Atomistry » Sodium » PDB 7ugj-7vm9 » 7ult
Atomistry »
  Sodium »
    PDB 7ugj-7vm9 »
      7ult »

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

Go back to Sodium Binding Sites List in 7ult
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

Go back to Sodium Binding Sites List in 7ult
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

Go back to Sodium Binding Sites List in 7ult
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

Go back to Sodium Binding Sites List in 7ult
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

Go back to Sodium Binding Sites List in 7ult
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

Go back to Sodium Binding Sites List in 7ult
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

Go back to Sodium Binding Sites List in 7ult
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: Mon Aug 18 12:11:04 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