Magnesium in PDB 8r57: Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain

The structure of Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain also contains other interesting chemical elements:

Potassium	(K)	6 atoms
Zinc	(Zn)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Magnesium atom in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain (pdb code 8r57). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 20 binding sites of Magnesium where determined in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain, PDB code: 8r57:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 20 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg301 b:10.7 occ:1.00 O P:ASN161 2.2 19.6 1.0 O P:ALA158 2.5 16.4 1.0 O P:LYS163 2.6 23.6 1.0 OP1 A:PSU1480 2.7 13.8 1.0 C P:ASN161 3.3 19.6 1.0 O2' A:C1479 3.3 15.0 1.0 C P:ALA158 3.5 16.4 1.0 C3' A:C1479 3.7 15.0 1.0 P A:PSU1480 3.7 13.8 1.0 C2' A:C1479 3.7 15.0 1.0 C P:LYS163 3.8 23.6 1.0 N P:ASN161 3.8 19.6 1.0 O A:HOH2021 3.8 15.7 1.0 CA P:ASN161 3.9 19.6 1.0 CA P:ALA158 4.0 16.4 1.0 O3' A:C1479 4.0 15.0 1.0 CB P:ALA158 4.1 16.4 1.0 CB P:ASN161 4.1 19.6 1.0 OP2 A:PSU1480 4.2 13.8 1.0 C P:VAL162 4.2 22.3 1.0 N P:VAL162 4.4 22.3 1.0 N P:LYS163 4.4 23.6 1.0 O A:HOH2138 4.4 10.9 1.0 O P:VAL162 4.4 22.3 1.0 N P:THR164 4.6 21.1 1.0 CA P:THR164 4.6 21.1 1.0 CA P:VAL162 4.7 22.3 1.0 CA P:LYS163 4.7 23.6 1.0 N P:PHE159 4.7 15.2 1.0 OP2 A:C1479 4.9 15.0 1.0 N P:ARG160 4.9 16.9 1.0 C P:THR164 4.9 21.1 1.0 N P:ILE165 4.9 19.6 1.0 CG P:ASN161 5.0 19.6 1.0

Magnesium binding site 2 out of 20 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1906 b:13.6 occ:1.00 OP1 A:C1598 1.9 22.0 1.0 O A:HOH2186 2.0 19.4 1.0 O A:HOH2155 2.3 14.6 1.0 O T:HOH206 2.6 14.0 1.0 O A:HOH2137 3.0 10.2 1.0 P A:C1598 3.3 22.0 1.0 OP1 A:U1475 3.8 6.1 1.0 O5' A:C1598 4.0 22.0 1.0 OP2 A:C1598 4.1 22.0 1.0 OP2 A:A1476 4.2 6.5 1.0 C5' A:C1598 4.3 22.0 1.0 O3' A:G1597 4.4 12.0 1.0 OP2 A:G1599 4.5 22.0 1.0 OP1 A:A1476 4.5 6.5 1.0 OP2 A:U1475 4.6 6.1 1.0 P A:U1475 4.6 6.1 1.0 CG T:PRO103 4.7 14.5 1.0 CD T:PRO103 4.8 14.5 1.0 P A:A1476 4.9 6.5 1.0 OP1 A:G1599 4.9 22.0 1.0

Magnesium binding site 3 out of 20 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1907 b:13.7 occ:1.00 OP2 A:A1165 1.9 14.8 1.0 OP1 A:G1588 2.0 13.0 1.0 O A:HOH2184 2.0 17.7 1.0 O Q:HOH203 2.0 12.8 1.0 O A:HOH2040 2.4 15.5 1.0 O A:HOH2012 2.7 11.9 1.0 P A:G1588 3.2 13.0 1.0 P A:A1165 3.2 14.8 1.0 O3' A:C1164 3.5 15.1 1.0 OP2 A:G1588 3.7 13.0 1.0 O5' A:G1588 3.9 13.0 1.0 OH Q:TYR148 3.9 21.3 1.0 C5' A:A1165 4.0 14.8 1.0 OP2 A:C1589 4.1 12.5 1.0 O5' A:A1165 4.1 14.8 1.0 OP1 A:A1165 4.3 14.8 1.0 O3' A:U1587 4.5 15.2 1.0 C5' A:G1588 4.5 13.0 1.0 O3' A:A1165 4.6 14.8 1.0 C4' A:A1165 4.7 14.8 1.0 OP1 A:C1166 4.7 15.2 1.0 O A:HOH2256 4.7 22.7 1.0 CZ Q:TYR148 4.8 21.3 1.0 C3' A:C1164 4.9 15.1 1.0

Magnesium binding site 4 out of 20 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1908 b:11.4 occ:1.00 O A:HOH2124 1.9 9.6 1.0 O A:HOH2054 2.1 10.4 1.0 O A:HOH2091 2.1 12.8 1.0 OP2 A:G1175 2.3 9.4 1.0 OP1 A:G1174 2.7 13.8 1.0 P A:G1174 3.5 13.8 1.0 OP2 A:G1174 3.6 13.8 1.0 P A:G1175 3.7 9.4 1.0 N7 A:A1176 3.8 7.6 1.0 O5' A:G1174 3.8 13.8 1.0 O A:HOH2227 3.9 22.0 1.0 OP2 A:A1176 4.1 7.6 1.0 O5' A:G1175 4.2 9.4 1.0 C5' A:G1174 4.4 13.8 1.0 OP1 A:G1175 4.4 9.4 1.0 C8 A:A1176 4.5 7.6 1.0 O6 A:G1177 4.6 5.2 1.0 C5 A:A1176 4.6 7.6 1.0 N6 A:A1176 4.7 7.6 1.0 O6 A:G1473 4.7 4.6 1.0 O3' A:G1174 4.8 13.8 1.0 O3' A:U1173 5.0 13.2 1.0 N7 A:G1175 5.0 9.4 1.0

Magnesium binding site 5 out of 20 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1909 b:13.0 occ:1.00 O A:HOH2276 1.8 17.5 1.0 O A:HOH2146 2.0 13.6 1.0 OP2 A:C1167 2.2 15.9 1.0 O A:HOH2044 2.2 13.2 1.0 P A:C1167 3.3 15.9 1.0 OP1 A:C1167 3.8 15.9 1.0 N7 A:G1169 3.8 13.7 1.0 O6 A:G1169 3.9 13.7 1.0 O A:HOH2131 3.9 13.0 1.0 O5' A:C1167 4.0 15.9 1.0 O A:HOH2068 4.4 11.0 1.0 C5 A:G1169 4.6 13.7 1.0 C6 A:G1169 4.6 13.7 1.0 O3' A:C1166 4.6 15.2 1.0 N7 A:A1168 4.8 15.7 1.0 O A:HOH2214 4.9 10.3 1.0 C8 A:G1169 4.9 13.7 1.0 O A:HOH2145 4.9 14.4 1.0 OP2 A:A1168 4.9 15.7 1.0 N6 A:A1168 4.9 15.7 1.0

Magnesium binding site 6 out of 20 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1910 b:11.5 occ:1.00 O A:HOH2122 2.2 10.6 1.0 O A:HOH2255 2.2 13.8 1.0 OP2 A:A1208 2.4 12.8 1.0 OP1 A:A1207 2.6 10.4 1.0 O A:HOH2076 2.8 9.4 1.0 P A:A1207 3.5 10.4 1.0 OP2 A:A1207 3.5 10.4 1.0 P A:A1208 3.5 12.8 1.0 O A:HOH2142 3.8 12.2 1.0 O2 A:C1608 3.8 13.5 1.0 OP1 A:A1208 3.8 12.8 1.0 O3' A:A1207 4.5 10.4 1.0 O3' A:G1206 4.5 7.1 1.0 C2 A:C1608 4.6 13.5 1.0 O5' A:A1207 4.7 10.4 1.0 O5' A:A1208 4.7 12.8 1.0 C3' A:A1207 4.7 10.4 1.0 C2' A:G1206 4.8 7.1 1.0 C5' A:A1207 4.9 10.4 1.0 C5' A:A1208 4.9 12.8 1.0 N3 A:A1207 4.9 10.4 1.0 O2' A:G1206 5.0 7.1 1.0 N3 A:C1608 5.0 13.5 1.0 C2 A:A1207 5.0 10.4 1.0

Magnesium binding site 7 out of 20 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1911 b:22.0 occ:1.00 O6 A:G1462 1.8 7.7 1.0 O4 A:U1211 2.0 9.9 1.0 O A:HOH2049 2.1 12.3 1.0 OP2 A:C1210 2.1 10.9 1.0 O A:HOH2041 2.3 14.5 1.0 OP1 A:A1209 2.6 12.9 1.0 C6 A:G1462 3.0 7.7 1.0 C4 A:U1211 3.0 9.9 1.0 P A:C1210 3.5 10.9 1.0 C5 A:U1211 3.6 9.9 1.0 O2 A:U1212 3.7 10.3 1.0 P A:A1209 3.7 12.9 1.0 N4 A:C1463 3.8 7.8 1.0 N1 A:G1462 3.9 7.7 1.0 O5' A:A1209 4.0 12.9 1.0 O6 A:G1461 4.0 6.7 1.0 C5 A:G1462 4.0 7.7 1.0 OP1 A:C1210 4.2 10.9 1.0 C5' A:A1209 4.2 12.9 1.0 N3 A:U1211 4.2 9.9 1.0 N7 A:G1462 4.3 7.7 1.0 C2 A:U1212 4.4 10.3 1.0 OP2 A:A1209 4.4 12.9 1.0 O5' A:C1210 4.4 10.9 1.0 C4 A:C1463 4.5 7.8 1.0 O3' A:A1209 4.5 12.9 1.0 O2' A:U1212 4.5 10.3 1.0 N3 A:U1212 4.6 10.3 1.0 N3 A:C1463 4.8 7.8 1.0 C3' A:A1209 4.8 12.9 1.0 C6 A:G1461 4.9 6.7 1.0 C6 A:U1211 4.9 9.9 1.0 N4 A:C1214 5.0 8.4 1.0 O A:HOH2029 5.0 9.3 1.0

Magnesium binding site 8 out of 20 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1912 b:8.5 occ:1.00 OP1 A:C1210 2.0 10.9 1.0 O A:HOH2176 2.1 9.7 1.0 O A:HOH2029 2.1 9.3 1.0 O A:HOH2039 2.2 7.9 1.0 O A:HOH2169 2.2 7.2 1.0 P A:C1210 3.5 10.9 1.0 O6 A:G1460 3.8 8.1 1.0 O A:HOH2218 3.8 9.4 1.0 O4 A:U1459 3.9 10.6 1.0 O3' A:A1209 4.3 12.9 1.0 O5' A:C1210 4.3 10.9 1.0 C5' A:C1210 4.4 10.9 1.0 OP2 A:C1210 4.4 10.9 1.0 C5 A:U1459 4.4 10.6 1.0 C4 A:U1459 4.4 10.6 1.0 N7 A:G1460 4.5 8.1 1.0 O A:HOH2300 4.5 5.3 1.0 O6 A:G1461 4.5 6.7 1.0 O A:HOH2049 4.6 12.3 1.0 C6 A:G1460 4.7 8.1 1.0 O A:HOH2041 4.9 14.5 1.0 OP2 A:U1211 4.9 9.9 1.0 C5 A:G1460 5.0 8.1 1.0

Magnesium binding site 9 out of 20 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1913 b:12.9 occ:1.00 O A:HOH2217 1.8 10.6 1.0 O A:HOH2222 1.8 22.0 1.0 O A:HOH2235 2.1 15.4 1.0 OP2 A:OMG1435 2.2 8.4 1.0 OP2 A:C1279 2.5 16.4 1.0 P A:OMG1435 3.5 8.4 1.0 P A:C1279 3.6 16.4 1.0 O3' A:G1278 3.7 9.1 1.0 O2' A:G1278 3.8 9.1 1.0 N7 A:G1436 4.0 7.0 1.0 O4 A:U1437 4.1 7.5 1.0 OP1 A:OMG1435 4.1 8.4 1.0 O3' A:A1434 4.1 20.1 1.0 OP2 A:G1436 4.3 7.0 1.0 OP1 A:C1279 4.4 16.4 1.0 C8 A:G1436 4.6 7.0 1.0 O5' A:OMG1435 4.7 8.4 1.0 C2' A:G1278 4.8 9.1 1.0 C3' A:G1278 4.8 9.1 1.0 O5' A:C1279 4.9 16.4 1.0 O2' A:A1434 4.9 20.1 1.0 C8 A:OMG1435 4.9 8.4 1.0 N7 A:OMG1435 4.9 8.4 1.0 C4 A:U1437 5.0 7.5 1.0

Magnesium binding site 10 out of 20 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryoem Structure of Wheat 40S Ribosomal Subunit, Head Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1914 b:11.5 occ:1.00 O A:HOH2281 1.9 15.2 1.0 O A:HOH2264 2.2 13.9 1.0 OP1 A:C1279 2.2 16.4 1.0 OP2 A:G1436 2.4 7.0 1.0 OP1 A:OMG1435 2.4 8.4 1.0 O A:HOH2284 2.4 12.6 1.0 P A:G1436 3.3 7.0 1.0 OP1 A:G1436 3.4 7.0 1.0 P A:C1279 3.5 16.4 1.0 P A:OMG1435 3.8 8.4 1.0 O A:HOH2101 3.9 7.6 1.0 OP2 A:C1279 3.9 16.4 1.0 O2' A:A1434 4.0 20.1 1.0 O3' A:OMG1435 4.1 8.4 1.0 O5' A:C1279 4.3 16.4 1.0 C5' A:OMG1435 4.4 8.4 1.0 OP2 A:OMG1435 4.5 8.4 1.0 O5' A:G1436 4.6 7.0 1.0 C3' A:OMG1435 4.6 8.4 1.0 O3' A:G1278 4.6 9.1 1.0 O5' A:OMG1435 4.6 8.4 1.0 O3' A:A1434 4.7 20.1 1.0 C2' A:A1434 4.8 20.1 1.0 C3' A:A1434 4.9 20.1 1.0 C3' A:G1278 4.9 9.1 1.0

O.V.Kravchenko, T.N.Baymukhametov, Z.A.Afonina, K.S.Vassilenko. High-Resolution Structure and Internal Mobility of A Plant 40S Ribosomal Subunit Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS242417453