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Sodium in PDB 7ntw: Crystal Structure of the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site

Enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site, PDB code: 7ntw was solved by E.Dupre, V.Villeret, X.Hanoulle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.37 / 1.82
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.31, 53.68, 44.72, 90, 101.67, 90
R / Rfree (%) 19.7 / 25.7

Other elements in 7ntw:

The structure of Crystal Structure of the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site (pdb code 7ntw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site, PDB code: 7ntw:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 7ntw

Go back to Sodium Binding Sites List in 7ntw
Sodium binding site 1 out of 3 in the Crystal Structure of the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site


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 the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:38.1
occ:1.00
HD1 A:HIS41 2.0 32.8 0.0
HD1 A:HIS164 2.1 26.9 0.0
H A:HIS41 2.5 30.4 1.0
OD2 A:ASP187 2.7 29.2 1.0
ND1 A:HIS41 2.8 32.7 1.0
ND1 A:HIS164 2.8 26.8 1.0
HG2 A:ARG40 2.9 31.4 1.0
HB3 A:HIS41 3.1 32.9 1.0
HB2 A:ASP187 3.1 28.4 1.0
HB3 A:ASP187 3.2 28.4 1.0
HB3 A:PRO39 3.2 28.9 1.0
H A:ARG40 3.2 30.7 1.0
HE1 A:HIS164 3.3 26.9 1.0
N A:HIS41 3.3 29.5 1.0
CE1 A:HIS164 3.4 26.2 1.0
CB A:ASP187 3.4 28.0 1.0
HG3 A:ARG40 3.5 31.4 1.0
CG A:ASP187 3.5 28.4 1.0
HB3 A:CYS85 3.6 29.4 1.0
N A:ARG40 3.6 30.7 1.0
O A:CYS85 3.6 29.3 1.0
CG A:HIS41 3.6 35.7 1.0
CG A:ARG40 3.6 32.3 1.0
CB A:HIS41 3.7 32.2 1.0
HA A:PRO39 3.8 29.4 1.0
CE1 A:HIS41 3.9 38.1 1.0
CB A:PRO39 3.9 28.7 1.0
HB3 A:HIS164 4.0 25.4 1.0
CG A:HIS164 4.0 25.6 1.0
HE1 A:HIS41 4.0 36.2 1.0
CA A:HIS41 4.1 31.6 1.0
C A:PRO39 4.1 30.7 1.0
HE A:ARG40 4.1 32.3 1.0
CA A:PRO39 4.1 29.6 1.0
HB2 A:PRO39 4.1 28.9 1.0
HH A:TYR54 4.2 35.7 0.0
C A:ARG40 4.2 31.1 1.0
CA A:ARG40 4.3 30.5 1.0
OH A:TYR54 4.4 35.6 1.0
CB A:ARG40 4.5 29.7 1.0
CB A:CYS85 4.5 29.8 1.0
CB A:HIS164 4.5 25.0 1.0
HB2 A:HIS41 4.5 32.9 1.0
HA A:HIS41 4.6 31.4 1.0
NE2 A:HIS164 4.7 28.4 1.0
C A:CYS85 4.7 27.2 1.0
OD1 A:ASP187 4.7 32.2 1.0
NE A:ARG40 4.8 32.8 1.0
CD A:ARG40 4.8 31.2 1.0
HB3 A:ARG40 4.8 30.5 1.0
HE1 A:PHE181 4.8 30.0 1.0
HE1 A:TYR54 4.8 35.5 1.0
CD2 A:HIS41 4.8 38.2 1.0
CZ A:TYR54 4.9 34.8 1.0
CA A:ASP187 4.9 29.2 1.0
HA A:CYS85 4.9 28.3 1.0
NE2 A:HIS41 4.9 35.9 1.0
HZ A:PHE181 5.0 30.6 1.0
HB2 A:CYS85 5.0 29.4 1.0
CD2 A:HIS164 5.0 26.6 1.0

Sodium binding site 2 out of 3 in 7ntw

Go back to Sodium Binding Sites List in 7ntw
Sodium binding site 2 out of 3 in the Crystal Structure of the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site


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 the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:38.9
occ:1.00
H A:GLY174 2.1 25.4 1.0
HA A:ALA173 2.6 25.9 1.0
O A:PHE134 2.7 39.5 1.0
O A:TYR182 2.8 32.3 1.0
HB2 A:TYR182 2.8 30.4 1.0
N A:GLY174 3.0 25.0 1.0
HD2 A:PHE185 3.1 31.6 1.0
O A:GLY174 3.2 28.3 1.0
HB1 A:ALA173 3.2 26.1 1.0
CA A:ALA173 3.3 25.8 1.0
HB2 A:ALA173 3.5 26.1 1.0
CB A:ALA173 3.5 26.2 1.0
HD2 A:PHE181 3.5 31.1 1.0
C A:TYR182 3.6 31.3 1.0
C A:ALA173 3.6 26.3 1.0
CB A:TYR182 3.6 30.6 1.0
H A:TYR182 3.7 30.6 1.0
HE1 A:TYR161 3.8 27.6 1.0
HB3 A:PHE134 3.8 35.2 1.0
CD2 A:PHE185 3.8 31.4 1.0
HE2 A:PHE185 3.9 31.7 1.0
HA A:THR135 3.9 32.9 1.0
HB3 A:TYR182 3.9 30.4 1.0
C A:PHE134 4.0 36.1 1.0
CA A:TYR182 4.0 30.5 1.0
C A:GLY174 4.0 25.4 1.0
CA A:GLY174 4.1 25.4 1.0
N A:TYR182 4.1 29.8 1.0
CE2 A:PHE185 4.3 31.6 1.0
HH A:TYR161 4.3 26.1 0.0
HD2 A:TYR182 4.4 27.8 1.0
CD2 A:PHE181 4.4 31.3 1.0
HB3 A:ALA173 4.5 26.1 1.0
HE1 A:MET130 4.5 36.6 1.0
HB2 A:PHE185 4.6 32.2 1.0
O A:HIS172 4.6 28.3 1.0
N A:ALA173 4.6 25.3 1.0
CB A:PHE134 4.7 34.7 1.0
HA3 A:GLY174 4.7 25.3 1.0
HA2 A:GLY174 4.7 25.3 1.0
HE2 A:PHE181 4.7 31.1 1.0
CE1 A:TYR161 4.7 27.1 1.0
CA A:THR135 4.7 33.4 1.0
HA3 A:GLY183 4.7 29.0 1.0
N A:GLY183 4.8 29.1 1.0
N A:THR135 4.8 33.5 1.0
CG A:TYR182 4.8 29.7 1.0
HB2 A:PHE134 4.9 35.2 1.0
HB3 A:PHE181 4.9 29.2 1.0
O A:ALA173 4.9 26.5 1.0
CA A:PHE134 4.9 34.1 1.0
CG A:PHE185 4.9 32.0 1.0
HA A:TYR182 4.9 30.5 1.0
CD2 A:TYR182 5.0 27.3 1.0

Sodium binding site 3 out of 3 in 7ntw

Go back to Sodium Binding Sites List in 7ntw
Sodium binding site 3 out of 3 in the Crystal Structure of the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site


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 the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:44.5
occ:1.00
H A:VAL148 2.2 28.9 1.0
HB3 A:LEU115 2.6 27.4 1.0
O A:LEU115 2.7 26.8 1.0
HG21 A:VAL148 2.8 29.2 1.0
HA A:SER147 2.9 29.5 1.0
N A:VAL148 3.0 28.5 1.0
HE2 A:MET17 3.2 34.3 1.0
SD A:MET17 3.3 32.6 1.0
HG A:CYS117 3.3 33.6 0.0
HD23 A:LEU115 3.4 29.3 1.0
HE1 A:MET17 3.4 34.3 1.0
CE A:MET17 3.5 35.1 1.0
CB A:LEU115 3.5 27.3 1.0
HG23 A:VAL148 3.5 29.2 1.0
SG A:CYS117 3.6 33.5 1.0
CG2 A:VAL148 3.6 29.1 1.0
CA A:SER147 3.6 28.3 1.0
HG3 A:MET17 3.6 31.9 1.0
C A:LEU115 3.7 27.2 1.0
HB3 A:SER147 3.7 31.8 1.0
H A:LEU115 3.7 25.0 1.0
HG A:LEU115 3.8 29.3 1.0
C A:SER147 3.8 30.3 1.0
HG11 A:VAL13 3.8 28.9 1.0
O A:VAL148 3.8 23.8 1.0
HG13 A:VAL148 4.0 31.2 1.0
CA A:LEU115 4.0 26.1 1.0
CA A:VAL148 4.0 28.4 1.0
CG A:LEU115 4.0 29.0 1.0
CG A:MET17 4.1 31.3 1.0
CB A:SER147 4.1 31.9 1.0
HG12 A:VAL13 4.1 28.9 1.0
CD2 A:LEU115 4.1 29.4 1.0
HB2 A:LEU115 4.2 27.4 1.0
CB A:VAL148 4.2 29.5 1.0
HB2 A:CYS117 4.2 33.2 1.0
N A:LEU115 4.3 24.4 1.0
HG22 A:VAL148 4.4 29.2 1.0
C A:VAL148 4.4 26.7 1.0
CG1 A:VAL13 4.4 29.1 1.0
OG A:SER147 4.4 35.7 1.0
HE3 A:MET17 4.4 34.3 1.0
HG2 A:MET17 4.5 31.9 1.0
CB A:CYS117 4.6 34.1 1.0
CG1 A:VAL148 4.6 32.0 1.0
HD21 A:LEU115 4.6 29.3 1.0
HD22 A:LEU115 4.8 29.3 1.0
HG13 A:VAL13 4.8 28.9 1.0
O A:GLY146 4.8 33.3 1.0
HA A:VAL148 4.8 28.3 1.0
N A:SER147 4.9 29.0 1.0
N A:ALA116 4.9 26.2 1.0
HG A:SER147 4.9 35.7 0.0
HA A:LEU115 4.9 26.2 1.0
HB2 A:SER147 5.0 31.8 1.0

Reference:

E.Dupre, V.Villeret, X.Hanoulle. Crystal Structure of the Sars-Cov-2 Main Protease with A Zinc Ion Coordinated in the Active Site To Be Published.
Page generated: Tue Oct 8 18:12:15 2024

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