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Sodium in PDB 9p0f: Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 From Sars-Cov-2

Protein crystallography data

The structure of Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 From Sars-Cov-2, PDB code: 9p0f was solved by G.Minasov, L.Shuvalova, J.S.Brunzelle, K.J.F.Satchell, Center Forstructural Biology Of Infectious Diseases (Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.69 / 2.35
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.691, 125.541, 89.862, 90, 90, 90
R / Rfree (%) 21.6 / 25.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 From Sars-Cov-2 (pdb code 9p0f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 From Sars-Cov-2, PDB code: 9p0f:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 9p0f

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Sodium binding site 1 out of 4 in the Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 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 Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 From Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:97.1
occ:1.00
 O A:LEU436 2.3 76.2 1.0
O A:HOH702 2.3 87.8 1.0
O A:HOH707 2.3 97.7 1.0
O A:ASP433 2.3 80.3 1.0
O A:HOH706 2.3 96.6 1.0
O A:HOH705 2.3 102.1 1.0
C A:ASP433 3.4 71.7 1.0
C A:LEU436 3.4 76.6 1.0
N A:GLY409 3.8 83.8 1.0
OD1 A:ASP433 4.0 79.8 1.0
N A:LEU436 4.2 70.7 1.0
CA A:LEU436 4.2 75.1 1.0
N A:VAL434 4.2 71.1 1.0
CA A:ASP433 4.2 69.8 1.0
CA A:VAL434 4.3 68.7 1.0
CB A:LEU436 4.4 73.5 1.0
N A:PRO437 4.4 84.0 1.0
CG A:ASP433 4.4 79.8 1.0
CA A:GLY409 4.5 81.8 1.0
CD A:PRO437 4.6 82.7 1.0
C A:VAL434 4.8 70.0 1.0
N A:LEU435 4.8 67.3 1.0
O A:SER432 4.8 74.0 1.0
OD2 A:ASP433 4.9 87.1 1.0
CB A:ASP433 5.0 73.2 1.0

Sodium binding site 2 out of 4 in 9p0f

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Sodium binding site 2 out of 4 in the Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 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 Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 From Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:126.7
occ:1.00
 O A:HOH703 2.4 90.2 1.0
O A:THR461 2.4 208.2 1.0
O A:GLN500 2.8 163.4 1.0
OG1 A:THR461 3.0 205.4 1.0
C A:THR461 3.5 205.7 1.0
O A:SER496 3.5 124.8 1.0
OG A:SER496 3.7 111.9 1.0
C A:GLN500 3.8 161.0 1.0
CB A:THR461 3.8 196.4 1.0
OXT A:GLN500 4.0 135.6 1.0
CA A:THR461 4.2 197.3 1.0
C A:SER496 4.4 125.3 1.0
N A:SER462 4.5 105.4 1.0
N A:TYR463 4.7 86.2 1.0
CA A:SER462 4.7 101.3 1.0
O A:LEU499 4.7 171.6 1.0
CB A:SER496 4.8 119.5 1.0
N A:THR461 4.9 202.2 1.0
C A:SER462 5.0 94.6 1.0

Sodium binding site 3 out of 4 in 9p0f

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Sodium binding site 3 out of 4 in the Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 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 Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 From Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:95.7
occ:1.00
 O B:HOH704 2.3 86.4 1.0
O B:LEU436 2.3 76.1 1.0
O B:HOH707 2.3 90.5 1.0
O B:ASP433 2.3 77.8 1.0
O B:HOH703 2.3 98.8 1.0
O B:HOH706 2.3 88.6 1.0
C B:ASP433 3.4 70.2 1.0
C B:LEU436 3.4 77.5 1.0
N B:GLY409 3.8 83.4 1.0
OD1 B:ASP433 4.0 82.3 1.0
N B:LEU436 4.2 73.5 1.0
CA B:LEU436 4.2 77.4 1.0
N B:VAL434 4.2 72.0 1.0
CA B:ASP433 4.2 70.1 1.0
CA B:VAL434 4.3 69.0 1.0
CB B:LEU436 4.4 75.6 1.0
N B:PRO437 4.4 87.5 1.0
CG B:ASP433 4.4 82.0 1.0
CA B:GLY409 4.5 81.9 1.0
CD B:PRO437 4.6 86.7 1.0
C B:VAL434 4.8 70.5 1.0
N B:LEU435 4.8 70.5 1.0
O B:SER432 4.8 74.9 1.0
OD2 B:ASP433 4.9 89.6 1.0
CB B:ASP433 5.0 75.7 1.0

Sodium binding site 4 out of 4 in 9p0f

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Sodium binding site 4 out of 4 in the Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 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 Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 From Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:93.7
occ:1.00
 O C:LEU436 2.3 78.5 1.0
O C:HOH705 2.3 80.2 1.0
O C:HOH708 2.3 98.6 1.0
O C:ASP433 2.3 79.7 1.0
O C:HOH707 2.3 95.3 1.0
O C:HOH704 2.3 99.6 1.0
C C:ASP433 3.4 69.9 1.0
C C:LEU436 3.4 78.9 1.0
N C:GLY409 3.8 83.2 1.0
OD1 C:ASP433 4.0 81.8 1.0
N C:LEU436 4.2 75.6 1.0
CA C:LEU436 4.2 79.7 1.0
CA C:VAL434 4.2 68.9 1.0
N C:VAL434 4.2 69.1 1.0
CA C:ASP433 4.3 69.6 1.0
CB C:LEU436 4.4 76.4 1.0
N C:PRO437 4.4 85.2 1.0
CG C:ASP433 4.5 85.6 1.0
CA C:GLY409 4.5 81.1 1.0
CD C:PRO437 4.6 86.4 1.0
C C:VAL434 4.7 71.4 1.0
N C:LEU435 4.8 69.3 1.0
O C:SER432 4.8 79.8 1.0
OD2 C:ASP433 4.9 93.9 1.0

Reference:

G.Minasov, L.Shuvalova, J.S.Brunzelle, K.J.F.Satchell, Center For Structural Biology Of Infectious Diseases (Csbid). Crystal Structure of the C-Terminal Cytoplasmic Domain of NSP4 From Sars-Cov-2 To Be Published.
Page generated: Mon Aug 18 17:31:53 2025

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