Sodium in PDB 8drw: Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
Enzymatic activity of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
All present enzymatic activity of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence:
3.4.22.69;
Protein crystallography data
The structure of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence, PDB code: 8drw
was solved by
J.Lee,
C.Kenward,
L.J.Worrall,
M.Vuckovic,
M.Paetzel,
N.C.J.Strynadka,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
67.10 /
2.67
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
275.644,
217.218,
104.635,
90,
110.98,
90
|
R / Rfree (%)
|
20.5 /
23.9
|
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Sodium atom in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
(pdb code 8drw). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the
Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence, PDB code: 8drw:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 12 in 8drw
Go back to
Sodium Binding Sites List in 8drw
Sodium binding site 1 out
of 12 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na401
b:81.9
occ:1.00
|
OD1
|
A:ASP263
|
2.3
|
109.0
|
1.0
|
OD1
|
A:ASN221
|
2.3
|
85.0
|
1.0
|
OG
|
A:SER267
|
2.3
|
78.7
|
1.0
|
O
|
A:ASN221
|
2.3
|
84.9
|
1.0
|
O
|
A:ASP263
|
2.4
|
91.7
|
1.0
|
O
|
A:PHE223
|
2.9
|
93.0
|
1.0
|
C
|
A:ASN221
|
3.3
|
81.6
|
1.0
|
CG
|
A:ASN221
|
3.3
|
80.2
|
1.0
|
N
|
A:SER267
|
3.4
|
75.7
|
1.0
|
C
|
A:ASP263
|
3.4
|
87.9
|
1.0
|
CG
|
A:ASP263
|
3.5
|
108.9
|
1.0
|
CB
|
A:SER267
|
3.5
|
73.4
|
1.0
|
CA
|
A:SER267
|
3.7
|
72.9
|
1.0
|
N
|
A:PHE223
|
3.7
|
89.8
|
1.0
|
N
|
A:ASN221
|
3.8
|
71.2
|
1.0
|
CA
|
A:ASN221
|
3.9
|
75.3
|
1.0
|
C
|
A:PHE223
|
3.9
|
98.1
|
1.0
|
CA
|
A:ASP263
|
4.0
|
88.8
|
1.0
|
CB
|
A:ALA266
|
4.1
|
87.8
|
1.0
|
C
|
A:ALA266
|
4.1
|
82.1
|
1.0
|
CB
|
A:ASN221
|
4.2
|
78.0
|
1.0
|
ND2
|
A:ASN221
|
4.2
|
77.5
|
1.0
|
N
|
A:ARG222
|
4.2
|
81.7
|
1.0
|
CB
|
A:ASP263
|
4.3
|
92.9
|
1.0
|
OD2
|
A:ASP263
|
4.3
|
115.8
|
1.0
|
CA
|
A:PHE223
|
4.4
|
97.4
|
1.0
|
N
|
A:MET264
|
4.4
|
81.8
|
1.0
|
C
|
A:ARG222
|
4.5
|
88.3
|
1.0
|
CA
|
A:ARG222
|
4.6
|
82.3
|
1.0
|
CA
|
A:ALA266
|
4.6
|
87.5
|
1.0
|
CA
|
A:MET264
|
4.8
|
76.2
|
1.0
|
CB
|
A:PHE223
|
4.8
|
96.4
|
1.0
|
N
|
A:ALA266
|
4.8
|
78.4
|
1.0
|
O
|
A:ALA266
|
4.9
|
77.5
|
1.0
|
C
|
A:LEU220
|
5.0
|
73.9
|
1.0
|
|
Sodium binding site 2 out
of 12 in 8drw
Go back to
Sodium Binding Sites List in 8drw
Sodium binding site 2 out
of 12 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na401
b:52.4
occ:1.00
|
OD1
|
B:ASN221
|
2.3
|
56.8
|
1.0
|
OD1
|
B:ASP263
|
2.3
|
50.6
|
1.0
|
O
|
B:ASN221
|
2.3
|
55.8
|
1.0
|
O
|
B:ASP263
|
2.3
|
57.4
|
1.0
|
O
|
B:PHE223
|
2.6
|
52.4
|
1.0
|
OG
|
B:SER267
|
2.8
|
52.5
|
1.0
|
C
|
B:ASP263
|
3.3
|
52.5
|
1.0
|
C
|
B:ASN221
|
3.3
|
56.2
|
1.0
|
CG
|
B:ASN221
|
3.5
|
50.6
|
1.0
|
CG
|
B:ASP263
|
3.5
|
49.2
|
1.0
|
N
|
B:SER267
|
3.5
|
50.7
|
1.0
|
C
|
B:PHE223
|
3.7
|
52.4
|
1.0
|
CB
|
B:ALA266
|
3.8
|
50.6
|
1.0
|
CA
|
B:ASP263
|
3.9
|
48.5
|
1.0
|
N
|
B:PHE223
|
3.9
|
52.7
|
1.0
|
CB
|
B:SER267
|
3.9
|
49.7
|
1.0
|
N
|
B:ASN221
|
4.0
|
48.9
|
1.0
|
CA
|
B:ASN221
|
4.1
|
48.9
|
1.0
|
CA
|
B:SER267
|
4.1
|
51.3
|
1.0
|
C
|
B:ARG222
|
4.2
|
52.1
|
1.0
|
C
|
B:ALA266
|
4.2
|
50.1
|
1.0
|
CB
|
B:ASN221
|
4.3
|
46.2
|
1.0
|
CB
|
B:ASP263
|
4.3
|
45.3
|
1.0
|
N
|
B:ARG222
|
4.3
|
55.3
|
1.0
|
CA
|
B:PHE223
|
4.4
|
51.5
|
1.0
|
N
|
B:MET264
|
4.4
|
47.3
|
1.0
|
CA
|
B:ALA266
|
4.4
|
50.1
|
1.0
|
OD2
|
B:ASP263
|
4.5
|
52.0
|
1.0
|
ND2
|
B:ASN221
|
4.5
|
49.2
|
1.0
|
CA
|
B:ARG222
|
4.5
|
48.8
|
1.0
|
O
|
B:ARG222
|
4.7
|
60.8
|
1.0
|
N
|
B:ALA266
|
4.7
|
49.0
|
1.0
|
CA
|
B:MET264
|
4.7
|
48.5
|
1.0
|
N
|
B:THR224
|
4.8
|
51.0
|
1.0
|
CB
|
B:PHE223
|
5.0
|
52.5
|
1.0
|
|
Sodium binding site 3 out
of 12 in 8drw
Go back to
Sodium Binding Sites List in 8drw
Sodium binding site 3 out
of 12 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na401
b:99.9
occ:1.00
|
OD1
|
C:ASP263
|
1.3
|
106.6
|
1.0
|
CG
|
C:ASP263
|
2.0
|
102.0
|
1.0
|
O
|
C:ASN221
|
2.3
|
114.9
|
1.0
|
OD2
|
C:ASP263
|
2.4
|
102.3
|
1.0
|
C
|
C:ASN221
|
3.1
|
106.2
|
1.0
|
O
|
C:ASP263
|
3.1
|
87.6
|
1.0
|
O
|
C:PHE223
|
3.3
|
99.5
|
1.0
|
CB
|
C:ASP263
|
3.3
|
82.6
|
1.0
|
N
|
C:ASN221
|
3.4
|
94.7
|
1.0
|
OG
|
C:SER267
|
3.4
|
85.1
|
1.0
|
CA
|
C:ASN221
|
3.5
|
96.4
|
1.0
|
CB
|
C:ASN221
|
3.5
|
97.2
|
1.0
|
C
|
C:ASP263
|
3.6
|
82.8
|
1.0
|
CA
|
C:ASP263
|
3.7
|
81.7
|
1.0
|
N
|
C:ARG222
|
4.2
|
119.0
|
1.0
|
C
|
C:PHE223
|
4.4
|
100.6
|
1.0
|
N
|
C:PHE223
|
4.5
|
109.0
|
1.0
|
C
|
C:LEU220
|
4.6
|
85.4
|
1.0
|
C
|
C:ARG222
|
4.6
|
115.8
|
1.0
|
CB
|
C:SER267
|
4.7
|
73.4
|
1.0
|
CA
|
C:ARG222
|
4.7
|
124.1
|
1.0
|
N
|
C:MET264
|
4.7
|
80.2
|
1.0
|
CD2
|
C:LEU220
|
4.7
|
73.6
|
1.0
|
N
|
C:SER267
|
4.7
|
79.4
|
1.0
|
CG
|
C:ASN221
|
4.9
|
103.5
|
1.0
|
CB
|
C:ALA266
|
4.9
|
86.0
|
1.0
|
CA
|
C:LEU220
|
5.0
|
74.4
|
1.0
|
|
Sodium binding site 4 out
of 12 in 8drw
Go back to
Sodium Binding Sites List in 8drw
Sodium binding site 4 out
of 12 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na401
b:76.3
occ:1.00
|
OD1
|
D:ASP263
|
2.3
|
75.2
|
1.0
|
O
|
D:ASN221
|
2.4
|
88.3
|
1.0
|
OD1
|
D:ASN221
|
2.4
|
81.2
|
1.0
|
O
|
D:PHE223
|
2.4
|
78.5
|
1.0
|
O
|
D:ASP263
|
2.7
|
71.4
|
1.0
|
OG
|
D:SER267
|
2.8
|
71.7
|
1.0
|
N
|
D:PHE223
|
3.2
|
87.9
|
1.0
|
C
|
D:ASN221
|
3.2
|
89.3
|
1.0
|
C
|
D:PHE223
|
3.4
|
82.5
|
1.0
|
CG
|
D:ASN221
|
3.4
|
77.5
|
1.0
|
N
|
D:SER267
|
3.5
|
66.7
|
1.0
|
CG
|
D:ASP263
|
3.5
|
69.8
|
1.0
|
C
|
D:ASP263
|
3.6
|
64.2
|
1.0
|
CB
|
D:ALA266
|
3.6
|
72.0
|
1.0
|
CA
|
D:PHE223
|
3.8
|
84.3
|
1.0
|
C
|
D:ARG222
|
3.9
|
92.8
|
1.0
|
CA
|
D:ASP263
|
4.0
|
65.7
|
1.0
|
CB
|
D:SER267
|
4.0
|
65.5
|
1.0
|
N
|
D:ARG222
|
4.0
|
98.3
|
1.0
|
CA
|
D:ARG222
|
4.1
|
99.4
|
1.0
|
CA
|
D:SER267
|
4.1
|
64.1
|
1.0
|
C
|
D:ALA266
|
4.1
|
66.4
|
1.0
|
CA
|
D:ASN221
|
4.1
|
80.7
|
1.0
|
N
|
D:ASN221
|
4.2
|
83.7
|
1.0
|
ND2
|
D:ASN221
|
4.2
|
80.3
|
1.0
|
CB
|
D:PHE223
|
4.2
|
78.7
|
1.0
|
CB
|
D:ASN221
|
4.3
|
75.0
|
1.0
|
CA
|
D:ALA266
|
4.4
|
66.7
|
1.0
|
CB
|
D:ASP263
|
4.4
|
63.3
|
1.0
|
OD2
|
D:ASP263
|
4.4
|
66.8
|
1.0
|
N
|
D:THR224
|
4.6
|
104.4
|
1.0
|
N
|
D:ALA266
|
4.7
|
67.5
|
1.0
|
N
|
D:MET264
|
4.8
|
63.5
|
1.0
|
O
|
D:ARG222
|
4.8
|
92.0
|
1.0
|
O
|
D:ALA266
|
4.9
|
65.0
|
1.0
|
|
Sodium binding site 5 out
of 12 in 8drw
Go back to
Sodium Binding Sites List in 8drw
Sodium binding site 5 out
of 12 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na401
b:58.5
occ:1.00
|
OD1
|
E:ASN221
|
2.4
|
62.3
|
1.0
|
OD1
|
E:ASP263
|
2.6
|
68.9
|
1.0
|
O
|
E:ASN221
|
2.7
|
65.3
|
1.0
|
O
|
E:ASP263
|
2.9
|
63.0
|
1.0
|
OG
|
E:SER267
|
3.1
|
59.3
|
1.0
|
N
|
E:ASN221
|
3.3
|
53.8
|
1.0
|
CG
|
E:ASN221
|
3.3
|
61.2
|
1.0
|
C
|
E:ASN221
|
3.4
|
69.1
|
1.0
|
O
|
E:PHE223
|
3.5
|
65.2
|
1.0
|
CG
|
E:ASP263
|
3.6
|
66.9
|
1.0
|
CA
|
E:ASN221
|
3.8
|
62.9
|
1.0
|
C
|
E:ASP263
|
3.8
|
59.7
|
1.0
|
CB
|
E:SER267
|
4.1
|
52.1
|
1.0
|
CB
|
E:ASN221
|
4.1
|
59.9
|
1.0
|
ND2
|
E:ASN221
|
4.2
|
62.7
|
1.0
|
CD2
|
E:LEU220
|
4.2
|
50.6
|
1.0
|
OD2
|
E:ASP263
|
4.2
|
66.0
|
1.0
|
N
|
E:SER267
|
4.2
|
49.4
|
1.0
|
C
|
E:LEU220
|
4.4
|
55.9
|
1.0
|
OG1
|
A:THR196
|
4.4
|
65.6
|
1.0
|
N
|
E:PHE223
|
4.5
|
67.1
|
1.0
|
N
|
E:ARG222
|
4.5
|
72.1
|
1.0
|
CA
|
E:ASP263
|
4.5
|
57.0
|
1.0
|
CA
|
E:LEU220
|
4.5
|
53.0
|
1.0
|
CB
|
E:ASP263
|
4.6
|
59.3
|
1.0
|
CA
|
E:SER267
|
4.6
|
49.0
|
1.0
|
C
|
E:PHE223
|
4.6
|
65.6
|
1.0
|
CB
|
E:ALA266
|
4.7
|
55.1
|
1.0
|
N
|
E:MET264
|
4.7
|
54.2
|
1.0
|
C
|
E:ARG222
|
4.9
|
71.3
|
1.0
|
CA
|
E:MET264
|
5.0
|
50.5
|
1.0
|
CB
|
E:LEU220
|
5.0
|
49.5
|
1.0
|
|
Sodium binding site 6 out
of 12 in 8drw
Go back to
Sodium Binding Sites List in 8drw
Sodium binding site 6 out
of 12 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na401
b:88.1
occ:1.00
|
OD1
|
F:ASP263
|
2.2
|
89.5
|
1.0
|
OD1
|
F:ASN221
|
2.2
|
83.2
|
1.0
|
O
|
F:PHE223
|
2.4
|
82.2
|
1.0
|
O
|
F:ASN221
|
2.4
|
90.9
|
1.0
|
O
|
F:ASP263
|
2.6
|
72.4
|
1.0
|
OG
|
F:SER267
|
3.3
|
79.3
|
1.0
|
CG
|
F:ASN221
|
3.3
|
80.6
|
1.0
|
CG
|
F:ASP263
|
3.4
|
84.5
|
1.0
|
C
|
F:ASN221
|
3.4
|
86.6
|
1.0
|
C
|
F:PHE223
|
3.5
|
88.8
|
1.0
|
C
|
F:ASP263
|
3.5
|
70.7
|
1.0
|
N
|
F:PHE223
|
3.8
|
91.0
|
1.0
|
CB
|
F:ALA266
|
3.8
|
72.7
|
1.0
|
CA
|
F:ASP263
|
3.9
|
74.8
|
1.0
|
N
|
F:SER267
|
4.0
|
68.5
|
1.0
|
N
|
F:ASN221
|
4.0
|
75.2
|
1.0
|
CA
|
F:ASN221
|
4.1
|
77.7
|
1.0
|
C
|
F:ARG222
|
4.1
|
93.7
|
1.0
|
ND2
|
F:ASN221
|
4.1
|
86.9
|
1.0
|
CA
|
F:PHE223
|
4.2
|
91.9
|
1.0
|
CB
|
F:ASP263
|
4.2
|
73.6
|
1.0
|
OD2
|
F:ASP263
|
4.2
|
85.3
|
1.0
|
CB
|
F:ASN221
|
4.3
|
80.3
|
1.0
|
N
|
F:ARG222
|
4.4
|
88.6
|
1.0
|
CB
|
F:SER267
|
4.4
|
72.2
|
1.0
|
C
|
F:ALA266
|
4.5
|
72.2
|
1.0
|
CA
|
F:ARG222
|
4.6
|
91.8
|
1.0
|
CA
|
F:SER267
|
4.6
|
70.2
|
1.0
|
N
|
F:THR224
|
4.6
|
94.0
|
1.0
|
CA
|
F:ALA266
|
4.6
|
75.4
|
1.0
|
O
|
F:ARG222
|
4.6
|
96.8
|
1.0
|
N
|
F:MET264
|
4.7
|
70.4
|
1.0
|
CB
|
F:PHE223
|
4.7
|
86.7
|
1.0
|
N
|
F:ALA266
|
4.9
|
71.8
|
1.0
|
CA
|
F:THR224
|
4.9
|
83.6
|
1.0
|
|
Sodium binding site 7 out
of 12 in 8drw
Go back to
Sodium Binding Sites List in 8drw
Sodium binding site 7 out
of 12 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Na401
b:103.1
occ:1.00
|
OD1
|
H:ASP263
|
1.7
|
109.9
|
1.0
|
O
|
H:PHE223
|
2.0
|
103.3
|
1.0
|
O
|
H:ASN221
|
2.1
|
112.4
|
1.0
|
O
|
H:ASP263
|
2.6
|
91.1
|
1.0
|
OD1
|
H:ASN221
|
2.8
|
106.6
|
1.0
|
CG
|
H:ASP263
|
2.9
|
106.7
|
1.0
|
C
|
H:PHE223
|
3.1
|
106.0
|
1.0
|
C
|
H:ASN221
|
3.2
|
105.2
|
1.0
|
C
|
H:ASP263
|
3.4
|
86.8
|
1.0
|
N
|
H:PHE223
|
3.5
|
115.8
|
1.0
|
C
|
H:ARG222
|
3.5
|
117.6
|
1.0
|
CA
|
H:ASP263
|
3.6
|
91.0
|
1.0
|
O
|
H:ARG222
|
3.8
|
122.3
|
1.0
|
OD2
|
H:ASP263
|
3.8
|
108.8
|
1.0
|
OG
|
H:SER267
|
3.8
|
81.5
|
1.0
|
CB
|
H:ASP263
|
3.8
|
96.5
|
1.0
|
CA
|
H:PHE223
|
3.9
|
110.3
|
1.0
|
CB
|
H:ALA266
|
3.9
|
87.4
|
1.0
|
CG
|
H:ASN221
|
3.9
|
99.2
|
1.0
|
OG1
|
H:THR224
|
4.0
|
99.9
|
1.0
|
N
|
H:ARG222
|
4.1
|
113.0
|
1.0
|
CA
|
H:ARG222
|
4.1
|
115.5
|
1.0
|
N
|
H:THR224
|
4.2
|
104.3
|
1.0
|
CA
|
H:ASN221
|
4.2
|
91.5
|
1.0
|
N
|
H:ASN221
|
4.2
|
87.3
|
1.0
|
N
|
H:SER267
|
4.3
|
85.0
|
1.0
|
CA
|
H:THR224
|
4.4
|
99.3
|
1.0
|
CB
|
H:ASN221
|
4.6
|
95.3
|
1.0
|
N
|
H:MET264
|
4.6
|
84.4
|
1.0
|
CB
|
H:PHE223
|
4.6
|
104.3
|
1.0
|
C
|
H:ALA266
|
4.7
|
85.9
|
1.0
|
CA
|
H:ALA266
|
4.8
|
87.2
|
1.0
|
CB
|
H:SER267
|
4.9
|
78.3
|
1.0
|
CB
|
H:THR224
|
4.9
|
98.2
|
1.0
|
N
|
H:ALA266
|
4.9
|
85.1
|
1.0
|
CA
|
H:SER267
|
5.0
|
78.5
|
1.0
|
N
|
H:ASP263
|
5.0
|
91.2
|
1.0
|
|
Sodium binding site 8 out
of 12 in 8drw
Go back to
Sodium Binding Sites List in 8drw
Sodium binding site 8 out
of 12 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Na401
b:116.1
occ:1.00
|
O
|
I:ASN221
|
1.8
|
128.8
|
1.0
|
OD1
|
I:ASN221
|
2.1
|
128.1
|
1.0
|
OD2
|
I:ASP263
|
2.3
|
108.5
|
1.0
|
O
|
I:ASP263
|
2.5
|
89.3
|
1.0
|
OG
|
I:SER267
|
2.6
|
88.7
|
1.0
|
C
|
I:ASN221
|
2.7
|
119.2
|
1.0
|
N
|
I:ASN221
|
2.7
|
131.9
|
1.0
|
CG
|
I:ASP263
|
2.9
|
99.9
|
1.0
|
CG
|
I:ASN221
|
2.9
|
122.8
|
1.0
|
CA
|
I:ASN221
|
3.1
|
117.1
|
1.0
|
C
|
I:ASP263
|
3.3
|
85.5
|
1.0
|
OD1
|
I:ASP263
|
3.4
|
107.9
|
1.0
|
O
|
I:PHE223
|
3.5
|
127.1
|
1.0
|
CB
|
I:ASN221
|
3.5
|
113.1
|
1.0
|
CA
|
I:ASP263
|
3.7
|
89.7
|
1.0
|
CB
|
I:ASP263
|
3.8
|
86.4
|
1.0
|
C
|
I:LEU220
|
3.9
|
106.0
|
1.0
|
CB
|
I:SER267
|
3.9
|
78.6
|
1.0
|
N
|
I:ARG222
|
3.9
|
109.8
|
1.0
|
ND2
|
I:ASN221
|
3.9
|
129.9
|
1.0
|
N
|
I:SER267
|
4.0
|
78.8
|
1.0
|
N
|
I:MET264
|
4.2
|
79.6
|
1.0
|
CA
|
I:LEU220
|
4.3
|
97.4
|
1.0
|
N
|
I:PHE223
|
4.4
|
121.1
|
1.0
|
CA
|
I:SER267
|
4.4
|
78.5
|
1.0
|
CA
|
I:ARG222
|
4.5
|
106.3
|
1.0
|
CB
|
I:ALA266
|
4.5
|
82.5
|
1.0
|
CA
|
I:MET264
|
4.7
|
72.3
|
1.0
|
C
|
I:PHE223
|
4.7
|
123.7
|
1.0
|
C
|
I:ARG222
|
4.7
|
111.7
|
1.0
|
CB
|
I:LEU220
|
4.8
|
92.2
|
1.0
|
C
|
I:ALA266
|
4.9
|
79.1
|
1.0
|
O
|
I:LEU220
|
5.0
|
98.0
|
1.0
|
CD2
|
I:LEU220
|
5.0
|
72.2
|
1.0
|
|
Sodium binding site 9 out
of 12 in 8drw
Go back to
Sodium Binding Sites List in 8drw
Sodium binding site 9 out
of 12 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Na401
b:104.3
occ:1.00
|
OD1
|
J:ASN221
|
2.2
|
110.8
|
1.0
|
OD1
|
J:ASP263
|
2.2
|
112.1
|
1.0
|
O
|
J:ASN221
|
2.4
|
117.1
|
1.0
|
O
|
J:ASP263
|
2.7
|
88.4
|
1.0
|
O
|
J:PHE223
|
2.8
|
111.2
|
1.0
|
CG
|
J:ASP263
|
3.1
|
109.9
|
1.0
|
C
|
J:ASN221
|
3.3
|
110.8
|
1.0
|
CG
|
J:ASN221
|
3.4
|
107.8
|
1.0
|
OG
|
J:SER267
|
3.4
|
95.3
|
1.0
|
C
|
J:ASP263
|
3.4
|
84.1
|
1.0
|
CA
|
J:ASP263
|
3.7
|
91.0
|
1.0
|
CB
|
J:ASP263
|
3.8
|
92.1
|
1.0
|
OD2
|
J:ASP263
|
3.8
|
120.7
|
1.0
|
N
|
J:ASN221
|
3.9
|
95.1
|
1.0
|
CB
|
J:ALA266
|
4.0
|
90.3
|
1.0
|
CA
|
J:ASN221
|
4.0
|
107.2
|
1.0
|
C
|
J:PHE223
|
4.0
|
114.1
|
1.0
|
N
|
J:PHE223
|
4.2
|
114.2
|
1.0
|
N
|
J:ARG222
|
4.2
|
105.2
|
1.0
|
N
|
J:SER267
|
4.2
|
89.4
|
1.0
|
CB
|
J:ASN221
|
4.3
|
106.0
|
1.0
|
C
|
J:ARG222
|
4.3
|
115.1
|
1.0
|
ND2
|
J:ASN221
|
4.4
|
102.3
|
1.0
|
CA
|
J:ARG222
|
4.4
|
109.3
|
1.0
|
N
|
J:MET264
|
4.6
|
78.6
|
1.0
|
CB
|
J:SER267
|
4.6
|
84.5
|
1.0
|
CA
|
J:PHE223
|
4.7
|
114.6
|
1.0
|
OG1
|
J:THR224
|
4.8
|
111.7
|
1.0
|
C
|
J:ALA266
|
4.8
|
88.1
|
1.0
|
CA
|
J:ALA266
|
4.9
|
85.7
|
1.0
|
CA
|
J:SER267
|
4.9
|
86.7
|
1.0
|
O
|
J:ARG222
|
4.9
|
116.0
|
1.0
|
|
Sodium binding site 10 out
of 12 in 8drw
Go back to
Sodium Binding Sites List in 8drw
Sodium binding site 10 out
of 12 in the Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Product Structure of Sars-Cov-2 Mpro C145A Mutant in Complex with NSP9-NSP10 (C9) Cut Site Sequence within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Na401
b:62.5
occ:1.00
|
OD1
|
L:ASN221
|
2.4
|
69.1
|
1.0
|
OD1
|
L:ASP263
|
2.4
|
64.1
|
1.0
|
O
|
L:ASN221
|
2.5
|
64.4
|
1.0
|
O
|
L:PHE223
|
2.7
|
65.6
|
1.0
|
O
|
L:ASP263
|
2.7
|
60.3
|
1.0
|
OG
|
L:SER267
|
3.0
|
68.8
|
1.0
|
C
|
L:ASN221
|
3.3
|
61.6
|
1.0
|
CG
|
L:ASN221
|
3.4
|
68.6
|
1.0
|
CG
|
L:ASP263
|
3.5
|
63.6
|
1.0
|
N
|
L:PHE223
|
3.6
|
61.9
|
1.0
|
C
|
L:ASP263
|
3.6
|
60.3
|
1.0
|
C
|
L:PHE223
|
3.7
|
66.3
|
1.0
|
N
|
L:ASN221
|
3.8
|
57.8
|
1.0
|
N
|
L:SER267
|
3.8
|
65.1
|
1.0
|
CA
|
L:ASN221
|
3.9
|
62.9
|
1.0
|
C
|
L:ARG222
|
4.0
|
62.0
|
1.0
|
CA
|
L:ASP263
|
4.1
|
62.0
|
1.0
|
CB
|
L:SER267
|
4.1
|
57.9
|
1.0
|
CB
|
L:ALA266
|
4.1
|
64.8
|
1.0
|
N
|
L:ARG222
|
4.1
|
68.5
|
1.0
|
CA
|
L:PHE223
|
4.2
|
67.1
|
1.0
|
CB
|
L:ASN221
|
4.2
|
62.8
|
1.0
|
CA
|
L:SER267
|
4.3
|
62.4
|
1.0
|
OD2
|
L:ASP263
|
4.3
|
64.6
|
1.0
|
ND2
|
L:ASN221
|
4.3
|
70.5
|
1.0
|
O
|
L:HOH509
|
4.4
|
51.1
|
1.0
|
CB
|
L:ASP263
|
4.4
|
59.0
|
1.0
|
C
|
L:ALA266
|
4.5
|
65.5
|
1.0
|
CA
|
L:ARG222
|
4.5
|
62.9
|
1.0
|
O
|
L:ARG222
|
4.5
|
65.8
|
1.0
|
N
|
L:MET264
|
4.7
|
56.3
|
1.0
|
CA
|
L:ALA266
|
4.8
|
59.5
|
1.0
|
CB
|
L:PHE223
|
4.9
|
68.8
|
1.0
|
N
|
L:THR224
|
4.9
|
68.4
|
1.0
|
C
|
L:LEU220
|
5.0
|
64.4
|
1.0
|
|
Reference:
J.Lee,
C.Kenward,
L.J.Worrall,
M.Vuckovic,
F.Gentile,
A.T.Ton,
M.Ng,
A.Cherkasov,
N.C.J.Strynadka,
M.Paetzel.
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ISSN: ESSN 2041-1723
PubMed: 36057636
DOI: 10.1038/S41467-022-32854-4
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