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Sodium in PDB 5y3e: Crystal Structure of Sars Coronavirus Papain-Like Protease in Complex with Glycerol

Enzymatic activity of Crystal Structure of Sars Coronavirus Papain-Like Protease in Complex with Glycerol

All present enzymatic activity of Crystal Structure of Sars Coronavirus Papain-Like Protease in Complex with Glycerol:
3.4.19.12; 3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars Coronavirus Papain-Like Protease in Complex with Glycerol, PDB code: 5y3e 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) 74.47 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 151.179, 33.357, 90.890, 90.00, 124.98, 90.00
R / Rfree (%) 16.2 / 19.9

Other elements in 5y3e:

The structure of Crystal Structure of Sars Coronavirus Papain-Like Protease in Complex with Glycerol 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 in Complex with Glycerol (pdb code 5y3e). 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 in Complex with Glycerol, PDB code: 5y3e:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5y3e

Go back to Sodium Binding Sites List in 5y3e
Sodium binding site 1 out of 5 in the Crystal Structure of Sars Coronavirus Papain-Like Protease in Complex with Glycerol


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 in Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:30.9
occ:1.00
 O A:LYS218 2.6 22.7 1.0
O A:LEU235 2.7 21.4 1.0
OG1 A:THR313 2.7 24.5 1.0
OH A:TYR311 2.8 24.1 1.0
CB A:THR313 3.3 25.0 1.0
C A:LYS218 3.5 21.0 1.0
CA A:LYS218 3.7 19.9 1.0
CZ A:TYR311 3.7 23.7 1.0
CE2 A:TYR311 3.7 24.4 1.0
CB A:LYS218 3.8 19.1 1.0
C A:LEU235 3.8 21.6 1.0
CA A:THR313 3.9 24.4 1.0
CD1 A:ILE315 4.0 32.0 1.0
CD1 A:TYR234 4.0 27.0 1.0
N A:LEU235 4.3 20.1 1.0
CG A:LYS218 4.4 19.8 1.0
CA A:LEU235 4.5 19.1 1.0
CB A:LEU235 4.5 20.1 1.0
CG1 A:ILE315 4.6 32.9 1.0
CG2 A:THR313 4.6 25.4 1.0
CE1 A:TYR234 4.7 26.4 1.0
N A:THR219 4.7 20.8 1.0
N A:THR313 4.7 24.2 1.0
CG A:TYR234 4.9 25.1 1.0
N A:VAL236 4.9 21.4 1.0
CB A:TYR234 4.9 24.3 1.0
N A:THR314 5.0 29.5 1.0

Sodium binding site 2 out of 5 in 5y3e

Go back to Sodium Binding Sites List in 5y3e
Sodium binding site 2 out of 5 in the Crystal Structure of Sars Coronavirus Papain-Like Protease in Complex with Glycerol


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 in Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:34.7
occ:1.00
 OD1 A:ASN263 2.3 37.2 0.5
OG A:SER116 2.7 18.3 0.5
ND1 A:HIS276 2.8 22.3 1.0
CG A:ASN263 3.0 25.1 0.5
O A:SER116 3.1 21.1 0.5
O A:SER116 3.2 21.5 0.5
O A:ALA262 3.3 20.1 1.0
ND2 A:ASN263 3.3 31.8 0.5
CE1 A:HIS276 3.5 22.9 1.0
C A:ALA262 3.7 19.5 1.0
C A:SER116 3.8 20.7 0.5
C A:SER116 3.8 21.0 0.5
CB A:SER116 3.8 22.9 0.5
CB A:ALA120 3.9 21.1 1.0
CB A:SER116 3.9 19.9 0.5
CG A:HIS276 3.9 21.4 1.0
N A:ASN263 3.9 18.2 0.5
OG A:SER116 3.9 23.2 0.5
N A:ASN263 4.0 19.1 0.5
CA A:ASN263 4.0 20.1 0.5
CB A:ASN263 4.0 19.7 0.5
CA A:SER116 4.0 21.0 0.5
CA A:SER116 4.0 19.9 0.5
CA A:ASN263 4.0 22.1 0.5
CB A:ASN263 4.1 23.5 0.5
CB A:HIS276 4.2 19.3 1.0
CE1 A:PHE305 4.3 22.3 1.0
CA A:HIS276 4.4 18.7 1.0
OD1 A:ASN263 4.5 18.7 0.5
N A:ALA120 4.5 19.5 1.0
CA A:ALA120 4.6 20.8 1.0
CA A:ALA262 4.6 19.7 1.0
N A:ALA262 4.7 19.6 1.0
NE2 A:HIS276 4.7 22.5 1.0
N A:VAL117 4.8 20.0 1.0
CG A:ASN263 4.8 20.0 0.5
CD1 A:PHE305 4.9 21.0 1.0
CD2 A:HIS276 4.9 22.5 1.0
O A:THR275 5.0 18.3 0.5

Sodium binding site 3 out of 5 in 5y3e

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Sodium binding site 3 out of 5 in the Crystal Structure of Sars Coronavirus Papain-Like Protease in Complex with Glycerol


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 in Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:27.4
occ:1.00
 OG A:SER115 2.9 21.3 1.0
O A:HOH530 2.9 29.0 1.0
O A:ILE286 3.0 18.2 1.0
N A:GLY288 3.0 18.1 1.0
CB A:SER115 3.5 19.6 1.0
CD1 A:LEU119 3.5 20.3 1.0
C A:ILE286 3.8 18.3 1.0
CA A:ASP287 3.8 18.2 1.0
CA A:GLY288 3.9 18.6 1.0
C A:ASP287 3.9 17.8 1.0
OG A:SER104 3.9 21.1 1.0
N A:ASP287 4.1 18.1 1.0
N A:SER116 4.1 20.0 0.5
N A:SER116 4.1 19.4 0.5
C A:SER115 4.2 19.6 1.0
N A:HIS276 4.3 19.7 1.0
CG2 A:ILE286 4.3 19.6 1.0
CB A:HIS276 4.4 19.3 1.0
CA A:SER115 4.4 19.2 1.0
O A:SER115 4.6 20.2 1.0
O A:CYS112 4.6 20.3 1.0
OG A:SER116 4.6 23.2 0.5
O A:TYR274 4.6 16.6 0.5
CA A:SER116 4.7 19.9 0.5
CA A:SER116 4.7 21.0 0.5
O A:GLY288 4.7 20.4 1.0
CA A:THR275 4.7 20.5 0.5
CA A:THR275 4.7 20.2 0.5
O A:HOH674 4.8 22.6 1.0
CB A:ILE286 4.8 17.8 1.0
C A:GLY288 4.8 19.1 1.0
OD1 A:ASP287 4.9 22.8 1.0
O A:HOH617 4.9 21.8 1.0
CG A:LEU119 4.9 19.4 1.0
CA A:ILE286 4.9 17.0 1.0
C A:THR275 4.9 19.5 0.5
O A:TYR274 5.0 18.5 0.5

Sodium binding site 4 out of 5 in 5y3e

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Sodium binding site 4 out of 5 in the Crystal Structure of Sars Coronavirus Papain-Like Protease in Complex with Glycerol


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 in Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:37.7
occ:1.00
 OH A:TYR72 2.7 35.1 1.0
O A:HOH678 2.8 42.9 1.0
O A:ALA132 2.9 22.7 1.0
ND2 A:ASN147 3.0 24.2 0.5
C A:ALA132 3.7 23.3 1.0
CZ A:TYR72 3.7 28.4 1.0
CA A:ALA132 3.8 24.8 1.0
CB A:ALA136 3.9 25.6 1.0
N A:ALA136 3.9 26.4 1.0
CD1 A:LEU151 4.0 25.1 1.0
CE2 A:TYR72 4.1 28.1 1.0
CB A:GLU135 4.2 28.7 1.0
CG A:ASN147 4.2 23.6 0.5
CA A:ALA136 4.3 26.1 1.0
CB A:ALA132 4.3 25.2 1.0
OE1 A:GLU135 4.5 40.2 1.0
O A:HOH578 4.5 37.0 1.0
C A:GLU135 4.6 27.5 1.0
OH A:TYR84 4.6 30.4 1.0
O A:PRO131 4.7 26.2 1.0
CE1 A:TYR72 4.8 27.5 1.0
OD1 A:ASN147 4.9 24.7 0.5
CA A:GLU135 4.9 27.3 1.0
N A:ALA132 5.0 25.6 1.0

Sodium binding site 5 out of 5 in 5y3e

Go back to Sodium Binding Sites List in 5y3e
Sodium binding site 5 out of 5 in the Crystal Structure of Sars Coronavirus Papain-Like Protease in Complex with Glycerol


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 in Complex with Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:26.9
occ:1.00
 O A:VAL206 2.8 22.6 1.0
O A:MET244 2.9 19.3 1.0
NH1 A:ARG184 3.0 22.1 1.0
NH2 A:ARG184 3.1 22.1 1.0
SD A:MET245 3.3 20.6 1.0
N A:TYR208 3.4 21.3 1.0
CB A:TYR208 3.4 20.8 1.0
CZ A:ARG184 3.4 20.9 1.0
C A:VAL206 3.5 20.2 1.0
C A:MET244 3.6 18.7 1.0
N A:MET244 3.7 19.4 1.0
C A:MET207 3.7 20.9 1.0
CB A:VAL243 3.7 21.3 1.0
N A:MET207 3.9 20.2 1.0
CA A:MET207 3.9 21.2 1.0
CA A:TYR208 4.0 19.8 1.0
CA A:MET244 4.3 20.2 1.0
N A:MET245 4.3 20.5 1.0
CA A:VAL243 4.3 19.9 1.0
CA A:VAL206 4.3 19.8 1.0
O A:MET207 4.4 23.4 1.0
C A:VAL243 4.4 19.6 1.0
CG1 A:VAL243 4.4 19.6 1.0
CG A:MET245 4.4 18.6 1.0
CA A:MET245 4.6 18.7 1.0
CG2 A:VAL243 4.6 22.3 1.0
CE A:MET245 4.6 21.4 1.0
CG A:TYR208 4.7 21.2 1.0
NE A:ARG184 4.8 20.3 1.0
O A:ALA205 4.8 22.3 1.0
CD2 A:LEU217 4.9 21.0 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 01:20:14 2024

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