Atomistry » Sodium » PDB 5xvd-5ysu » 5y3q
Atomistry »
  Sodium »
    PDB 5xvd-5ysu »
      5y3q »

Sodium in PDB 5y3q: Crystal Structure of Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol

Enzymatic activity of Crystal Structure of Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol

All present enzymatic activity of Crystal Structure of Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol:
3.4.19.12; 3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol, PDB code: 5y3q was solved by M.H.Lin, C.Y.Chou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.27 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 151.412, 33.264, 90.677, 90.00, 125.01, 90.00
R / Rfree (%) 14.7 / 18.4

Other elements in 5y3q:

The structure of Crystal Structure of Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol (pdb code 5y3q). 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 Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol, PDB code: 5y3q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5y3q

Go back to Sodium Binding Sites List in 5y3q
Sodium binding site 1 out of 5 in the Crystal Structure of Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol


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 Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:19.5
occ:1.00
 O A:LYS218 2.6 11.6 1.0
O A:LEU235 2.7 10.9 1.0
OH A:TYR311 2.7 12.3 1.0
OG1 A:THR313 2.8 13.1 1.0
CB A:THR313 3.3 13.7 1.0
O A:HOH728 3.4 35.5 1.0
C A:LYS218 3.5 10.4 1.0
CA A:LYS218 3.6 9.8 1.0
CZ A:TYR311 3.6 11.5 1.0
CE2 A:TYR311 3.7 11.6 1.0
CB A:LYS218 3.7 10.0 1.0
C A:LEU235 3.8 10.3 1.0
O A:HOH659 3.9 26.9 1.0
CA A:THR313 3.9 13.9 1.0
CD1 A:TYR234 4.1 14.2 1.0
CD1 A:ILE315 4.1 19.9 1.0
CG A:LYS218 4.3 10.3 1.0
N A:LEU235 4.4 10.1 1.0
CA A:LEU235 4.5 9.9 1.0
CB A:LEU235 4.5 9.8 1.0
CG2 A:THR313 4.6 13.4 1.0
CG1 A:ILE315 4.7 21.1 1.0
N A:THR219 4.7 10.7 1.0
N A:THR313 4.7 12.8 1.0
CE1 A:TYR234 4.8 15.5 1.0
CB A:TYR234 4.9 11.7 1.0
CG A:TYR234 4.9 13.1 1.0
N A:VAL236 4.9 10.7 1.0
CE1 A:TYR311 5.0 11.9 1.0

Sodium binding site 2 out of 5 in 5y3q

Go back to Sodium Binding Sites List in 5y3q
Sodium binding site 2 out of 5 in the Crystal Structure of Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol


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 Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:26.2
occ:1.00
 OD1 A:ASN263 2.0 14.9 0.5
ND1 A:HIS276 2.6 12.6 1.0
OG A:SER116 2.7 8.7 0.5
CG A:ASN263 3.0 11.3 0.5
O A:SER116 3.1 10.5 0.5
O A:SER116 3.2 10.7 0.5
O A:ALA262 3.2 8.4 1.0
CE1 A:HIS276 3.4 13.1 1.0
ND2 A:ASN263 3.5 12.4 0.5
C A:ALA262 3.7 7.9 1.0
CG A:HIS276 3.7 11.4 1.0
OG A:SER116 3.8 11.0 0.5
C A:SER116 3.8 9.8 0.5
CB A:SER116 3.8 9.3 0.5
C A:SER116 3.8 10.0 0.5
CB A:SER116 3.8 10.5 0.5
CB A:ALA120 3.9 10.1 1.0
N A:ASN263 4.0 7.6 0.5
CA A:SER116 4.0 9.4 0.5
CA A:SER116 4.0 9.9 0.5
N A:ASN263 4.0 7.9 0.5
CA A:ASN263 4.0 8.2 0.5
CB A:ASN263 4.0 8.2 0.5
CA A:ASN263 4.1 9.0 0.5
CB A:ASN263 4.1 9.8 0.5
CB A:HIS276 4.1 9.8 1.0
CA A:HIS276 4.3 8.7 1.0
CE1 A:PHE305 4.3 9.3 1.0
N A:ALA120 4.5 9.0 1.0
OD1 A:ASN263 4.5 8.3 0.5
NE2 A:HIS276 4.6 12.8 1.0
CA A:ALA120 4.6 9.8 1.0
CA A:ALA262 4.6 7.9 1.0
N A:ALA262 4.7 7.6 1.0
CD2 A:HIS276 4.8 12.3 1.0
CG A:ASN263 4.8 8.2 0.5
N A:VAL117 4.9 9.7 1.0
O A:THR275 4.9 7.7 0.5
CD1 A:PHE305 5.0 8.6 1.0

Sodium binding site 3 out of 5 in 5y3q

Go back to Sodium Binding Sites List in 5y3q
Sodium binding site 3 out of 5 in the Crystal Structure of Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol


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 Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:15.9
occ:1.00
 O A:HOH517 2.7 23.2 1.0
OG A:SER115 2.9 9.3 1.0
O A:ILE286 2.9 7.1 1.0
N A:GLY288 3.0 7.6 1.0
O A:HOH531 3.0 14.9 1.0
CB A:SER115 3.5 9.2 1.0
CD1 A:LEU119 3.5 9.4 1.0
C A:ILE286 3.7 8.0 1.0
CA A:GLY288 3.8 8.3 1.0
CA A:ASP287 3.8 8.5 1.0
C A:ASP287 3.9 8.1 1.0
OG A:SER104 4.0 8.8 1.0
N A:ASP287 4.1 8.2 1.0
C A:SER115 4.2 9.1 1.0
N A:SER116 4.2 9.6 0.5
N A:SER116 4.2 9.3 0.5
N A:HIS276 4.3 8.5 1.0
CG2 A:ILE286 4.3 9.0 1.0
CB A:HIS276 4.4 9.8 1.0
CA A:SER115 4.5 8.8 1.0
O A:SER115 4.6 9.3 1.0
CA A:THR275 4.6 8.8 0.5
O A:TYR274 4.7 7.8 0.5
O A:CYS112 4.7 9.0 1.0
CA A:THR275 4.7 9.2 0.5
O A:GLY288 4.7 8.7 1.0
CA A:SER116 4.8 9.4 0.5
CB A:ILE286 4.8 8.5 1.0
CA A:SER116 4.8 9.9 0.5
O A:HOH738 4.8 12.4 1.0
C A:GLY288 4.8 8.0 1.0
OG A:SER116 4.8 11.0 0.5
C A:THR275 4.8 8.4 0.5
CA A:ILE286 4.9 8.1 1.0
CG A:LEU119 4.9 9.3 1.0
C A:THR275 4.9 8.6 0.5
OD1 A:ASP287 5.0 10.7 1.0
O A:HOH636 5.0 12.0 1.0

Sodium binding site 4 out of 5 in 5y3q

Go back to Sodium Binding Sites List in 5y3q
Sodium binding site 4 out of 5 in the Crystal Structure of Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol


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 Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:27.4
occ:1.00
 O A:HOH723 2.8 34.1 1.0
OH A:TYR72 2.9 23.7 1.0
ND2 A:ASN147 2.9 16.8 0.5
O A:ALA132 2.9 13.2 1.0
C A:ALA132 3.7 13.8 1.0
CB A:ALA136 3.7 16.3 1.0
CA A:ALA132 3.8 14.0 1.0
CZ A:TYR72 3.8 17.5 1.0
N A:ALA136 3.8 16.4 1.0
CD1 A:LEU151 4.0 13.4 1.0
CE2 A:TYR72 4.1 17.2 1.0
CA A:ALA136 4.2 15.9 1.0
CG A:ASN147 4.2 16.1 0.5
CB A:GLU135 4.2 18.9 1.0
CB A:ALA132 4.4 14.4 1.0
OE1 A:GLU135 4.5 27.3 1.0
OH A:TYR84 4.6 20.7 1.0
C A:GLU135 4.6 16.8 1.0
O A:HOH629 4.6 29.6 1.0
O A:PRO131 4.8 14.9 1.0
OD1 A:ASN147 4.9 18.9 0.5
CE1 A:TYR72 4.9 16.4 1.0
CA A:GLU135 4.9 17.4 1.0

Sodium binding site 5 out of 5 in 5y3q

Go back to Sodium Binding Sites List in 5y3q
Sodium binding site 5 out of 5 in the Crystal Structure of Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol


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 Sars Coronavirus Papain-Like Protease Conjugated with Beta-Mercaptoethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:17.0
occ:1.00
 O A:VAL206 2.8 10.5 1.0
O A:MET244 2.9 8.1 1.0
NH1 A:ARG184 3.0 9.8 1.0
NH2 A:ARG184 3.0 9.9 1.0
SD A:MET245 3.3 8.1 1.0
CZ A:ARG184 3.4 9.4 1.0
N A:TYR208 3.4 9.4 1.0
CB A:TYR208 3.5 8.9 1.0
C A:VAL206 3.5 9.4 1.0
C A:MET244 3.6 7.2 1.0
N A:MET244 3.6 7.5 1.0
CB A:VAL243 3.7 8.5 1.0
C A:MET207 3.7 9.4 1.0
CA A:MET207 3.9 9.5 1.0
N A:MET207 3.9 9.1 1.0
CA A:TYR208 4.0 9.2 1.0
CA A:MET244 4.3 7.4 1.0
N A:MET245 4.3 6.9 1.0
CA A:VAL243 4.3 7.9 1.0
CG1 A:VAL243 4.3 8.6 1.0
C A:VAL243 4.3 7.9 1.0
O A:MET207 4.3 11.2 1.0
CA A:VAL206 4.4 9.0 1.0
CG A:MET245 4.4 7.1 1.0
CG2 A:VAL243 4.5 8.9 1.0
CA A:MET245 4.6 7.1 1.0
CE A:MET245 4.6 8.9 1.0
CG A:TYR208 4.7 8.8 1.0
NE A:ARG184 4.7 8.9 1.0
CD2 A:LEU217 4.8 9.6 1.0
O A:ALA205 4.8 9.4 1.0

Reference:

M.H.Lin, D.C.Moses, C.H.Hsieh, S.C.Cheng, Y.H.Chen, C.Y.Sun, C.Y.Chou. Disulfiram Can Inhibit Mers and Sars Coronavirus Papain-Like Proteases Via Different Modes Antiviral Res. V. 150 155 2017.
ISSN: ISSN 1872-9096
PubMed: 29289665
DOI: 10.1016/J.ANTIVIRAL.2017.12.015
Page generated: Tue Oct 8 01:20:13 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy