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

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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

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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

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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

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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

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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

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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

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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: Tue Dec 15 15:30:47 2020

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