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Sodium 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:

Chlorine (Cl) 5 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Human USP2 in Complex with Ubiquitin and 6- Thioguanine, PDB code: 5xu8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5xu8

Go back to Sodium Binding Sites List in 5xu8
Sodium 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 Sodium with other atoms in the Na 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:Na705

b:73.7
occ:1.00
 O A:SER508 2.7 49.4 1.0
O A:SER506 3.0 47.8 1.0
OG1 A:THR512 3.2 57.9 1.0
CB A:THR512 3.5 56.5 1.0
C A:GLU507 3.6 58.3 1.0
N A:SER508 3.6 55.0 1.0
C A:SER508 3.6 52.9 1.0
CD1 B:LEU71 3.8 27.6 1.0
CG1 B:ILE36 3.8 38.5 1.0
CA A:GLU507 3.9 60.1 1.0
O A:GLU507 4.0 57.0 1.0
C A:SER506 4.0 49.5 1.0
CD1 B:ILE36 4.1 46.7 1.0
CA A:SER508 4.2 55.0 1.0
CD1 B:LEU8 4.3 33.4 1.0
CA A:THR512 4.4 52.9 1.0
N A:GLU507 4.4 55.5 1.0
CG2 B:ILE36 4.6 39.9 1.0
CG2 A:THR512 4.7 54.5 1.0
N A:ARG509 4.7 52.5 1.0
CB B:ILE36 4.8 40.1 1.0
CB A:SER508 4.9 54.3 1.0
OG A:SER506 4.9 48.3 1.0

Sodium binding site 2 out of 5 in 5xu8

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Sodium 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 Sodium with other atoms in the Na 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:Na706

b:41.8
occ:1.00
 O B:ALA46 2.6 29.6 1.0
O A:HOH991 2.7 55.8 1.0
OH A:TYR403 2.8 40.7 1.0
CB B:ALA46 3.7 29.1 1.0
CZ A:TYR403 3.7 35.5 1.0
C B:ALA46 3.8 31.1 1.0
CE1 A:TYR403 3.8 39.7 1.0
CE B:LYS48 3.9 57.9 1.0
NE1 A:TRP439 4.0 35.4 1.0
CG B:LYS48 4.1 42.6 1.0
CD B:LYS48 4.2 49.7 1.0
NZ B:LYS48 4.3 63.6 1.0
CA B:ALA46 4.3 30.0 1.0
O A:HOH982 4.4 61.1 1.0
CG A:GLU407 4.5 43.0 1.0
O B:HOH219 4.6 48.9 1.0
CD A:GLU407 4.7 44.5 1.0
CD1 A:TRP439 4.8 32.0 1.0
OE1 A:GLU407 4.8 45.6 1.0
CE2 A:TRP439 4.8 38.5 1.0
N B:GLY47 4.9 30.2 1.0

Sodium binding site 3 out of 5 in 5xu8

Go back to Sodium Binding Sites List in 5xu8
Sodium 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 Sodium with other atoms in the Na 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
A:Na707

b:38.6
occ:1.00
 NA A:NA708 2.7 42.3 1.0
OG A:SER421 2.7 24.8 1.0
O B:GLU64 2.9 26.9 1.0
CB A:SER421 3.6 24.4 1.0
O B:HOH207 3.6 26.3 1.0
CE A:LYS487 3.7 26.4 1.0
CE2 B:PHE4 3.7 28.3 1.0
CB B:GLU64 3.8 30.0 1.0
CG2 A:VAL434 3.8 32.6 1.0
CD2 B:PHE4 3.9 26.6 1.0
C B:GLU64 3.9 29.3 1.0
O A:SER421 4.1 27.1 1.0
CB A:LEU423 4.2 27.0 1.0
CA B:GLU64 4.3 28.6 1.0
C A:SER421 4.3 26.3 1.0
NZ A:LYS487 4.4 25.9 1.0
CG A:LYS487 4.4 28.6 1.0
CD A:LYS487 4.5 30.3 1.0
CA A:SER421 4.6 25.8 1.0
CG B:GLU64 4.6 34.6 1.0
OG1 B:THR66 4.7 26.3 1.0
OE1 B:GLU64 4.8 42.6 1.0
CD2 A:LEU423 4.8 30.3 1.0
CZ B:PHE4 4.9 27.5 1.0
N A:LEU423 4.9 24.9 1.0
CB A:VAL434 4.9 33.2 1.0
N A:SER422 4.9 25.4 1.0

Sodium binding site 4 out of 5 in 5xu8

Go back to Sodium Binding Sites List in 5xu8
Sodium 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 Sodium with other atoms in the Na 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
A:Na708

b:42.3
occ:1.00
 NA A:NA707 2.7 38.6 1.0
O A:SER432 2.8 31.4 1.0
OE1 B:GLU64 3.1 42.6 1.0
O A:SER421 3.4 27.1 1.0
C A:SER432 3.5 33.4 1.0
CB A:LEU423 3.6 27.0 1.0
N A:VAL434 3.7 29.9 1.0
CB B:GLU64 3.9 30.0 1.0
N A:LEU423 3.9 24.9 1.0
CG1 A:VAL434 3.9 35.7 1.0
CA A:THR433 3.9 34.5 1.0
C A:THR433 3.9 34.4 1.0
N A:THR433 3.9 31.4 1.0
CD B:GLU64 4.0 42.1 1.0
CB A:SER432 4.0 33.9 1.0
CG2 A:VAL434 4.0 32.6 1.0
OG A:SER432 4.1 43.2 1.0
C A:SER421 4.3 26.3 1.0
CB A:VAL434 4.3 33.2 1.0
CA A:SER432 4.4 32.2 1.0
CG B:GLU64 4.4 34.6 1.0
CA A:LEU423 4.4 25.3 1.0
CD2 A:LEU423 4.5 30.3 1.0
OG A:SER421 4.5 24.8 1.0
C A:SER422 4.6 26.7 1.0
O B:GLU64 4.6 26.9 1.0
CA A:VAL434 4.6 30.5 1.0
CA A:SER422 4.6 26.8 0.5
O A:THR433 4.6 39.2 1.0
CA A:SER422 4.7 25.0 0.5
CG A:LEU423 4.7 28.5 1.0
N A:SER422 4.8 25.4 1.0
OE2 B:GLU64 4.9 44.5 1.0
CB A:SER421 4.9 24.4 1.0

Sodium binding site 5 out of 5 in 5xu8

Go back to Sodium Binding Sites List in 5xu8
Sodium 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 Sodium with other atoms in the Na 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
A:Na709

b:56.1
occ:1.00
 OD1 A:ASN309 3.2 78.0 1.0
OG A:SER308 3.2 61.7 1.0
CG A:ASN309 3.7 86.7 1.0
CB A:ASN309 3.9 87.2 1.0
CB A:SER308 4.0 64.5 1.0
C A:SER308 4.3 73.2 1.0
N A:ASN309 4.4 79.1 1.0
O A:SER308 4.5 78.4 1.0
ND2 A:ASN309 4.7 91.9 1.0
CA A:ASN309 4.8 86.6 1.0
CA A:SER308 4.8 64.9 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: Tue Oct 8 01:17:03 2024

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