Atomistry » Sodium » PDB 7u34-7v8o » 7ult
Atomistry »
  Sodium »
    PDB 7u34-7v8o »
      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: Wed Oct 9 09:15:25 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy