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:

Zinc (Zn) 4 atoms

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

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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

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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 Dec 15 15:39:51 2020

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