Atomistry » Sodium » PDB 6w26-6wo2 » 6w75
Atomistry »
  Sodium »
    PDB 6w26-6wo2 »
      6w75 »

Sodium in PDB 6w75: 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2

Protein crystallography data

The structure of 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2, PDB code: 6w75 was solved by G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, G.Wiersum, A.Godzik, L.Jaroszewski, P.J.Stogios, T.Skarina, K.J.F.Satchell, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 1.95
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.245, 166.245, 98.279, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 17.5

Other elements in 6w75:

The structure of 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2 (pdb code 6w75). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2, PDB code: 6w75:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 6w75

Go back to Sodium Binding Sites List in 6w75
Sodium binding site 1 out of 7 in the 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na7101

b:45.3
occ:1.00
O B:HOH4504 2.3 41.3 1.0
O A:LEU6887 2.3 26.4 1.0
O A:HOH7392 2.3 52.1 1.0
O A:GLN6885 2.5 25.0 1.0
O A:ARG6884 2.7 25.9 0.5
O A:ARG6884 2.7 26.8 0.5
C A:GLN6885 3.2 24.6 1.0
C A:LEU6887 3.5 27.2 1.0
O A:HOH7247 3.5 28.9 1.0
CA A:GLN6885 3.7 25.1 1.0
C A:ARG6884 3.8 26.1 0.5
C A:ARG6884 3.8 25.4 0.5
N A:LEU6887 4.0 24.9 1.0
C A:TRP6886 4.0 24.9 1.0
N A:TRP6886 4.0 23.7 1.0
OG1 A:THR6889 4.1 33.2 0.5
N A:THR6889 4.2 31.1 0.5
N A:GLN6885 4.2 25.4 1.0
N A:THR6889 4.2 31.4 0.5
O A:HOH7328 4.2 37.1 1.0
C A:PRO6888 4.2 29.9 1.0
O A:TRP6886 4.3 24.5 1.0
CA A:LEU6887 4.3 25.9 1.0
OG1 B:THR4311 4.3 36.4 1.0
N A:PRO6888 4.4 28.1 1.0
CG2 A:THR6889 4.4 33.8 0.5
CA A:PRO6888 4.5 29.7 1.0
CA A:TRP6886 4.6 23.8 1.0
CA A:THR6889 4.7 32.1 0.5
O A:PRO6888 4.7 28.1 1.0
O A:HOH7347 4.7 36.0 1.0
CA A:THR6889 4.7 31.8 0.5
CB B:THR4311 4.7 33.4 1.0
O B:HOH4586 4.7 50.0 1.0
O B:VAL4310 4.7 27.7 1.0

Sodium binding site 2 out of 7 in 6w75

Go back to Sodium Binding Sites List in 6w75
Sodium binding site 2 out of 7 in the 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4403

b:66.1
occ:0.75
O B:HOH4584 2.3 44.3 0.5
O B:HOH4589 2.3 43.9 0.5
O B:HOH4544 2.4 42.6 0.5
O B:HOH4529 2.4 46.0 0.8
O B:THR4355 2.8 45.2 1.0
O B:HOH4589 2.8 43.4 0.5
OD1 B:ASN4358 3.0 45.6 1.0
CG B:ASN4358 3.5 45.7 1.0
C B:THR4355 3.7 42.4 1.0
CB B:ASN4358 4.1 43.4 1.0
ND2 B:ASN4358 4.1 47.6 1.0
CA B:THR4355 4.4 43.9 1.0
O B:HOH4585 4.5 37.7 0.5
O B:THR4354 4.6 40.3 1.0
N B:CYS4356 4.6 39.8 1.0
N B:ASN4358 4.7 38.3 1.0
CA B:CYS4356 4.8 39.5 1.0

Sodium binding site 3 out of 7 in 6w75

Go back to Sodium Binding Sites List in 6w75
Sodium binding site 3 out of 7 in the 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na7101

b:38.4
occ:1.00
O C:HOH7436 2.2 42.4 1.0
O C:LEU6887 2.2 21.7 1.0
O C:HOH7381 2.4 39.8 1.0
O C:GLN6885 2.5 19.6 1.0
O C:ARG6884 2.7 22.4 0.7
O C:ARG6884 2.7 21.2 0.3
C C:GLN6885 3.1 20.4 1.0
C C:LEU6887 3.4 22.1 1.0
O C:HOH7268 3.5 24.7 1.0
CA C:GLN6885 3.7 21.0 1.0
C C:ARG6884 3.7 23.0 0.7
C C:ARG6884 3.8 21.1 0.3
N C:LEU6887 3.9 20.5 1.0
C C:TRP6886 4.0 20.6 1.0
N C:TRP6886 4.0 19.7 1.0
N C:GLN6885 4.2 21.3 1.0
OG1 D:THR4311 4.2 34.0 1.0
CA C:LEU6887 4.3 21.1 1.0
O C:TRP6886 4.3 20.1 1.0
N C:THR6889 4.3 26.6 1.0
O C:HOH7230 4.3 25.7 1.0
C C:PRO6888 4.3 25.4 1.0
N C:PRO6888 4.4 22.8 1.0
OG1 C:THR6889 4.4 32.0 1.0
CA C:PRO6888 4.5 24.6 1.0
CA C:TRP6886 4.5 20.0 1.0
CB D:THR4311 4.6 29.7 1.0
O D:HOH4580 4.7 47.5 1.0
O C:PRO6888 4.8 23.6 1.0
O C:HOH7357 4.8 19.9 0.6
O D:VAL4310 4.9 25.8 1.0
CA C:THR6889 4.9 30.0 1.0

Sodium binding site 4 out of 7 in 6w75

Go back to Sodium Binding Sites List in 6w75
Sodium binding site 4 out of 7 in the 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na7102

b:59.9
occ:1.00
O C:HOH7442 2.2 43.4 1.0
O C:HOH7429 2.3 59.7 1.0
O C:HOH7418 2.4 35.8 1.0
O C:LEU6855 2.5 36.4 1.0
O C:HOH7294 2.6 42.4 1.0
O C:ASN6853 2.7 24.6 1.0
O C:HOH7274 3.2 32.2 1.0
O C:HOH7248 3.4 35.3 0.6
C C:ASN6853 3.7 24.2 1.0
C C:LEU6855 3.7 29.3 1.0
N C:LEU6855 4.1 26.1 1.0
O C:HOH7421 4.1 33.1 0.5
O C:HOH7316 4.2 39.7 0.6
O C:HOH7460 4.3 46.3 1.0
C C:THR6854 4.3 26.3 1.0
O C:HOH7287 4.4 26.9 1.0
O C:HOH7316 4.4 37.8 0.4
CA C:ASN6853 4.5 22.9 1.0
N C:THR6854 4.6 23.7 1.0
CA C:LEU6855 4.6 27.6 1.0
O C:LEU6852 4.6 21.6 1.0
CA C:THR6854 4.6 25.6 1.0
N C:THR6856 4.7 28.1 1.0
CA C:THR6856 4.7 28.1 1.0
O C:HOH7415 4.7 32.3 1.0
N C:LEU6857 4.8 25.5 1.0
O C:THR6854 4.8 27.1 1.0
O C:HOH7248 4.9 33.0 0.4

Sodium binding site 5 out of 7 in 6w75

Go back to Sodium Binding Sites List in 6w75
Sodium binding site 5 out of 7 in the 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na7103

b:50.5
occ:1.00
O C:HOH7226 2.3 42.0 0.5
O C:HOH7439 2.3 29.4 0.3
OH C:TYR7009 2.6 29.6 1.0
O C:GLN6956 2.6 31.4 1.0
O C:HOH7477 2.7 33.7 0.5
O C:HOH7434 2.7 65.0 1.0
O C:HOH7439 3.2 44.3 0.7
C C:GLN6956 3.6 31.0 1.0
CZ C:TYR7009 3.6 28.2 1.0
O C:HOH7312 3.6 25.7 1.0
CE2 C:TYR7009 3.9 27.6 1.0
O C:HOH7221 3.9 37.0 1.0
CA C:GLN6956 4.0 30.8 1.0
O C:HOH7490 4.1 34.0 0.3
O C:GLY7011 4.2 36.7 1.0
CA C:GLY7011 4.2 33.3 1.0
C C:GLY7011 4.6 35.6 1.0
N C:GLN6957 4.7 31.1 1.0
CB C:GLN6956 4.7 33.2 1.0
O C:HOH7340 4.8 34.3 1.0
O C:ILE6955 4.8 28.0 1.0
CE1 C:TYR7009 4.9 27.7 1.0

Sodium binding site 6 out of 7 in 6w75

Go back to Sodium Binding Sites List in 6w75
Sodium binding site 6 out of 7 in the 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na7104

b:53.4
occ:1.00
O C:HOH7309 2.2 65.7 1.0
O C:HOH7241 2.3 47.5 1.0
O C:ILE6910 2.4 31.0 1.0
OG C:SER7090 2.5 41.5 1.0
CB C:SER7090 3.5 36.6 1.0
C C:ILE6910 3.6 30.3 1.0
O C:ASP7091 3.8 44.3 1.0
CA C:GLY6911 4.2 30.1 1.0
O C:SER7090 4.2 32.9 1.0
CG1 C:VAL7092 4.2 48.0 0.6
O C:HOH7398 4.2 35.6 1.0
C C:SER7090 4.4 34.8 1.0
N C:GLY6911 4.4 29.1 1.0
CA C:SER7090 4.5 34.9 1.0
CG2 C:VAL7092 4.6 45.9 0.4
OG1 C:THR6915 4.7 31.2 1.0
C C:ASP7091 4.7 42.5 1.0
CA C:ILE6910 4.8 28.8 1.0
N C:ILE6910 4.8 28.7 1.0

Sodium binding site 7 out of 7 in 6w75

Go back to Sodium Binding Sites List in 6w75
Sodium binding site 7 out of 7 in the 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na4403

b:64.5
occ:1.00
O D:HOH4576 2.1 40.7 0.5
O D:HOH4511 2.3 73.2 1.0
O D:ASN4367 2.6 45.4 1.0
O D:THR4364 2.6 44.7 1.0
O D:HOH4575 3.1 45.1 0.5
O D:HOH4576 3.3 41.0 0.5
O D:HOH4537 3.7 41.4 1.0
C D:ASN4367 3.8 45.3 1.0
C D:THR4364 3.8 41.2 1.0
CZ3 D:TRP4376 4.4 37.9 1.0
CA D:THR4368 4.4 45.3 1.0
O D:LEU4365 4.4 51.7 0.6
N D:THR4368 4.5 45.6 1.0
CH2 D:TRP4376 4.7 35.6 1.0
CA D:THR4364 4.7 38.6 1.0
O D:LEU4365 4.7 50.7 0.4
N D:LEU4365 4.7 43.3 0.6
N D:ASN4367 4.7 47.3 1.0
N D:LEU4365 4.8 43.2 0.4
C D:LEU4365 4.8 48.2 0.6
CA D:LEU4365 4.8 46.0 0.6
O D:HOH4527 4.8 55.2 1.0
O D:HOH4584 4.8 50.5 1.0
CA D:LEU4365 4.8 45.8 0.4
C D:LEU4365 4.9 48.1 0.4
CA D:ASN4367 4.9 46.4 1.0
OD2 D:ASP4344 4.9 62.8 1.0

Reference:

G.Minasov, L.Shuvalova, M.Rosas-Lemus, O.Kiryukhina, G.Wiersum, A.Godzik, L.Jaroszewski, P.J.Stogios, T.Skarina, K.J.F.Satchell. 1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex From Sars-Cov-2 To Be Published.
Page generated: Mon Aug 18 08:02:12 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy