Magnesium in PDB 8r6f: Cryoem Structure of Wheat 40S Ribosomal Subunit, Body Domain

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

Potassium	(K)	14 atoms
Zinc	(Zn)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Magnesium atom in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body Domain (pdb code 8r6f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 32 binding sites of Magnesium where determined in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body Domain, PDB code: 8r6f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 32 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body 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, Body Domain within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg301 b:17.4 occ:1.00 OE1 G:GLN181 2.1 20.5 1.0 OP1 A:C271 2.3 22.7 1.0 CD G:GLN181 3.1 20.5 1.0 NE2 G:GLN181 3.5 20.5 1.0 P A:C271 3.6 22.7 1.0 O3' A:U270 3.9 22.4 1.0 C5' A:C271 4.0 22.7 1.0 O5' A:C271 4.3 22.7 1.0 OP1 A:OMU168 4.3 14.8 1.0 OP1 A:U64 4.4 13.7 1.0 OP2 A:OMU168 4.4 14.8 1.0 CG G:GLN181 4.5 20.5 1.0 N G:ARG182 4.5 23.4 1.0 O A:HOH2345 4.7 19.8 1.0 CB G:GLN181 4.7 20.5 1.0 CA G:GLN181 4.7 20.5 1.0 OP2 A:C271 4.8 22.7 1.0 C5' A:A167 4.8 13.5 1.0 P A:OMU168 4.8 14.8 1.0

Magnesium binding site 2 out of 32 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body 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, Body Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1915 b:10.8 occ:1.00 O A:HOH2541 2.1 10.1 1.0 O A:HOH2024 2.2 11.2 1.0 OP2 A:C428 2.2 12.7 1.0 O A:HOH2626 2.3 11.2 1.0 O A:HOH2616 2.3 11.4 1.0 O A:HOH2005 2.4 9.4 1.0 P A:C428 3.6 12.7 1.0 O4' A:G407 3.8 10.3 1.0 N7 A:G430 3.9 11.7 1.0 O5' A:C428 4.1 12.7 1.0 N1 A:A55 4.1 10.8 1.0 OP2 A:G407 4.2 10.3 1.0 C8 A:G430 4.3 11.7 1.0 N6 A:A55 4.3 10.8 1.0 OP1 A:C428 4.4 12.7 1.0 O4' A:C428 4.5 12.7 1.0 C1' A:G407 4.6 10.3 1.0 O3' A:G427 4.7 19.0 1.0 C6 A:A55 4.7 10.8 1.0 C8 A:G407 4.8 10.3 1.0 C4' A:G407 4.8 10.3 1.0 C3' A:G427 4.9 19.0 1.0 C4' A:C428 4.9 12.7 1.0 OP1 A:G430 4.9 11.7 1.0 C5' A:G407 5.0 10.3 1.0 N9 A:G407 5.0 10.3 1.0 C5 A:G430 5.0 11.7 1.0

Magnesium binding site 3 out of 32 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body 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, Body Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1916 b:18.9 occ:1.00 O A:HOH2001 2.0 12.7 1.0 O A:HOH2922 2.0 17.1 1.0 O A:HOH2261 2.5 13.3 1.0 O A:HOH2283 2.8 15.3 1.0 O6 A:OMG1300 3.6 13.4 1.0 K A:K1907 3.8 21.0 1.0 O A:HOH2390 3.9 11.1 1.0 O6 A:G1299 3.9 15.1 1.0 N6 A:A1301 4.0 12.5 1.0 N7 A:OMG1300 4.1 13.4 1.0 N7 A:G1299 4.2 15.1 1.0 O4 A:U1307 4.2 13.4 1.0 O A:HOH2360 4.4 14.0 1.0 C6 A:OMG1300 4.4 13.4 1.0 C6 A:G1299 4.5 15.1 1.0 C5 A:G1299 4.6 15.1 1.0 C5 A:OMG1300 4.6 13.4 1.0

Magnesium binding site 4 out of 32 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body 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, Body Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1917 b:17.1 occ:1.00 O A:HOH2115 1.8 17.2 1.0 OP1 A:G1779 1.9 19.7 1.0 O A:HOH2587 2.1 17.8 1.0 O A:HOH2182 2.2 15.1 1.0 O2P A:6MZ1774 2.4 20.7 1.0 OP1 A:U1782 2.6 19.5 1.0 P A:G1779 3.3 19.7 1.0 O3' A:U1781 3.4 20.1 1.0 P A:U1782 3.6 19.5 1.0 K A:K1909 3.8 22.7 1.0 P A:6MZ1774 3.8 20.7 1.0 O A:HOH2747 3.8 17.0 1.0 O2' A:U1780 3.8 25.0 1.0 OP1 A:G1778 3.8 17.4 1.0 C5' A:G1779 3.9 19.7 1.0 O5' A:G1779 4.0 19.7 1.0 OP2 A:G1779 4.2 19.7 1.0 C3' A:G1778 4.3 17.4 1.0 O3' A:G1778 4.3 17.4 1.0 O1P A:6MZ1774 4.3 20.7 1.0 C2' A:U1780 4.3 25.0 1.0 OP2 A:G1778 4.6 17.4 1.0 C3' A:U1781 4.6 20.1 1.0 OP2 A:U1782 4.6 19.5 1.0 O3' A:A1773 4.6 27.8 1.0 O5' A:U1782 4.7 19.5 1.0 P A:G1778 4.7 17.4 1.0 C4' A:U1781 4.7 20.1 1.0 C5' A:U1782 4.8 19.5 1.0 C5' A:U1781 4.8 20.1 1.0 O5' A:6MZ1774 4.8 20.7 1.0 O2' A:G1778 4.9 17.4 1.0 OP2 A:C1775 5.0 18.6 1.0 C2' A:G1778 5.0 17.4 1.0

Magnesium binding site 5 out of 32 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body 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, Body Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1918 b:22.8 occ:1.00 O2 A:PSU255 1.8 25.3 1.0 OP2 A:A254 1.9 24.2 1.0 O A:HOH2356 2.0 25.1 1.0 O A:HOH2706 2.4 22.2 1.0 OP2 A:C253 2.4 22.6 1.0 C2 A:PSU255 2.7 25.3 1.0 N1 A:PSU255 3.1 25.3 1.0 P A:A254 3.4 24.2 1.0 P A:C253 3.7 22.6 1.0 O A:HOH2190 3.8 26.6 1.0 O A:HOH2903 3.9 31.3 1.0 N3 A:PSU255 4.0 25.3 1.0 N2 A:G211 4.0 28.7 1.0 OP1 A:A254 4.1 24.2 1.0 OP1 A:C253 4.2 22.6 1.0 O5' A:A254 4.2 24.2 1.0 O3' A:C253 4.3 22.6 1.0 N6 A:A210 4.4 26.7 1.0 C6 A:PSU255 4.4 25.3 1.0 C3' A:C253 4.5 22.6 1.0 N1 A:G211 4.7 28.7 1.0 O5' A:C253 4.7 22.6 1.0 O3' A:U252 4.7 20.9 1.0 C2 A:G211 4.7 28.7 1.0

Magnesium binding site 6 out of 32 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body 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, Body Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1919 b:15.2 occ:1.00 OP1 A:C629 2.2 13.8 1.0 O A:HOH2724 2.2 15.1 1.0 O A:HOH2288 2.2 13.3 1.0 O A:HOH2477 2.3 11.8 1.0 O A:HOH2279 2.4 12.7 1.0 O A:HOH2873 2.4 16.9 1.0 P A:C629 3.5 13.8 1.0 O3' A:G628 3.8 13.9 1.0 O A:HOH2376 3.9 14.8 1.0 OP2 A:A627 4.0 15.2 1.0 OP2 A:C1033 4.0 14.4 1.0 OP1 A:U1036 4.3 12.4 1.0 OP2 A:C629 4.5 13.8 1.0 O5' A:C629 4.5 13.8 1.0 O2' A:A626 4.6 14.3 1.0 C5' A:G1037 4.6 12.1 1.0 C5' A:C629 4.6 13.8 1.0 O3' A:A626 4.7 14.3 1.0 C4' A:G1037 4.7 12.1 1.0 P A:C1033 4.8 14.4 1.0 C5' A:C1033 4.9 14.4 1.0 OP1 A:C1033 4.9 14.4 1.0 P A:A627 4.9 15.2 1.0

Magnesium binding site 7 out of 32 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body 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, Body Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1920 b:15.1 occ:1.00 O A:HOH2573 1.9 10.6 1.0 O A:HOH2752 2.1 15.1 1.0 OP1 A:A627 2.1 15.2 1.0 O A:HOH2287 2.5 12.2 1.0 O A:HOH2579 3.3 12.0 1.0 O A:HOH2023 3.5 11.5 1.0 P A:A627 3.5 15.2 1.0 OP2 A:A627 4.1 15.2 1.0 C5 A:C1033 4.2 14.4 1.0 O5' A:A627 4.2 15.2 1.0 OP1 A:U1036 4.5 12.4 1.0 OP1 A:C1033 4.6 14.4 1.0 O3' A:A626 4.6 14.3 1.0 O A:HOH2279 4.7 12.7 1.0 C3' A:A626 4.7 14.3 1.0 C6 A:C1033 4.7 14.4 1.0 OP2 A:A626 4.9 14.3 1.0 OP2 A:G628 4.9 13.9 1.0 O3' A:A1035 5.0 13.0 1.0

Magnesium binding site 8 out of 32 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body 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, Body Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1921 b:12.2 occ:1.00 O A:HOH2151 2.0 12.1 1.0 OP2 A:A1030 2.0 13.2 1.0 O A:HOH2804 2.1 14.2 1.0 O A:HOH2581 2.2 11.8 1.0 O A:HOH2425 2.3 19.3 1.0 O A:HOH2598 2.5 18.5 1.0 P A:A1030 3.1 13.2 1.0 OP1 A:A1030 3.5 13.2 1.0 O A:HOH2695 3.6 15.6 1.0 C5' A:A1030 3.9 13.2 1.0 O5' A:A1030 4.0 13.2 1.0 OP1 A:G628 4.0 13.9 1.0 OP2 A:G628 4.2 13.9 1.0 OP1 A:A1031 4.3 14.0 1.0 O3' A:U1029 4.3 14.2 1.0 N7 A:A1032 4.4 13.3 1.0 P A:G628 4.6 13.9 1.0 N6 A:A1032 4.7 13.3 1.0 O A:HOH2287 4.8 12.2 1.0 OP2 A:A1031 4.8 14.0 1.0 C3' A:U1029 4.9 14.2 1.0

Magnesium binding site 9 out of 32 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body 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, Body Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1922 b:23.0 occ:1.00 O A:HOH2689 2.2 12.0 1.0 OP2 A:A2M623 2.2 9.3 1.0 OP2 A:A624 2.3 23.0 1.0 OP2 A:A625 2.3 20.3 1.0 O A:HOH2808 2.4 14.9 1.0 O A:HOH2136 2.4 14.4 1.0 P A:A2M623 3.3 9.3 1.0 P A:A625 3.5 20.3 1.0 P A:A624 3.6 23.0 1.0 O5' A:A2M623 3.6 9.3 1.0 OP1 A:A2M623 3.7 9.3 1.0 OP1 A:A625 4.0 20.3 1.0 OP1 A:U622 4.0 9.7 1.0 C5' A:A2M623 4.0 9.3 1.0 OP1 A:A624 4.1 23.0 1.0 O A:HOH2249 4.5 16.3 1.0 OP2 A:U622 4.5 9.7 1.0 P A:U622 4.5 9.7 1.0 O3' A:A2M623 4.6 9.3 1.0 O3' A:A624 4.6 23.0 1.0 O5' A:A625 4.6 20.3 1.0 N7 A:A625 4.6 20.3 1.0 C3' A:A624 4.6 23.0 1.0 O5' A:A624 4.6 23.0 1.0 C3' A:A2M623 4.6 9.3 1.0 O3' A:U622 4.6 9.7 1.0 O5' A:U622 4.7 9.7 1.0 C8 A:A625 4.7 20.3 1.0 C2 A:A1035 4.8 13.0 1.0 C4' A:A2M623 4.9 9.3 1.0 C5' A:U622 4.9 9.7 1.0

Magnesium binding site 10 out of 32 in the Cryoem Structure of Wheat 40S Ribosomal Subunit, Body 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, Body Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1923 b:18.5 occ:1.00 O A:HOH2509 1.9 17.0 1.0 OP1 A:A2M623 2.0 9.3 1.0 O A:HOH2819 2.1 14.0 1.0 O A:HOH2249 2.1 16.3 1.0 O A:HOH2161 2.3 17.4 1.0 P A:A2M623 3.4 9.3 1.0 O A:HOH2808 3.9 14.9 1.0 O3' A:U622 4.0 9.7 1.0 O5' A:A2M623 4.2 9.3 1.0 N1 A:A1035 4.2 13.0 1.0 N6 A:A1035 4.2 13.0 1.0 OP2 A:A2M623 4.4 9.3 1.0 OP1 A:A624 4.6 23.0 1.0 C6 A:A1035 4.7 13.0 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