Sodium in PDB 7l0n: Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity

Enzymatic activity of Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity

All present enzymatic activity of Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity:
3.4.17.23;

Protein crystallography data

The structure of Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity, PDB code: 7l0n was solved by G.Snell, N.Czudnochowski, J.Dillen, J.C.Nix, T.I.Croll, D.Corti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.90 / 2.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.98, 186.58, 194.52, 90, 96.4, 90
R / Rfree (%) 29 / 32.5

Other elements in 7l0n:

The structure of Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 27 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity (pdb code 7l0n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity, PDB code: 7l0n:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 7l0n

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Sodium binding site 1 out of 6 in the Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na701

b:38.2
occ:1.00
 O H:TYR59 3.2 65.5 1.0
O R:PHE377 3.5 69.8 1.0
CG L:PRO95 4.0 67.8 1.0
CD L:PRO95 4.2 67.2 1.0
C H:TYR59 4.4 68.0 1.0
C R:PHE377 4.5 70.6 1.0
CG2 L:THR96 4.7 68.1 1.0
N R:PHE377 4.7 72.3 1.0
N H:TYR59 4.8 64.0 1.0
CA R:PHE377 5.0 71.5 1.0
CB R:PHE377 5.0 72.6 1.0

Sodium binding site 2 out of 6 in 7l0n

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Sodium binding site 2 out of 6 in the Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na704

b:56.9
occ:1.00
 CL H:CL703 2.7 81.7 1.0
OE2 H:GLU72 2.8 89.5 1.0
CD H:GLU72 3.6 88.4 1.0
OE1 H:GLU72 3.7 89.2 1.0
CD H:LYS75 4.1 76.2 1.0
NZ H:LYS75 4.3 76.0 1.0
CE H:LYS75 4.5 76.6 1.0

Sodium binding site 3 out of 6 in 7l0n

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Sodium binding site 3 out of 6 in the Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na705

b:52.4
occ:1.00
 OD2 H:ASP99 2.9 68.2 1.0
OH H:TYR106 3.1 54.7 1.0
OD2 H:ASP108 3.5 52.8 1.0
CL H:CL706 3.7 82.1 1.0
O L:HOH802 3.8 62.0 1.0
CE1 H:TYR106 3.9 54.2 1.0
CG H:ASP99 4.0 68.2 1.0
CZ H:TYR106 4.0 54.2 1.0
NH2 H:ARG97 4.2 59.4 1.0
CB H:ASP99 4.3 66.6 1.0
CG H:ASP108 4.6 53.2 1.0
OE1 L:GLN55 4.9 68.0 1.0
CB H:ASP108 4.9 53.5 1.0

Sodium binding site 4 out of 6 in 7l0n

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Sodium binding site 4 out of 6 in the Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na708

b:90.8
occ:1.00
 O F:HOH819 2.3 58.4 1.0
OD1 F:ASN578 3.0 91.6 1.0
O F:ASP216 3.3 68.7 1.0
CG F:ASN578 4.0 89.8 1.0
CG2 F:THR567 4.1 65.4 1.0
CD2 F:TYR217 4.1 59.6 1.0
ND2 F:ASN578 4.4 89.9 1.0
O F:TYR215 4.4 74.6 1.0
C F:ASP216 4.4 69.3 1.0
C F:TYR215 4.5 74.9 1.0
O F:GLY214 4.5 81.7 1.0
CB F:LYS577 4.5 79.2 1.0
CB F:THR567 4.8 65.2 1.0
CA F:TYR215 4.8 76.5 1.0
CE2 F:TYR217 4.8 59.1 1.0
N F:ASP216 4.8 72.7 1.0
CD F:LYS577 5.0 78.9 1.0

Sodium binding site 5 out of 6 in 7l0n

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Sodium binding site 5 out of 6 in the Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na711

b:84.1
occ:1.00
 O F:GLN531 3.2 104.8 1.0
O F:ALA532 3.6 107.1 1.0
CD F:LYS534 4.1 108.0 1.0
C F:ALA532 4.1 106.2 1.0
CA F:ALA532 4.1 105.8 1.0
C F:GLN531 4.3 104.5 1.0
CB F:LYS534 4.3 106.9 1.0
CG F:LYS534 4.7 107.7 1.0
N F:ALA532 4.7 105.0 1.0
N F:LYS534 4.7 104.7 1.0
CA F:LYS534 4.8 105.4 1.0

Sodium binding site 6 out of 6 in 7l0n

Go back to Sodium Binding Sites List in 7l0n
Sodium binding site 6 out of 6 in the Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Na603

b:50.4
occ:1.00
 OG R:SER494 3.5 82.3 1.0
O R:LEU492 3.8 73.8 1.0
CD2 R:LEU452 4.1 71.4 1.0
CE2 R:PHE490 4.3 84.5 1.0
CD2 R:PHE490 4.5 83.1 1.0
C R:LEU492 4.7 73.2 1.0
CB R:SER494 4.9 79.8 1.0
N R:SER494 5.0 78.9 1.0

Reference:

E.C.Thomson, L.E.Rosen, J.G.Shepherd, R.Spreafico, D.L.Robertson, G.Snell. Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity To Be Published.
Page generated: Tue Oct 8 17:31:35 2024

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