Magnesium in PDB 6zol: Sars-Cov-2-NSP1-40S Complex, Focused on Head

All present enzymatic activity of Sars-Cov-2-NSP1-40S Complex, Focused on Head:
4.2.99.18;

The structure of Sars-Cov-2-NSP1-40S Complex, Focused on Head also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 57;

Binding sites:

The binding sites of Magnesium atom in the Sars-Cov-2-NSP1-40S Complex, Focused on Head (pdb code 6zol). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 57 binding sites of Magnesium where determined in the Sars-Cov-2-NSP1-40S Complex, Focused on Head, PDB code: 6zol:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 57 in the Sars-Cov-2-NSP1-40S Complex, Focused on Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sars-Cov-2-NSP1-40S Complex, Focused on Head within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg2001 b:16.7 occ:1.00 O6 2:G1517 1.9 12.3 1.0 OP2 2:C1262 2.1 16.3 1.0 O4 2:U1263 2.5 16.4 1.0 OP1 2:C1261 2.9 15.5 1.0 C6 2:G1517 3.1 12.3 1.0 O5' 2:C1261 3.2 15.5 1.0 P 2:C1262 3.4 16.3 1.0 C4 2:U1263 3.6 16.4 1.0 P 2:C1261 3.7 15.5 1.0 OP1 2:C1262 4.0 16.3 1.0 C5 2:G1517 4.0 12.3 1.0 O6 2:G1516 4.1 12.2 1.0 O3' 2:C1261 4.1 15.5 1.0 C5 2:U1263 4.1 16.4 1.0 N1 2:G1517 4.1 12.3 1.0 N7 2:G1517 4.3 12.3 1.0 O2 2:C1264 4.3 16.2 1.0 N4 2:C1518 4.4 12.4 1.0 C5' 2:C1261 4.4 15.5 1.0 O5' 2:C1262 4.5 16.3 1.0 C3' 2:C1261 4.6 15.5 1.0 OP2 2:C1261 4.6 15.5 1.0 N3 2:U1263 4.8 16.4 1.0 N3 2:C1264 4.8 16.2 1.0 O3' 2:A1260 4.8 13.6 1.0 C2 2:C1264 4.8 16.2 1.0 C6 2:G1516 4.9 12.2 1.0

Magnesium binding site 2 out of 57 in the Sars-Cov-2-NSP1-40S Complex, Focused on Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sars-Cov-2-NSP1-40S Complex, Focused on Head within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg2002 b:20.6 occ:1.00 OP2 2:G1387 2.6 19.1 1.0 N7 2:A1388 3.7 20.1 1.0 P 2:G1387 4.0 19.1 1.0 N6 2:A1388 4.1 20.1 1.0 N4 2:C1389 4.3 18.7 1.0 OP1 2:A1386 4.3 19.0 1.0 N7 2:G1387 4.4 19.1 1.0 OP2 2:A1386 4.4 19.0 1.0 N3 2:C1482 4.4 18.1 1.0 O6 2:G1481 4.4 14.8 1.0 C8 2:G1387 4.5 19.1 1.0 O2 2:C1482 4.5 18.1 1.0 C4 2:C1389 4.5 18.7 1.0 C5 2:A1388 4.6 20.1 1.0 OP1 2:G1387 4.6 19.1 1.0 C8 2:A1388 4.6 20.1 1.0 P 2:A1386 4.7 19.0 1.0 C6 2:A1388 4.8 20.1 1.0 O3' 2:A1386 4.8 19.0 1.0 O5' 2:A1386 4.9 19.0 1.0 C5 2:C1389 4.9 18.7 1.0 N3 2:C1389 4.9 18.7 1.0 C2 2:C1482 4.9 18.1 1.0 O5' 2:G1387 5.0 19.1 1.0

Magnesium binding site 3 out of 57 in the Sars-Cov-2-NSP1-40S Complex, Focused on Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Sars-Cov-2-NSP1-40S Complex, Focused on Head within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg2003 b:10.9 occ:1.00 O4 2:U1492 2.8 13.8 1.0 O6 2:G1335 3.0 14.4 1.0 O6 2:G1491 3.5 13.6 1.0 N4 2:C1336 3.6 13.3 1.0 N2 2:G1330 3.8 15.8 1.0 C4 2:U1492 3.8 13.8 1.0 C6 2:G1335 4.1 14.4 1.0 N3 2:U1492 4.1 13.8 1.0 OP2 2:G1334 4.3 15.9 1.0 C2 2:G1330 4.3 15.8 1.0 C6 2:G1491 4.4 13.6 1.0 N7 2:G1335 4.4 14.4 1.0 N3 2:G1330 4.5 15.8 1.0 C5 2:G1335 4.6 14.4 1.0 C4 2:C1336 4.6 13.3 1.0

Magnesium binding site 4 out of 57 in the Sars-Cov-2-NSP1-40S Complex, Focused on Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Sars-Cov-2-NSP1-40S Complex, Focused on Head within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg2004 b:14.4 occ:1.00 MG 2:MG2030 2.7 20.9 1.0 OP2 2:G1603 2.8 18.9 1.0 O6 2:G1605 2.8 13.8 1.0 OP2 2:G1604 2.8 14.2 1.0 O5' 2:G1603 3.1 18.9 1.0 O6 2:G1606 3.2 13.7 1.0 N7 2:G1605 3.4 13.8 1.0 P 2:G1603 3.5 18.9 1.0 C6 2:G1605 3.6 13.8 1.0 C5 2:G1605 3.8 13.8 1.0 NH2 S:ARG38 3.9 16.2 1.0 C6 2:G1606 4.1 13.7 1.0 P 2:G1604 4.2 14.2 1.0 OP1 2:G1603 4.4 18.9 1.0 C5' 2:G1603 4.4 18.9 1.0 N7 2:G1604 4.4 14.2 1.0 O5' 2:G1604 4.6 14.2 1.0 C8 2:G1605 4.6 13.8 1.0 N1 2:G1606 4.6 13.7 1.0 C8 2:G1604 4.6 14.2 1.0 C4' 2:G1603 4.7 18.9 1.0 O3' 2:U1602 4.8 20.9 1.0 C3' 2:G1603 4.8 18.9 1.0 N1 2:G1605 4.9 13.8 1.0

Magnesium binding site 5 out of 57 in the Sars-Cov-2-NSP1-40S Complex, Focused on Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Sars-Cov-2-NSP1-40S Complex, Focused on Head within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg2005 b:25.9 occ:1.00 O6 2:G1540 3.2 12.9 1.0 O4 2:U1539 3.8 14.3 1.0 N7 2:G1540 3.9 12.9 1.0 O6 2:G1541 4.0 12.8 1.0 C6 2:G1540 4.1 12.9 1.0 C5 2:G1540 4.3 12.9 1.0 C4 2:U1539 4.4 14.3 1.0 N4 2:C1592 4.6 15.0 1.0 C5 2:U1539 4.8 14.3 1.0 C6 2:G1541 5.0 12.8 1.0

Magnesium binding site 6 out of 57 in the Sars-Cov-2-NSP1-40S Complex, Focused on Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Sars-Cov-2-NSP1-40S Complex, Focused on Head within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg2006 b:10.0 occ:1.00 O6 2:G1656 2.9 9.4 1.0 O4 2:U1667 3.1 8.8 1.0 O4 2:U1668 3.2 8.8 1.0 N4 2:C1655 3.3 14.5 1.0 O6 2:G1669 3.4 11.5 1.0 C6 2:G1656 3.9 9.4 1.0 C4 2:U1667 4.1 8.8 1.0 O6 2:G1657 4.1 7.6 1.0 C4 2:U1668 4.2 8.8 1.0 C6 2:G1669 4.2 11.5 1.0 C4 2:C1655 4.3 14.5 1.0 N7 2:G1656 4.3 9.4 1.0 N3 2:U1668 4.4 8.8 1.0 C5 2:G1656 4.5 9.4 1.0 N3 2:C1655 4.8 14.5 1.0 N1 2:G1669 4.8 11.5 1.0 N3 2:U1667 4.8 8.8 1.0

Magnesium binding site 7 out of 57 in the Sars-Cov-2-NSP1-40S Complex, Focused on Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Sars-Cov-2-NSP1-40S Complex, Focused on Head within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg2007 b:13.0 occ:1.00 OP1 2:U1519 2.3 15.6 1.0 P 2:U1519 3.5 15.6 1.0 OP2 2:U1519 3.8 15.6 1.0 OP1 2:G1233 4.3 15.2 1.0 C5' 2:G1233 4.4 15.2 1.0 N7 2:A1259 4.5 12.2 1.0 O3' 2:C1518 4.5 12.4 1.0 O5' 2:U1519 4.6 15.6 1.0 N6 2:A1259 4.6 12.2 1.0 O5' 2:G1233 4.7 15.2 1.0 OP2 2:C1234 4.7 14.6 1.0 O2' 2:C1518 4.7 12.4 1.0 N2 2:G1257 4.7 14.8 1.0 C5' 2:U1519 4.8 15.6 1.0 C2' 2:C1518 4.8 12.4 1.0 MG 2:MG2046 4.9 14.9 1.0 P 2:G1233 4.9 15.2 1.0

Magnesium binding site 8 out of 57 in the Sars-Cov-2-NSP1-40S Complex, Focused on Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Sars-Cov-2-NSP1-40S Complex, Focused on Head within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg2008 b:15.4 occ:1.00 OP1 2:G1226 2.1 19.5 1.0 OP2 2:G1227 2.8 16.3 1.0 P 2:G1226 3.2 19.5 1.0 OP2 2:G1226 3.5 19.5 1.0 P 2:G1227 3.8 16.3 1.0 O5' 2:G1226 3.8 19.5 1.0 OP1 2:G1227 3.9 16.3 1.0 C5' 2:G1226 4.2 19.5 1.0 N7 2:A1228 4.3 14.6 1.0 O6 2:G1528 4.4 12.4 1.0 OP2 2:A1228 4.5 14.6 1.0 O3' 2:U1225 4.5 18.5 1.0 O6 2:G1229 4.7 17.0 1.0 N6 2:A1228 4.8 14.6 1.0 O5' 2:G1227 4.9 16.3 1.0 O3' 2:G1226 5.0 19.5 1.0

Magnesium binding site 9 out of 57 in the Sars-Cov-2-NSP1-40S Complex, Focused on Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Sars-Cov-2-NSP1-40S Complex, Focused on Head within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg2009 b:14.8 occ:1.00 OP1 2:C1262 2.4 16.3 1.0 O6 2:G1515 3.8 14.1 1.0 P 2:C1262 3.8 16.3 1.0 N7 2:G1515 4.1 14.1 1.0 MG 2:MG2053 4.2 20.3 1.0 O3' 2:C1261 4.3 15.5 1.0 N7 2:G1514 4.6 16.7 1.0 C6 2:G1515 4.6 14.1 1.0 OP2 2:C1262 4.7 16.3 1.0 C5' 2:C1262 4.7 16.3 1.0 C5 2:G1515 4.8 14.1 1.0 O5' 2:C1262 4.8 16.3 1.0 O6 2:G1514 4.8 16.7 1.0 O6 2:G1516 4.8 12.2 1.0

Magnesium binding site 10 out of 57 in the Sars-Cov-2-NSP1-40S Complex, Focused on Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Sars-Cov-2-NSP1-40S Complex, Focused on Head within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg2010 b:10.6 occ:1.00 OP1 2:A1259 2.3 12.2 1.0 OP2 2:A1260 2.5 13.6 1.0 P 2:A1259 3.4 12.2 1.0 OP2 2:A1259 3.6 12.2 1.0 P 2:A1260 3.7 13.6 1.0 OP1 2:A1260 4.1 13.6 1.0 N1 2:A1663 4.3 16.5 1.0 O5' 2:A1259 4.5 12.2 1.0 O3' 2:A1258 4.5 13.4 1.0 C5' 2:A1259 4.5 12.2 1.0 C2 2:A1663 4.6 16.5 1.0 O3' 2:A1259 4.7 12.2 1.0 C3' 2:A1259 4.7 12.2 1.0 O2' 2:A1258 4.8 13.4 1.0 O5' 2:A1260 4.8 13.6 1.0 C2' 2:A1258 4.8 13.4 1.0 N3 2:A1259 4.9 12.2 1.0 C2 2:A1259 4.9 12.2 1.0

K.Schubert, E.D.Karousis, A.Jomaa, A.Scaiola, B.Echeverria, L.A.Gurzeler, M.Leibundgut, V.Thiel, O.Muhlemann, N.Ban. Sars-Cov-2 NSP1 Binds the Ribosomal Mrna Channel to Inhibit Translation. Nat.Struct.Mol.Biol. V. 27 959 2020.
ISSN: ESSN 1545-9985
PubMed: 32908316
DOI: 10.1038/S41594-020-0511-8