Magnesium in PDB 8cbj: Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex

All present enzymatic activity of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex:
2.7.11.1;

The structure of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex 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 - 46;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex (pdb code 8cbj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 46 binding sites of Magnesium where determined in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex, PDB code: 8cbj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 46 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg3001 b:82.8 occ:1.00 OP2 2:A620 2.1 37.0 1.0 OP2 2:A621 2.2 37.9 1.0 P 2:A620 2.8 37.0 1.0 OP1 2:A620 2.8 37.0 1.0 P 2:A621 3.3 37.9 1.0 OP2 2:A619 3.3 34.9 1.0 OP1 2:A621 3.6 37.9 1.0 O5' 2:A620 3.7 37.0 1.0 C5' 2:A620 3.8 37.0 1.0 C5' 2:A619 4.2 34.9 1.0 O3' 2:A620 4.2 37.0 1.0 O3' 2:A619 4.2 34.9 1.0 C3' 2:A620 4.2 37.0 1.0 P 2:A619 4.4 34.9 1.0 O5' 2:A621 4.5 37.9 1.0 C4' 2:A620 4.6 37.0 1.0 OP1 2:U618 4.6 34.9 1.0 C3' 2:A619 4.7 34.9 1.0 O5' 2:A619 4.7 34.9 1.0 N7 2:A621 4.8 37.9 1.0 OP1 2:A619 4.9 34.9 1.0 C4' 2:A619 5.0 34.9 1.0 C8 2:A621 5.0 37.9 1.0

Magnesium binding site 2 out of 46 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg3002 b:94.7 occ:1.00 OP2 2:U82 3.2 107.2 1.0 OP1 2:A62 3.4 46.3 1.0 OP1 2:U82 3.5 107.2 1.0 P 2:U82 3.6 107.2 1.0 O5' 2:U82 3.9 107.2 1.0 P 2:A62 4.4 46.3 1.0 OP2 2:A62 4.6 46.3 1.0 O3' 2:A61 4.7 54.3 1.0 OP2 2:G83 4.7 89.9 1.0 C5' 2:U82 4.9 107.2 1.0

Magnesium binding site 3 out of 46 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg3003 b:82.8 occ:1.00 OP2 2:G95 2.1 82.8 1.0 P 2:G95 3.4 82.8 1.0 O5' 2:G95 3.9 82.8 1.0 OP1 2:G95 4.2 82.8 1.0 N7 2:G96 4.3 46.2 1.0 O3' 2:U94 4.6 50.3 1.0 O6 2:G96 4.7 46.2 1.0 N7 2:G95 4.7 82.8 1.0 C8 2:G95 4.8 82.8 1.0 OP2 2:U94 5.0 50.3 1.0 C3' 2:U94 5.0 50.3 1.0

Magnesium binding site 4 out of 46 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg3004 b:82.8 occ:1.00 OP2 2:A401 2.1 33.7 1.0 OP1 2:A387 3.3 29.9 1.0 P 2:A401 3.3 33.7 1.0 OP1 2:A401 3.9 33.7 1.0 O5' 2:A401 4.0 33.7 1.0 P 2:A387 4.3 29.9 1.0 NZ I:LYS23 4.3 41.4 1.0 OP2 2:A387 4.4 29.9 1.0 O4' 2:C402 4.5 33.8 1.0 O3' 2:A400 4.6 82.8 1.0 C2 2:C402 4.7 33.8 1.0 O2 2:C402 4.7 33.8 1.0 O6 2:G392 4.8 33.1 1.0 O5' 2:A387 4.9 29.9 1.0 N1 2:C402 4.9 33.8 1.0 OP2 2:C402 4.9 33.8 1.0

Magnesium binding site 5 out of 46 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg3005 b:82.8 occ:1.00 OP1 2:A550 2.1 45.7 1.0 P 2:A550 3.2 45.7 1.0 O3' 2:G549 3.2 39.9 1.0 C5' 2:A550 4.1 45.7 1.0 O6 2:G553 4.2 45.1 1.0 O5' 2:A550 4.2 45.7 1.0 OP2 2:A550 4.3 45.7 1.0 C3' 2:G549 4.6 39.9 1.0

Magnesium binding site 6 out of 46 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg3006 b:82.8 occ:1.00 OP1 2:G403 2.2 32.5 1.0 P 2:G403 3.5 32.5 1.0 O6 2:G95 3.8 82.8 1.0 O3' 2:C402 3.8 33.8 1.0 OP2 2:A93 4.1 32.1 1.0 O5' 2:C402 4.1 33.8 1.0 NH2 E:ARG3 4.4 18.0 1.0 O5' 2:G403 4.5 32.5 1.0 OP2 2:G403 4.6 32.5 1.0 C5' 2:C402 4.9 33.8 1.0 N6 2:A387 4.9 29.9 1.0 OP1 2:C402 4.9 33.8 1.0 C3' 2:C402 5.0 33.8 1.0

Magnesium binding site 7 out of 46 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg3007 b:44.7 occ:1.00 OP2 2:G91 2.1 32.4 1.0 O6 2:G398 2.7 35.1 1.0 P 2:G91 3.0 32.4 1.0 O5' 2:G91 3.1 32.4 1.0 OP1 2:G91 3.6 32.4 1.0 C6 2:G398 3.8 35.1 1.0 N1 2:A93 4.0 32.1 1.0 N1 2:G398 4.2 35.1 1.0 O2' 2:G396 4.2 35.5 1.0 O3' 2:C90 4.4 31.0 1.0 C2 2:A93 4.4 32.1 1.0 C5' 2:G91 4.4 32.4 1.0 OP2 2:A92 4.5 30.1 1.0 C8 2:G91 4.5 32.4 1.0 N7 2:A92 4.6 30.1 1.0 C3' 2:C90 4.8 31.0 1.0 C6 2:A93 4.9 32.1 1.0 N7 2:G91 4.9 32.4 1.0 N7 2:A397 4.9 35.5 1.0 C3' 2:G91 5.0 32.4 1.0 C5 2:G398 5.0 35.1 1.0

Magnesium binding site 8 out of 46 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg3008 b:82.8 occ:1.00 OP1 2:G1035 3.7 36.4 1.0 OP1 2:G866 4.0 32.4 1.0 CG2 N:ILE11 4.2 71.0 1.0 O N:LYS9 4.3 72.9 1.0 N N:GLY2 4.3 79.7 1.0 OP1 2:A1036 4.5 40.2 1.0 OP2 2:A865 4.6 31.6 1.0 O2' 2:U864 4.6 32.9 1.0 C N:LYS9 4.9 72.9 1.0 O3' 2:A865 5.0 31.6 1.0 P 2:G866 5.0 32.4 1.0

Magnesium binding site 9 out of 46 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg3009 b:36.1 occ:1.00 OP2 2:A1025 2.1 45.6 1.0 P 2:A1025 3.2 45.6 1.0 OP1 2:A1025 3.4 45.6 1.0 OP2 2:G624 3.7 40.7 1.0 OP1 2:G624 3.8 40.7 1.0 O5' 2:A1025 4.2 45.6 1.0 P 2:G624 4.3 40.7 1.0 O3' 2:U1024 4.3 44.1 1.0 C5' 2:A1025 4.5 45.6 1.0 N6 2:A1027 4.6 45.4 1.0 C3' 2:U1024 4.8 44.1 1.0 O5' 2:U1024 4.9 44.1 1.0 OP2 2:A1026 4.9 43.0 1.0 N7 2:A1027 4.9 45.4 1.0

Magnesium binding site 10 out of 46 in the Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of OTU2-Bound Cytoplasmic Pre-40S Ribosome Biogenesis Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg3010 b:82.8 occ:1.00 OP2 2:C427 3.0 30.6 1.0 O2' 2:C424 3.7 36.5 1.0 O6 2:G429 3.9 39.0 1.0 C5 2:C427 4.0 30.6 1.0 C2' 2:C424 4.3 36.5 1.0 P 2:C427 4.3 30.6 1.0 C6 2:C427 4.5 30.6 1.0 O5' 2:C427 4.6 30.6 1.0 N7 2:A428 4.6 30.2 1.0 C6 2:G429 4.7 39.0 1.0 O2 2:C424 4.8 36.5 1.0 N7 2:G429 4.8 39.0 1.0 OP2 2:A425 4.9 36.3 1.0 C4 2:C427 5.0 30.6 1.0

K.Ikeuchi, N.Ivic, R.Buschauer, J.Cheng, T.Frohlich, Y.Matsuo, O.Berninghausen, T.Inada, T.Becker, R.Beckmann. Molecular Basis For Recognition and Deubiquitination of 40S Ribosomes By OTU2. Nat Commun V. 14 2730 2023.
ISSN: ESSN 2041-1723
PubMed: 37169754
DOI: 10.1038/S41467-023-38161-W