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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

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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

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