Magnesium in PDB 9dtr: Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution

All present enzymatic activity of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution:
2.3.2.27; 3.6.4.13;

The structure of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Zinc	(Zn)	7 atoms

The binding sites of Magnesium atom in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution (pdb code 9dtr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution, PDB code: 9dtr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 6:Mg201 b:29.0 occ:1.00 OP1 6:U80 1.7 24.5 1.0 OP1 6:A59 1.8 20.5 1.0 O2' I:G95 1.9 30.2 1.0 OP2 6:G60 2.0 28.0 1.0 O 6:HOH401 2.1 77.7 1.0 O3' I:G95 2.2 23.2 1.0 P 6:U80 3.0 17.8 1.0 C2' I:G95 3.0 24.9 1.0 C3' I:G95 3.1 22.8 1.0 P 6:A59 3.2 18.3 1.0 P 6:G60 3.4 22.0 1.0 OP2 6:U80 3.6 28.6 1.0 O5' 6:A59 3.7 19.9 1.0 OP1 E:A1 3.8 60.9 1.0 C5' 6:A59 3.8 24.9 1.0 C1' I:G95 3.9 24.2 1.0 K 6:K202 3.9 32.4 1.0 O5' 6:U80 4.0 23.1 1.0 O3' 6:A79 4.0 22.3 1.0 OP1 6:G60 4.1 40.7 1.0 O5' 6:G60 4.1 21.5 1.0 OP2 6:A59 4.1 28.3 1.0 O3' 6:C58 4.2 22.7 1.0 C4' I:G95 4.3 24.9 1.0 N1 6:A51 4.5 29.9 1.0 O3' 6:A59 4.5 22.0 1.0 C2 6:A51 4.5 29.2 1.0 O4' I:G95 4.5 22.2 1.0 C4' 6:A59 4.8 22.4 1.0 C3' 6:A59 4.9 21.3 1.0 C5' 6:G60 5.0 27.6 1.0 K E:K101 5.0 52.6 1.0

Magnesium binding site 2 out of 2 in the Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Yeast Post-Catalytic P Complex Spliceosome at 2.3 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2502 b:55.6 occ:1.00 O2G C:GTP2501 1.9 39.6 1.0 O2B C:GTP2501 1.9 25.8 1.0 OG C:SER190 2.0 51.4 1.0 OG1 C:THR147 2.2 55.8 1.0 PG C:GTP2501 2.8 30.6 1.0 PB C:GTP2501 3.0 19.0 1.0 O3B C:GTP2501 3.0 27.6 1.0 CB C:SER190 3.2 36.9 1.0 O3G C:GTP2501 3.2 35.7 1.0 CB C:THR147 3.4 46.1 1.0 OD2 C:ASP179 3.7 69.6 1.0 N C:SER190 3.8 33.0 1.0 O1A C:GTP2501 3.9 37.0 1.0 O1B C:GTP2501 4.0 24.9 1.0 N C:THR147 4.0 30.9 1.0 CA C:SER190 4.1 32.6 1.0 O1G C:GTP2501 4.1 37.0 1.0 OD1 C:ASP179 4.1 86.7 1.0 O3A C:GTP2501 4.1 23.9 1.0 OD2 C:ASP214 4.3 124.4 1.0 CA C:THR147 4.3 31.6 1.0 CG C:ASP179 4.3 52.6 1.0 CG2 C:THR147 4.4 64.7 1.0 PA C:GTP2501 4.5 24.7 1.0 OD1 C:ASP214 4.6 105.7 1.0 CE C:LYS146 4.8 32.8 1.0 CG C:ASP214 4.8 108.6 1.0 NZ C:LYS146 4.9 32.0 1.0 C C:LEU189 4.9 29.0 1.0 O C:ALA215 4.9 65.0 1.0 CB C:LYS146 4.9 29.8 1.0 O2A C:GTP2501 4.9 28.7 1.0

K.A.Senn, K.A.Lipinski, N.J.Zeps, A.F.Griffin, M.E.Wilkinson, A.A.Hoskins. Control of 3' Splice Site Selection By the Yeast Splicing Factor FYV6. Elife 2024.
ISSN: ESSN 2050-084X
PubMed: 38746449
DOI: 10.1038/S41422-019-0143-X