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Sodium in PDB 7ult: Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form., PDB code: 7ult was solved by G.Minasov, L.Shuvalova, J.S.Brunzelle, 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) 29.90 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.681, 166.681, 98.55, 90, 90, 120
R / Rfree (%) 16.4 / 18.8

Other elements in 7ult:

The structure of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. (pdb code 7ult). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form., PDB code: 7ult:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7ult

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Sodium binding site 1 out of 8 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na7101

b:37.7
occ:1.00
 O A:HOH7399 2.2 42.5 1.0
O A:LEU6887 2.3 26.7 1.0
O B:HOH4523 2.3 33.2 1.0
O A:GLN6885 2.5 25.3 1.0
O A:ARG6884 2.7 24.9 1.0
C A:GLN6885 3.1 24.4 1.0
C A:LEU6887 3.5 26.3 1.0
CA A:GLN6885 3.6 24.5 1.0
O A:HOH7308 3.7 26.1 1.0
C A:ARG6884 3.7 24.5 1.0
N A:LEU6887 4.0 24.3 1.0
N A:TRP6886 4.1 24.0 1.0
C A:TRP6886 4.1 24.6 1.0
OG1 B:THR4311 4.1 35.4 1.0
N A:GLN6885 4.1 24.3 1.0
N A:THR6889 4.2 31.3 1.0
C A:PRO6888 4.3 29.4 1.0
O A:HOH7251 4.3 48.3 1.0
OG1 A:THR6889 4.3 36.2 1.0
CA A:LEU6887 4.3 25.1 1.0
O A:TRP6886 4.4 23.5 1.0
O A:HOH7267 4.4 34.1 1.0
N A:PRO6888 4.4 27.1 1.0
CB B:THR4311 4.5 32.5 1.0
CA A:PRO6888 4.5 28.7 1.0
CA A:TRP6886 4.6 23.9 1.0
O A:PRO6888 4.6 27.6 1.0
O B:VAL4310 4.6 29.4 1.0
CA A:THR6889 4.7 33.5 1.0
O B:HOH4591 4.7 52.5 1.0
O A:HOH7370 4.9 36.8 1.0
CA A:ARG6884 5.0 25.0 1.0

Sodium binding site 2 out of 8 in 7ult

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Sodium binding site 2 out of 8 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na7102

b:55.3
occ:1.00
 O C:HOH7230 2.3 49.7 1.0
O A:HOH7407 2.3 60.3 1.0
O A:HOH7375 2.4 40.8 1.0
O A:ASN7095 2.5 46.2 1.0
OD1 A:ASN7095 2.7 59.4 1.0
O C:HOH7223 3.2 39.0 1.0
C A:ASN7095 3.6 50.0 1.0
CG A:ASN7095 3.9 57.4 1.0
O C:ASP6906 3.9 25.5 1.0
N A:ASN7095 4.0 45.9 1.0
CA A:ASN7095 4.3 49.6 1.0
O C:HOH7377 4.3 42.9 0.5
CB C:ASP6906 4.6 24.9 1.0
CB A:ASN7095 4.6 53.9 1.0
C C:ASP6906 4.7 24.9 1.0
N A:ASN7096 4.7 52.4 1.0
CA C:ASP6906 4.8 24.5 1.0
ND2 A:ASN7095 4.9 62.5 1.0
OD1 C:ASP6906 5.0 26.6 1.0

Sodium binding site 3 out of 8 in 7ult

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Sodium binding site 3 out of 8 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4403

b:57.5
occ:1.00
 O B:HOH4589 2.2 38.7 0.5
O B:HOH4547 2.3 52.2 1.0
O B:HOH4577 2.4 63.2 1.0
O B:HOH4585 2.5 60.4 1.0
O B:THR4355 2.5 41.6 1.0
OD1 B:ASN4358 2.8 45.6 1.0
CG B:ASN4358 3.4 44.8 1.0
C B:THR4355 3.4 39.9 1.0
O B:HOH4528 4.0 62.6 1.0
CB B:ASN4358 4.0 41.6 1.0
ND2 B:ASN4358 4.1 46.5 1.0
CA B:THR4355 4.1 40.6 1.0
N B:CYS4356 4.2 38.5 1.0
CA B:CYS4356 4.5 38.0 1.0
O B:THR4354 4.5 35.7 0.7
O B:THR4354 4.5 35.4 0.3
N B:ASN4358 4.6 37.7 1.0
O B:HOH4555 4.6 55.1 1.0
O B:HOH4588 4.8 35.9 0.5
C B:CYS4356 4.8 38.0 1.0
N B:ALA4357 4.9 36.6 1.0
CA B:ASN4358 4.9 37.9 1.0

Sodium binding site 4 out of 8 in 7ult

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Sodium binding site 4 out of 8 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4404

b:54.5
occ:1.00
 O B:HOH4583 2.2 46.0 0.5
O B:HOH4580 2.4 41.6 0.5
O B:THR4364 2.5 41.7 1.0
O B:ASN4367 2.5 44.3 1.0
O B:HOH4583 3.3 36.5 0.5
C B:THR4364 3.7 40.7 1.0
C B:ASN4367 3.7 44.2 1.0
O B:HOH4552 3.8 46.1 1.0
CZ3 B:TRP4376 4.3 39.9 1.0
O B:LEU4365 4.3 48.3 1.0
O B:HOH4505 4.4 51.2 1.0
CA B:THR4364 4.5 38.0 1.0
CA B:THR4368 4.5 44.4 1.0
CH2 B:TRP4376 4.5 40.4 1.0
N B:THR4368 4.5 43.9 1.0
N B:ASN4367 4.6 45.1 1.0
C B:LEU4365 4.6 47.0 1.0
N B:LEU4365 4.6 43.6 1.0
O B:HOH4601 4.7 51.2 1.0
CA B:LEU4365 4.7 46.1 1.0
CA B:ASN4367 4.7 44.2 1.0
OD2 B:ASP4344 4.7 56.2 1.0

Sodium binding site 5 out of 8 in 7ult

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Sodium binding site 5 out of 8 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na7101

b:39.6
occ:1.00
 O C:HOH7213 2.3 43.7 1.0
O C:HOH7414 2.3 37.3 1.0
O C:HOH7362 2.4 36.5 1.0
O C:GLY6869 2.5 21.3 1.0
OD2 C:ASP6928 2.7 32.2 1.0
O C:ASP6928 2.8 24.2 1.0
O C:HOH7442 3.3 58.1 1.0
CG C:ASP6928 3.4 27.7 1.0
C C:GLY6869 3.5 21.6 1.0
C C:ASP6928 3.6 23.0 1.0
CB C:ASP6928 3.7 24.8 1.0
O C:HOH7376 3.9 44.5 1.0
CA C:GLY6869 4.0 22.0 1.0
O C:GLY6871 4.2 29.8 1.0
CA C:ASP6928 4.3 22.7 1.0
OD1 C:ASP6928 4.4 29.0 1.0
OD2 C:ASP6897 4.4 25.6 1.0
O C:HOH7255 4.4 38.7 1.0
N C:MET6929 4.5 22.8 1.0
O C:HOH7240 4.5 57.1 1.0
O C:HOH7390 4.5 36.0 1.0
O C:HOH7252 4.7 54.3 1.0
N C:ALA6870 4.7 21.4 1.0
CA C:MET6929 4.7 24.0 1.0

Sodium binding site 6 out of 8 in 7ult

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Sodium binding site 6 out of 8 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na7102

b:29.4
occ:1.00
 O C:HOH7436 2.2 38.8 1.0
O C:LEU6887 2.3 20.0 1.0
O D:HOH4542 2.4 31.9 1.0
O C:GLN6885 2.5 19.3 1.0
O C:ARG6884 2.6 20.1 1.0
C C:GLN6885 3.1 19.3 1.0
C C:LEU6887 3.4 20.7 1.0
O C:HOH7306 3.6 21.4 1.0
CA C:GLN6885 3.6 19.7 1.0
C C:ARG6884 3.7 20.2 1.0
N C:LEU6887 4.0 19.1 1.0
N C:TRP6886 4.0 18.6 1.0
C C:TRP6886 4.1 18.9 1.0
OG1 D:THR4311 4.1 29.1 1.0
N C:GLN6885 4.1 19.8 1.0
N C:THR6889 4.2 24.7 1.0
O C:HOH7212 4.2 50.3 1.0
C C:PRO6888 4.3 23.4 1.0
CA C:LEU6887 4.3 19.4 1.0
OG1 C:THR6889 4.3 28.7 1.0
O C:TRP6886 4.4 18.8 1.0
N C:PRO6888 4.4 21.4 1.0
O C:HOH7222 4.4 27.3 1.0
CA C:PRO6888 4.4 22.5 1.0
CB D:THR4311 4.5 27.4 1.0
CA C:TRP6886 4.6 18.7 1.0
O D:HOH4587 4.7 43.6 1.0
O C:PRO6888 4.7 22.1 1.0
O D:VAL4310 4.7 23.8 1.0
CA C:THR6889 4.8 26.5 1.0
O C:HOH7363 4.8 30.7 1.0
CA C:ARG6884 5.0 20.2 1.0

Sodium binding site 7 out of 8 in 7ult

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Sodium binding site 7 out of 8 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na7103

b:56.9
occ:1.00
 O C:HOH7265 2.2 39.0 0.5
O C:HOH7394 2.3 59.8 1.0
OG C:SER7090 2.6 44.2 1.0
O C:ILE6910 2.6 31.5 1.0
O C:ASP7091 3.4 40.2 1.0
CB C:SER7090 3.7 39.9 1.0
C C:ILE6910 3.8 32.5 1.0
CA C:GLY6911 4.2 34.1 1.0
O C:SER7090 4.3 36.8 1.0
C C:SER7090 4.4 37.2 1.0
C C:ASP7091 4.4 40.2 1.0
OG1 C:THR6915 4.4 33.0 1.0
N C:GLY6911 4.5 31.9 1.0
O C:HOH7380 4.5 36.4 1.0
CG2 C:VAL7092 4.5 42.9 1.0
O C:HOH7358 4.6 45.7 1.0
CA C:SER7090 4.7 36.7 1.0
O C:HOH7365 4.7 57.9 1.0
CA C:VAL7092 4.9 41.0 1.0
CA C:ILE6910 4.9 31.3 1.0
N C:ASP7091 5.0 37.0 1.0

Sodium binding site 8 out of 8 in 7ult

Go back to Sodium Binding Sites List in 7ult
Sodium binding site 8 out of 8 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na4403

b:65.6
occ:1.00
 O D:HOH4565 2.2 41.9 0.5
O D:HOH4522 2.3 74.4 1.0
O D:HOH4589 2.4 58.8 1.0
O D:THR4364 2.6 41.0 1.0
O D:ASN4367 2.6 45.1 1.0
O D:HOH4565 3.2 36.1 0.5
O D:HOH4524 3.4 56.3 1.0
O D:HOH4580 3.4 64.2 1.0
O D:HOH4547 3.7 41.9 1.0
C D:THR4364 3.8 40.5 1.0
C D:ASN4367 3.8 44.6 1.0
CZ3 D:TRP4376 4.3 37.9 1.0
O D:LEU4365 4.5 50.1 1.0
CA D:THR4368 4.5 44.3 1.0
CH2 D:TRP4376 4.6 37.8 1.0
N D:THR4368 4.6 44.0 1.0
OD2 D:ASP4344 4.6 53.8 1.0
CA D:THR4364 4.6 37.8 1.0
O D:HOH4534 4.7 46.0 1.0
O D:HOH4590 4.8 48.3 1.0
N D:LEU4365 4.8 43.5 1.0
N D:ASN4367 4.8 46.6 1.0
C D:LEU4365 4.8 49.0 1.0
CA D:LEU4365 4.9 48.0 1.0
CA D:ASN4367 4.9 45.4 1.0

Reference:

G.Minasov, L.Shuvalova, J.S.Brunzelle, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. To Be Published.
Page generated: Fri Apr 7 16:39:19 2023

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