5.0 56.2 1.0

Chlorine binding site 3 out of 5 in 5xu8

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Chlorine binding site 3 out of 5 in the Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine


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 USP2 in Complex with Ubiquitin and 6- Thioguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl101

b:68.0
occ:1.00
 NZ B:LYS27 3.0 46.4 1.0
O B:HOH222 3.0 37.6 1.0
O B:HOH212 3.0 28.8 1.0
O A:HOH850 3.0 51.5 1.0
NE2 B:GLN49 3.2 30.6 1.0
O B:GLN41 3.3 27.5 1.0
O B:HOH236 3.6 36.6 1.0
CE B:LYS27 3.9 40.1 1.0
CD B:GLN49 4.1 29.3 1.0
NH2 B:ARG72 4.1 30.4 1.0
CA B:ARG42 4.1 26.2 1.0
O B:LEU50 4.1 32.9 1.0
CG B:ARG42 4.2 23.3 1.0
NH2 A:ARG349 4.2 48.3 1.0
CG B:GLN49 4.4 27.6 1.0
C B:GLN41 4.4 28.6 1.0
CB B:ARG42 4.4 24.9 1.0
N B:ARG42 4.7 26.5 1.0
NH1 A:ARG349 4.9 51.7 1.0
OE1 A:GLU360 4.9 31.0 1.0

Chlorine binding site 4 out of 5 in 5xu8

Go back to Chlorine Binding Sites List in 5xu8
Chlorine binding site 4 out of 5 in the Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl102

b:69.0
occ:1.00
 OG1 B:THR7 2.7 29.4 1.0
OG1 B:THR9 2.8 42.5 1.0
N B:THR9 2.9 30.8 1.0
N B:LYS11 2.9 34.5 1.0
N B:GLY10 3.1 33.4 1.0
OE1 A:GLU507 3.4 73.8 1.0
CB B:LYS11 3.4 39.4 1.0
CA B:THR9 3.4 35.3 1.0
C B:THR9 3.5 35.9 1.0
CA B:LYS11 3.6 35.4 1.0
N B:LEU8 3.6 28.4 1.0
CB B:THR9 3.7 40.2 1.0
O B:HOH209 3.8 42.4 1.0
C B:THR7 3.8 28.4 1.0
O B:LYS11 3.9 31.4 1.0
C B:GLY10 3.9 37.0 1.0
O B:HOH214 3.9 36.1 1.0
CB B:THR7 3.9 31.0 1.0
C B:LEU8 4.0 31.9 1.0
CA B:GLY10 4.1 36.4 1.0
C B:LYS11 4.1 31.4 1.0
CE B:LYS11 4.2 61.2 1.0
CA B:THR7 4.3 27.1 1.0
CA B:LEU8 4.3 30.1 1.0
CG B:LYS11 4.4 50.2 1.0
O B:THR7 4.4 27.2 1.0
O B:THR9 4.4 39.5 1.0
CD B:LYS11 4.5 53.5 1.0
CD A:GLU507 4.6 72.5 1.0
NZ B:LYS11 4.6 57.3 1.0
CG2 B:THR9 4.6 46.8 1.0
N B:THR7 4.7 24.3 1.0

Chlorine binding site 5 out of 5 in 5xu8

Go back to Chlorine Binding Sites List in 5xu8
Chlorine binding site 5 out of 5 in the Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl103

b:74.5
occ:1.00
 N B:THR22 2.9 40.0 1.0
CB B:ASN25 3.0 43.5 1.0
OG1 B:THR22 3.0 39.3 1.0
ND2 B:ASN25 3.0 56.9 1.0
CG B:ASN25 3.3 50.4 1.0
CG2 B:THR22 3.6 39.3 1.0
CB B:THR22 3.6 37.0 1.0
CA B:ASP21 3.7 38.0 1.0
C B:ASP21 3.8 39.2 1.0
CA B:THR22 3.8 37.2 1.0
CA B:ASN25 4.3 36.8 1.0
O B:HOH204 4.3 59.7 1.0
CB B:ASP21 4.4 42.3 1.0
OD1 B:ASN25 4.4 61.6 1.0
O B:THR22 4.4 32.1 1.0
O B:HOH211 4.4 42.0 1.0
O B:SER20 4.5 38.4 1.0
N B:ASN25 4.5 37.8 1.0
C B:THR22 4.6 34.8 1.0
OD1 B:ASP21 4.6 44.3 1.0
CG B:ASP21 4.7 47.8 1.0
N B:ASP21 4.8 38.9 1.0
O B:ASP21 5.0 38.7 1.0

Reference:

S.J.Chuang, S.C.Cheng, H.C.Tang, C.Y.Sun, C.Y.Chou. 6-Thioguanine Is A Noncompetitive and Slow Binding Inhibitor of Human Deubiquitinating Protease USP2 Sci Rep V. 8 3102 2018.
ISSN: ESSN 2045-2322
PubMed: 29449607
DOI: 10.1038/S41598-018-21476-W
Page generated: Sat Dec 12 12:39:37 2020

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