Magnesium in PDB 8cah: Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex

The structure of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex also contains other interesting chemical elements:

Iron	(Fe)	8 atoms
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 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex (pdb code 8cah). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 80 binding sites of Magnesium where determined in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex, PDB code: 8cah:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation 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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1901 b:12.3 occ:1.00 MG 2:MG1967 3.8 16.1 1.0 O6 2:G1294 4.0 21.4 1.0 N7 2:G1294 4.0 21.4 1.0 O6 2:G1295 4.1 21.4 1.0 N7 2:G1295 4.5 21.4 1.0 C6 2:G1294 4.5 21.4 1.0 C5 2:G1294 4.5 21.4 1.0 O4 2:U1302 4.7 21.4 1.0 N6 2:A1296 4.8 21.4 1.0 C6 2:G1295 4.9 21.4 1.0 C8 2:G1294 5.0 21.4 1.0

Magnesium binding site 2 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation 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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range:

Magnesium binding site 3 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation 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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1903 b:14.3 occ:1.00 O6 2:G291 4.1 12.7 1.0 O4 2:U122 4.3 21.4 1.0 O6 2:G123 4.3 21.4 1.0 N6 2:A124 4.5 21.4 1.0 N7 2:G123 4.6 21.4 1.0 C4 2:U122 4.7 21.4 1.0 C5 2:U122 4.7 21.4 1.0

Magnesium binding site 4 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation 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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1904 b:2.0 occ:1.00 O6 2:G384 3.9 21.4 1.0 O4 2:U98 4.0 21.4 1.0 O6 2:G383 4.3 21.4 1.0 N4 2:C99 4.6 21.4 1.0 N6 2:A385 5.0 21.4 1.0 C6 2:G384 5.0 21.4 1.0

Magnesium binding site 5 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation 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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1905 b:3.8 occ:1.00 OP2 2:U101 2.1 21.4 1.0 OP2 2:C361 2.3 21.4 1.0 OP2 2:A100 2.5 21.4 1.0 P 2:U101 3.5 21.4 1.0 O4 2:U102 3.6 21.4 1.0 P 2:C361 3.6 21.4 1.0 P 2:A100 4.0 21.4 1.0 C3' 2:A360 4.0 21.4 1.0 O3' 2:A360 4.2 21.4 1.0 OP1 2:C361 4.3 21.4 1.0 OP1 2:U101 4.3 21.4 1.0 O5' 2:U101 4.3 21.4 1.0 C4 2:U102 4.4 21.4 1.0 OP2 2:A359 4.5 17.7 1.0 O3' 2:A100 4.5 21.4 1.0 O3' 2:C99 4.6 21.4 1.0 C5 2:U102 4.7 21.4 1.0 C3' 2:A100 4.7 21.4 1.0 OP1 2:A100 4.7 21.4 1.0 O5' 2:C361 4.8 21.4 1.0 C8 2:A360 4.8 21.4 1.0 C2' 2:A360 4.9 21.4 1.0 O5' 2:A100 4.9 21.4 1.0 C5' 2:A360 5.0 21.4 1.0

Magnesium binding site 6 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation 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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1906 b:3.5 occ:1.00 OP2 2:C424 2.1 21.4 1.0 P 2:C424 3.4 21.4 1.0 N7 2:G426 3.7 21.4 1.0 O5' 2:C424 3.9 21.4 1.0 OP1 2:C424 4.0 21.4 1.0 O4' 2:C424 4.0 21.4 1.0 C8 2:G426 4.2 21.4 1.0 C4' 2:C424 4.4 21.4 1.0 N1 2:A55 4.5 21.4 1.0 OP2 2:G403 4.6 21.4 1.0 O3' 2:G423 4.6 21.4 1.0 O4' 2:G403 4.7 21.4 1.0 C5 2:G426 4.7 21.4 1.0 N6 2:A55 4.7 21.4 1.0 OP1 2:G426 4.8 21.4 1.0 C5' 2:C424 4.8 21.4 1.0 C1' 2:C424 4.9 21.4 1.0

Magnesium binding site 7 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation 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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1907 b:6.5 occ:1.00 OP2 2:C49 2.2 21.4 1.0 P 2:C49 3.6 21.4 1.0 OP1 2:A425 3.8 21.4 1.0 N7 2:A425 3.8 21.4 1.0 C5' 2:G388 4.2 21.4 1.0 OP1 2:C49 4.2 21.4 1.0 C4' 2:G388 4.3 21.4 1.0 C8 2:A425 4.4 21.4 1.0 O5' 2:C49 4.4 21.4 1.0 O4' 2:G388 4.5 21.4 1.0 O3' 2:G48 4.6 21.4 1.0 C3' 2:G48 4.9 21.4 1.0 C5 2:A425 4.9 21.4 1.0

Magnesium binding site 8 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation 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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1908 b:12.7 occ:1.00 OP1 2:A100 2.3 21.4 1.0 OP1 2:C361 3.6 21.4 1.0 P 2:A100 3.7 21.4 1.0 C3' 2:C99 4.1 21.4 1.0 O3' 2:C99 4.2 21.4 1.0 OP2 2:A100 4.3 21.4 1.0 O2' 2:A43 4.4 21.4 1.0 C4' 2:U44 4.6 21.4 1.0 O4' 2:A378 4.6 21.4 1.0 C5' 2:U44 4.8 21.4 1.0 O5' 2:A100 4.8 21.4 1.0 P 2:C361 4.9 21.4 1.0

Magnesium binding site 9 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation 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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1909 b:2.1 occ:1.00 OP1 2:C402 3.2 21.4 1.0 OP2 2:C402 3.5 21.4 1.0 P 2:C402 3.8 21.4 1.0 OP2 2:G386 4.0 21.4 1.0 OP1 2:A400 4.1 21.4 1.0 O5' 2:A401 4.4 21.4 1.0 OP2 2:A387 4.4 21.4 1.0 C4' 2:A401 4.6 21.4 1.0 N7 2:G386 4.7 21.4 1.0 C8 2:G386 4.7 21.4 1.0 O3' 2:A401 4.7 21.4 1.0 N7 2:A387 4.8 21.4 1.0 NE S:ARG3 4.8 10.2 1.0 C5' 2:A401 4.9 21.4 1.0 C3' 2:A401 4.9 21.4 1.0 O5' 2:G386 4.9 21.4 1.0 CD S:ARG3 5.0 10.2 1.0

Magnesium binding site 10 out of 80 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation 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 Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1910 b:11.7 occ:1.00 OP1 2:A401 2.1 21.4 1.0 P 2:A401 3.5 21.4 1.0 OP2 2:A401 4.1 21.4 1.0 O4' 2:C402 4.1 21.4 1.0 O6 2:G404 4.2 21.4 1.0 O2 2:C402 4.3 21.4 1.0 O5' 2:A401 4.3 21.4 1.0 OP1 2:A387 4.4 21.4 1.0 C3' 2:A401 4.4 21.4 1.0 O3' 2:A400 4.4 21.4 1.0 O6 2:G392 4.5 21.4 1.0 C1' 2:C402 4.5 21.4 1.0 N4 2:C405 4.5 21.4 1.0 C2' 2:A401 4.6 21.4 1.0 C2 2:C402 4.6 21.4 1.0 OP2 2:C402 4.6 21.4 1.0 O2' 2:A401 4.7 21.4 1.0 N1 2:C402 4.7 21.4 1.0 OP2 2:A387 4.8 21.4 1.0 P 2:A387 5.0 21.4 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