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Potassium in PDB 9npy: Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head)

Other elements in 9npy:

The structure of Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head) also contains other interesting chemical elements:

Magnesium (Mg) 21 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head) (pdb code 9npy). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head), PDB code: 9npy:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 9npy

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Potassium binding site 1 out of 9 in the Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head) within 5.0Å range:
probe atom residue distance (Å) B Occ
d:K102

b:67.1
occ:1.00
O d:HIS28 2.7 65.9 1.0
O i:HOH2300 2.8 66.7 1.0
OE1 d:GLN41 2.9 64.7 1.0
OD1 d:ASN26 2.9 66.0 1.0
O4' i:G1495 3.1 63.0 1.0
CB d:CYS39 3.3 54.6 1.0
SG d:CYS39 3.6 66.9 1.0
C1' i:G1495 3.7 57.8 1.0
CG d:ASN26 3.7 61.3 1.0
CD d:GLN41 3.7 58.8 1.0
C d:HIS28 3.7 61.3 1.0
C4' i:G1495 3.8 55.9 1.0
NE2 d:GLN41 3.9 57.3 1.0
O2' i:G1495 4.1 63.2 1.0
CB d:ASN26 4.1 59.1 1.0
CA d:HIS28 4.5 59.1 1.0
C2' i:G1495 4.5 56.7 1.0
CB d:HIS28 4.5 59.1 1.0
N d:HIS28 4.5 59.6 1.0
CA d:CYS39 4.6 55.2 1.0
ND2 d:ASN26 4.6 59.5 1.0
N d:GLY29 4.6 61.3 1.0
C5' i:G1495 4.7 59.8 1.0
N9 i:G1495 4.8 58.2 1.0
CA d:GLY29 4.8 59.2 1.0
N d:ARG40 4.8 55.9 1.0
OP2 i:G1256 4.9 65.0 1.0
C3' i:G1495 4.9 57.6 1.0
O i:HOH2467 4.9 73.5 1.0
O d:GLY29 5.0 64.4 1.0

Potassium binding site 2 out of 9 in 9npy

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Potassium binding site 2 out of 9 in the Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head) within 5.0Å range:
probe atom residue distance (Å) B Occ
i:K1920

b:72.0
occ:1.00
OP2 i:U1225 2.9 75.2 1.0
OP2 i:G1226 2.9 69.7 1.0
N7 i:G1227 3.0 64.7 1.0
N7 i:G1226 3.0 66.6 1.0
O6 i:G1227 3.2 65.4 1.0
N7 i:G1638 3.5 68.1 1.0
O5' i:U1225 3.5 69.4 1.0
O i:HOH2337 3.5 77.1 1.0
C8 i:G1226 3.6 65.2 1.0
P i:U1225 3.7 72.5 1.0
C5 i:G1227 3.7 61.5 1.0
C6 i:G1227 3.8 60.5 1.0
C8 i:G1638 4.0 67.2 1.0
C8 i:G1227 4.1 63.7 1.0
P i:G1226 4.2 69.7 1.0
C5 i:G1226 4.2 64.9 1.0
C3' i:U1225 4.3 65.5 1.0
O i:HOH2070 4.3 72.6 1.0
OP1 i:U1225 4.3 71.8 1.0
C5 i:G1638 4.3 64.9 1.0
C6 i:U1225 4.3 62.5 1.0
C5 i:U1225 4.4 61.9 1.0
O5' i:G1226 4.4 69.6 1.0
C5' i:U1225 4.6 66.5 1.0
O3' i:U1225 4.7 67.9 1.0
O6 i:G1226 4.7 73.4 1.0
O6 i:G1638 4.8 69.6 1.0
C6 i:G1638 4.8 64.4 1.0
C6 i:G1226 4.9 68.5 1.0
N9 i:G1226 4.9 64.3 1.0
N1 i:U1225 4.9 63.5 1.0
N9 i:G1638 4.9 68.9 1.0
C4' i:U1225 5.0 66.7 1.0
C4 i:G1227 5.0 62.2 1.0

Potassium binding site 3 out of 9 in 9npy

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Potassium binding site 3 out of 9 in the Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head) within 5.0Å range:
probe atom residue distance (Å) B Occ
i:K1921

b:72.9
occ:1.00
O i:HOH2322 2.7 64.7 1.0
O4 i:U1492 2.8 61.5 1.0
O i:HOH2011 3.0 73.8 1.0
O6 i:G1335 3.0 59.3 1.0
O i:HOH2556 3.1 71.3 1.0
O6 i:G1491 3.2 59.0 1.0
O i:HOH2632 3.4 77.7 1.0
N4 i:C1336 3.5 56.6 1.0
N2 i:G1330 3.6 55.0 1.0
C4 i:U1492 3.8 56.6 1.0
N3 i:U1492 4.0 53.7 1.0
C6 i:G1335 4.1 56.0 1.0
C6 i:G1491 4.1 53.8 1.0
O i:HOH2436 4.1 76.2 1.0
C2 i:G1330 4.2 55.3 1.0
OP2 i:G1334 4.2 70.8 1.0
O i:HOH2561 4.3 68.4 1.0
O i:HOH2310 4.4 66.1 1.0
N7 i:G1335 4.4 58.8 1.0
N3 i:G1330 4.4 56.9 1.0
O i:HOH2430 4.5 66.7 1.0
C4 i:C1336 4.6 56.8 1.0
O i:HOH2121 4.6 67.6 1.0
C5 i:G1335 4.6 56.1 1.0
N1 i:G1491 4.8 52.9 1.0
C5 i:G1491 4.9 54.0 1.0
N3 i:C1336 5.0 58.4 1.0

Potassium binding site 4 out of 9 in 9npy

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Potassium binding site 4 out of 9 in the Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head) within 5.0Å range:
probe atom residue distance (Å) B Occ
i:K1922

b:69.9
occ:1.00
O i:HOH2280 2.7 70.1 1.0
O4 i:U1329 2.8 66.0 1.0
O2 i:C1493 2.9 61.1 1.0
O6 i:G1500 3.0 62.1 1.0
O6 i:OMG1328 3.1 67.5 1.0
O i:HOH2610 3.4 77.2 1.0
O2' i:C1493 3.5 79.5 1.0
C2 i:C1493 3.6 60.4 1.0
C4 i:U1329 3.8 60.5 1.0
N3 i:U1499 3.8 58.6 1.0
O4 i:U1499 3.9 72.7 1.0
N4 i:C1501 3.9 62.0 1.0
C2' i:C1493 3.9 65.8 1.0
N3 i:U1329 3.9 56.3 1.0
C6 i:OMG1328 4.1 63.6 1.0
C4 i:U1499 4.1 63.2 1.0
C6 i:G1500 4.1 60.9 1.0
N3 i:C1493 4.2 57.9 1.0
N1 i:C1493 4.3 60.3 1.0
N7 i:G1500 4.3 60.5 1.0
C1' i:C1493 4.4 63.0 1.0
C2 i:U1499 4.6 62.0 1.0
C5 i:G1500 4.6 60.0 1.0
O2 i:U1499 4.8 63.7 1.0
N1 i:OMG1328 4.9 59.7 1.0
C5 i:OMG1328 4.9 62.1 1.0
N6 i:A1332 4.9 58.8 1.0
C4 i:C1501 4.9 65.1 1.0
K i:K1926 5.0 87.4 1.0

Potassium binding site 5 out of 9 in 9npy

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Potassium binding site 5 out of 9 in the Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head) within 5.0Å range:
probe atom residue distance (Å) B Occ
i:K1923

b:76.7
occ:1.00
O6 i:G1257 2.6 67.5 1.0
O2 i:U1494 2.8 65.8 1.0
O i:HOH2502 2.9 69.9 1.0
N7 i:G1257 3.2 61.0 1.0
O i:HOH2145 3.3 70.5 1.0
O i:HOH2039 3.4 71.7 1.0
C6 i:G1257 3.4 61.4 1.0
C5 i:G1257 3.6 60.4 1.0
N2 i:G1255 3.7 61.1 1.0
N3 i:G1255 3.8 61.3 1.0
C2 i:G1255 3.8 60.5 1.0
O i:HOH2467 3.8 73.5 1.0
C2 i:U1494 4.0 63.9 1.0
OP1 i:G1256 4.1 72.8 1.0
C8 i:G1257 4.5 60.9 1.0
C4 i:G1255 4.5 59.9 1.0
C2' i:G1255 4.5 59.5 1.0
N1 i:G1255 4.5 58.6 1.0
C1' i:U1494 4.6 63.1 1.0
O2' i:U1494 4.6 70.1 1.0
O i:HOH2198 4.7 68.7 1.0
O2' i:G1255 4.7 63.7 1.0
N1 i:G1257 4.7 59.5 1.0
N1 i:U1494 4.8 63.8 1.0
N3 i:U1494 4.9 65.4 1.0
O i:HOH2313 4.9 71.1 1.0
C4 i:G1257 5.0 62.8 1.0

Potassium binding site 6 out of 9 in 9npy

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Potassium binding site 6 out of 9 in the Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head) within 5.0Å range:
probe atom residue distance (Å) B Occ
i:K1924

b:72.4
occ:1.00
O6 i:G1330 2.6 64.8 1.0
O i:HOH2286 2.7 65.9 1.0
O i:HOH2084 2.9 69.6 1.0
O6 i:G1334 3.0 59.2 1.0
O4 i:U1496 3.2 68.3 1.0
O i:HOH2009 3.5 68.7 1.0
C6 i:G1330 3.7 58.1 1.0
N2 i:G1335 3.8 58.5 1.0
C6 i:G1334 3.9 57.2 1.0
N6 i:A1498 3.9 58.7 1.0
N1 i:G1334 4.0 56.3 1.0
C4 i:U1496 4.1 67.3 1.0
C5 i:U1496 4.2 65.5 1.0
O2 i:U1492 4.2 60.3 1.0
N1 i:G1330 4.2 54.9 1.0
C2 i:G1335 4.2 56.7 1.0
N7 i:G1495 4.3 60.6 1.0
O2' i:U1492 4.3 62.6 1.0
N1 i:G1335 4.3 53.8 1.0
C2' i:U1492 4.5 57.2 1.0
O4' i:C1493 4.5 68.8 1.0
N7 i:A1498 4.6 62.0 1.0
C5' i:C1493 4.6 62.5 1.0
C4' i:C1493 4.6 64.3 1.0
C6 i:A1498 4.6 58.2 1.0
OP1 i:G1495 4.6 69.6 1.0
C5 i:A1498 4.8 59.8 1.0
C2 i:U1492 4.9 56.8 1.0
O6 i:G1495 4.9 68.3 1.0
C5 i:G1495 5.0 59.9 1.0
C8 i:G1495 5.0 59.6 1.0
C5 i:G1330 5.0 57.6 1.0

Potassium binding site 7 out of 9 in 9npy

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Potassium binding site 7 out of 9 in the Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head) within 5.0Å range:
probe atom residue distance (Å) B Occ
i:K1925

b:93.1
occ:1.00
O4 i:U1343 2.6 78.3 1.0
O i:HOH2497 2.7 73.5 1.0
O2 i:U1342 2.9 86.0 1.0
N7 i:A1484 2.9 64.8 1.0
O2 i:C1341 3.5 82.7 1.0
N3 i:C1341 3.5 73.9 1.0
C8 i:A1484 3.5 63.4 1.0
C2 i:U1342 3.6 83.4 1.0
C4 i:U1343 3.7 77.4 1.0
N3 i:U1342 3.8 82.4 1.0
C2 i:C1341 3.8 78.5 1.0
OP2 i:A1484 4.0 81.9 1.0
N6 i:A1344 4.1 73.7 1.0
C5 i:A1484 4.1 59.7 1.0
N1 i:A1344 4.2 67.7 1.0
C5 i:U1343 4.3 78.4 1.0
C6 i:A1344 4.4 71.2 1.0
O2' i:G1385 4.4 67.2 1.0
C4 i:C1341 4.5 74.3 1.0
N6 i:A1484 4.5 63.9 1.0
N3 i:U1343 4.7 76.5 1.0
C6 i:A1484 4.8 61.2 1.0
N4 i:C1341 4.8 74.1 1.0
C2' i:A1483 4.9 73.0 1.0
N9 i:A1484 4.9 60.7 1.0
N1 i:U1342 4.9 84.8 1.0
N1 i:C1341 4.9 77.8 1.0
N3 i:A1483 5.0 73.1 1.0

Potassium binding site 8 out of 9 in 9npy

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Potassium binding site 8 out of 9 in the Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head) within 5.0Å range:
probe atom residue distance (Å) B Occ
i:K1926

b:87.4
occ:1.00
O2' i:C1493 2.5 79.5 1.0
O i:HOH2243 2.6 74.6 1.0
O4 i:U1499 2.8 72.7 1.0
O i:HOH2491 2.8 86.1 1.0
O i:HOH2002 3.2 82.9 1.0
O3' i:C1493 3.3 74.1 1.0
OP2 i:U1494 3.5 72.2 1.0
O i:HOH2235 3.5 75.7 1.0
C2' i:C1493 3.8 65.8 1.0
C4 i:U1499 3.8 63.2 1.0
P i:U1494 4.1 75.2 1.0
C3' i:C1493 4.1 65.7 1.0
MG i:MG1906 4.2 84.4 1.0
O i:HOH2610 4.3 77.2 1.0
C5 i:U1499 4.4 62.6 1.0
OP2 i:G1497 4.4 83.4 1.0
O i:HOH2091 4.5 83.3 1.0
C4' i:C1493 4.7 64.3 1.0
OP2 i:U1496 4.8 72.2 1.0
C1' i:C1493 4.8 63.0 1.0
O i:HOH2084 4.8 69.6 1.0
N3 i:U1499 5.0 58.6 1.0
K i:K1922 5.0 69.9 1.0
C5' i:U1494 5.0 66.1 1.0

Potassium binding site 9 out of 9 in 9npy

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Potassium binding site 9 out of 9 in the Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Sars-Cov-2 NSP1 Bound to the Rhinolophus Lepidus 40S Ribosome (Local Refinement of the 40S Head) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K301

b:76.7
occ:1.00
O E:ASN165 2.5 76.3 1.0
O E:LYS167 2.6 78.0 1.0
OP1 i:U1535 2.6 73.8 1.0
O E:ALA162 2.7 71.0 1.0
O2' i:C1534 3.1 71.2 1.0
O i:HOH2223 3.3 75.0 1.0
C3' i:C1534 3.5 63.4 1.0
C2' i:C1534 3.6 63.2 1.0
P i:U1535 3.6 70.1 1.0
C E:LYS167 3.7 76.6 1.0
C E:ASN165 3.7 73.2 1.0
C E:ALA162 3.7 68.2 1.0
O3' i:C1534 3.7 69.5 1.0
CB E:ALA162 4.1 66.3 1.0
CA E:ALA162 4.1 65.7 1.0
CA E:THR168 4.1 73.8 1.0
OP2 i:U1535 4.2 69.2 1.0
N E:ASN165 4.3 71.7 1.0
N E:THR168 4.4 75.3 1.0
C E:ILE166 4.4 76.4 1.0
CA E:ASN165 4.4 70.4 1.0
N E:LYS167 4.5 74.3 1.0
C E:THR168 4.5 71.7 1.0
O E:ILE166 4.5 80.4 1.0
O i:HOH2183 4.5 71.8 1.0
N E:ILE169 4.6 68.7 1.0
N E:ILE166 4.7 71.8 1.0
CB E:ASN165 4.7 71.0 1.0
CA E:LYS167 4.7 75.2 1.0
CA E:ILE166 4.8 73.8 1.0
N E:PHE163 4.9 70.0 1.0
O4 i:U1599 4.9 73.3 1.0
O5' i:U1535 5.0 69.9 1.0
C4' i:C1534 5.0 63.4 1.0

Reference:

R.Gen, A.Addetia, D.Asarnow, Y.J.Park, J.Quispe, M.C.Chan, J.T.Brown, J.Lee, M.G.Campbell, C.P.Lapointe, D.Veesler. Sars-Cov-2 NSP1 Mediates Broad Inhibition of Translation in Mammals. Cell Rep V. 44 15696 2025.
ISSN: ESSN 2211-1247
PubMed: 40359110
DOI: 10.1016/J.CELREP.2025.115696
Page generated: Sat Aug 9 19:21:07 2025

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