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:
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
|