Sodium in PDB 6wkq: 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin
Protein crystallography data
The structure of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin, PDB code: 6wkq
was solved by
G.Minasov,
L.Shuvalova,
M.Rosas-Lemus,
O.Kiryukhina,
K.J.F.Satchell,
Center For Structural Genomics Of Infectious Diseases (Csgid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.92 /
1.98
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
166.247,
166.247,
98.139,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.2 /
18
|
Other elements in 6wkq:
The structure of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin
(pdb code 6wkq). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin, PDB code: 6wkq:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 6wkq
Go back to
Sodium Binding Sites List in 6wkq
Sodium binding site 1 out
of 4 in the 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na7101
b:48.1
occ:1.00
|
O
|
A:HOH7382
|
2.3
|
48.5
|
1.0
|
O
|
B:HOH4508
|
2.3
|
45.2
|
1.0
|
O
|
A:LEU6887
|
2.3
|
30.6
|
1.0
|
O
|
A:GLN6885
|
2.5
|
28.2
|
1.0
|
O
|
A:ARG6884
|
2.7
|
29.7
|
1.0
|
C
|
A:GLN6885
|
3.2
|
28.5
|
1.0
|
C
|
A:LEU6887
|
3.5
|
30.7
|
1.0
|
O
|
A:HOH7297
|
3.6
|
29.5
|
1.0
|
CA
|
A:GLN6885
|
3.7
|
29.0
|
1.0
|
C
|
A:ARG6884
|
3.8
|
29.3
|
1.0
|
N
|
A:LEU6887
|
4.1
|
28.6
|
1.0
|
OG1
|
A:THR6889
|
4.1
|
36.1
|
0.5
|
N
|
A:TRP6886
|
4.1
|
27.8
|
1.0
|
C
|
A:TRP6886
|
4.1
|
28.8
|
1.0
|
N
|
A:THR6889
|
4.2
|
35.1
|
0.5
|
N
|
A:GLN6885
|
4.2
|
29.1
|
1.0
|
O
|
A:HOH7246
|
4.2
|
38.4
|
1.0
|
OG1
|
B:THR4311
|
4.2
|
40.7
|
1.0
|
C
|
A:PRO6888
|
4.3
|
34.4
|
1.0
|
O
|
A:TRP6886
|
4.4
|
28.0
|
1.0
|
N
|
A:THR6889
|
4.4
|
36.9
|
0.5
|
CA
|
A:LEU6887
|
4.4
|
29.3
|
1.0
|
N
|
A:PRO6888
|
4.5
|
31.0
|
1.0
|
CB
|
B:THR4311
|
4.5
|
37.0
|
1.0
|
CA
|
A:PRO6888
|
4.5
|
33.2
|
1.0
|
CA
|
A:TRP6886
|
4.6
|
27.8
|
1.0
|
O
|
B:VAL4310
|
4.6
|
31.0
|
1.0
|
O
|
A:HOH7360
|
4.7
|
44.2
|
1.0
|
OG1
|
A:THR6889
|
4.7
|
40.6
|
0.5
|
CA
|
A:THR6889
|
4.7
|
35.3
|
0.5
|
O
|
A:PRO6888
|
4.7
|
32.2
|
1.0
|
O
|
B:HOH4574
|
4.8
|
58.5
|
1.0
|
CA
|
A:THR6889
|
4.8
|
38.3
|
0.5
|
|
Sodium binding site 2 out
of 4 in 6wkq
Go back to
Sodium Binding Sites List in 6wkq
Sodium binding site 2 out
of 4 in the 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na7102
b:53.4
occ:0.75
|
O
|
A:HOH7201
|
2.3
|
45.2
|
0.5
|
O
|
A:HOH7204
|
2.4
|
36.5
|
0.5
|
O
|
A:ILE6910
|
2.4
|
38.5
|
1.0
|
OG
|
A:SER7090
|
2.8
|
38.8
|
0.6
|
OG
|
A:SER7090
|
3.2
|
40.4
|
0.4
|
O
|
A:ASP7091
|
3.5
|
43.5
|
1.0
|
C
|
A:ILE6910
|
3.6
|
36.5
|
1.0
|
CB
|
A:SER7090
|
3.7
|
37.1
|
0.6
|
CB
|
A:SER7090
|
3.8
|
38.0
|
0.4
|
O
|
A:HOH7340
|
4.1
|
42.2
|
1.0
|
O
|
A:SER7090
|
4.1
|
38.9
|
0.4
|
O
|
A:SER7090
|
4.2
|
38.5
|
0.6
|
CA
|
A:GLY6911
|
4.2
|
35.6
|
1.0
|
C
|
A:SER7090
|
4.4
|
38.2
|
0.4
|
N
|
A:GLY6911
|
4.4
|
35.0
|
1.0
|
C
|
A:SER7090
|
4.4
|
37.7
|
0.6
|
C
|
A:ASP7091
|
4.4
|
43.4
|
1.0
|
CG2
|
A:VAL7092
|
4.5
|
53.7
|
1.0
|
CA
|
A:SER7090
|
4.7
|
36.6
|
0.6
|
CA
|
A:ILE6910
|
4.7
|
35.6
|
1.0
|
CA
|
A:SER7090
|
4.7
|
37.2
|
0.4
|
N
|
A:ILE6910
|
4.8
|
35.3
|
1.0
|
OG1
|
A:THR6915
|
4.9
|
35.7
|
1.0
|
CA
|
A:VAL7092
|
5.0
|
47.2
|
1.0
|
N
|
A:ASP7091
|
5.0
|
38.8
|
1.0
|
|
Sodium binding site 3 out
of 4 in 6wkq
Go back to
Sodium Binding Sites List in 6wkq
Sodium binding site 3 out
of 4 in the 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na7101
b:43.4
occ:1.00
|
O
|
C:HOH7406
|
2.2
|
42.6
|
1.0
|
O
|
C:LEU6887
|
2.3
|
24.7
|
1.0
|
O
|
C:HOH7350
|
2.4
|
42.8
|
1.0
|
O
|
C:GLN6885
|
2.5
|
23.7
|
1.0
|
O
|
C:ARG6884
|
2.7
|
26.1
|
1.0
|
C
|
C:GLN6885
|
3.2
|
24.3
|
1.0
|
C
|
C:LEU6887
|
3.4
|
25.2
|
1.0
|
O
|
C:HOH7293
|
3.6
|
27.4
|
1.0
|
CA
|
C:GLN6885
|
3.7
|
25.2
|
1.0
|
C
|
C:ARG6884
|
3.8
|
26.7
|
1.0
|
N
|
C:LEU6887
|
4.0
|
24.3
|
1.0
|
C
|
C:TRP6886
|
4.0
|
24.2
|
1.0
|
N
|
C:TRP6886
|
4.0
|
23.4
|
1.0
|
O
|
C:TRP6886
|
4.2
|
24.0
|
1.0
|
OG1
|
D:THR4311
|
4.2
|
38.6
|
1.0
|
N
|
C:GLN6885
|
4.2
|
25.6
|
1.0
|
N
|
C:THR6889
|
4.2
|
30.2
|
1.0
|
O
|
C:HOH7241
|
4.3
|
29.7
|
1.0
|
CA
|
C:LEU6887
|
4.3
|
24.4
|
1.0
|
C
|
C:PRO6888
|
4.3
|
28.8
|
1.0
|
N
|
C:PRO6888
|
4.4
|
26.9
|
1.0
|
OG1
|
C:THR6889
|
4.4
|
37.7
|
1.0
|
CA
|
C:PRO6888
|
4.4
|
28.2
|
1.0
|
CA
|
C:TRP6886
|
4.5
|
23.6
|
1.0
|
O
|
D:HOH4561
|
4.6
|
46.3
|
1.0
|
CB
|
D:THR4311
|
4.6
|
33.8
|
1.0
|
O
|
C:PRO6888
|
4.7
|
27.4
|
1.0
|
O
|
C:HOH7333
|
4.8
|
36.8
|
1.0
|
O
|
D:VAL4310
|
4.9
|
28.1
|
1.0
|
CA
|
C:THR6889
|
4.9
|
33.8
|
1.0
|
|
Sodium binding site 4 out
of 4 in 6wkq
Go back to
Sodium Binding Sites List in 6wkq
Sodium binding site 4 out
of 4 in the 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of 1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na7102
b:55.8
occ:0.75
|
O
|
C:HOH7421
|
2.3
|
42.0
|
0.5
|
O
|
C:HOH7278
|
2.3
|
54.7
|
1.0
|
O
|
C:ILE6910
|
2.4
|
34.1
|
1.0
|
OG
|
C:SER7090
|
2.7
|
45.0
|
1.0
|
C
|
C:ILE6910
|
3.6
|
33.3
|
1.0
|
CB
|
C:SER7090
|
3.6
|
40.5
|
1.0
|
O
|
C:HOH7389
|
4.0
|
26.9
|
0.6
|
O
|
C:ASP7091
|
4.1
|
45.7
|
1.0
|
CG1
|
C:VAL7092
|
4.2
|
51.5
|
0.6
|
CA
|
C:GLY6911
|
4.3
|
34.2
|
1.0
|
O
|
C:SER7090
|
4.3
|
38.9
|
1.0
|
N
|
C:GLY6911
|
4.4
|
32.8
|
1.0
|
C
|
C:SER7090
|
4.6
|
39.2
|
1.0
|
CG2
|
C:VAL7092
|
4.6
|
47.1
|
0.4
|
CA
|
C:ILE6910
|
4.7
|
32.0
|
1.0
|
O
|
C:HOH7389
|
4.7
|
26.9
|
0.4
|
CA
|
C:SER7090
|
4.7
|
38.9
|
1.0
|
N
|
C:ILE6910
|
4.8
|
32.2
|
1.0
|
CB
|
C:ILE6910
|
5.0
|
33.5
|
1.0
|
C
|
C:ASP7091
|
5.0
|
45.3
|
1.0
|
|
Reference:
G.Minasov,
L.Shuvalova,
M.Rosas-Lemus,
O.Kiryukhina,
K.J.F.Satchell.
1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer From Sars-Cov-2 in Complex with Sinefungin. To Be Published.
Page generated: Tue Oct 8 14:39:35 2024
|