Magnesium in PDB 8rap: Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex

All present enzymatic activity of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex:
2.7.7.6;

The structure of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Zinc	(Zn)	9 atoms

The binding sites of Magnesium atom in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex (pdb code 8rap). 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 SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex, PDB code: 8rap:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1803 b:91.2 occ:1.00 O3' P:U35 2.1 99.4 1.0 OD1 A:ASP483 2.2 95.8 1.0 CB A:ASP481 3.0 91.1 1.0 CG A:ASP483 3.1 95.8 1.0 OD2 A:ASP483 3.3 95.8 1.0 OD1 A:ASP481 3.3 91.1 1.0 CG A:ASP481 3.3 91.1 1.0 C3' P:U35 3.4 99.4 1.0 C4' P:U35 4.0 99.4 1.0 CA A:ASP481 4.0 91.1 1.0 N A:ASP481 4.1 91.1 1.0 OD2 A:ASP485 4.1 89.6 1.0 CB A:ASP485 4.1 89.6 1.0 C5' P:U35 4.2 99.4 1.0 OD2 A:ASP481 4.2 91.1 1.0 CB A:ASP483 4.5 95.8 1.0 O2' P:U35 4.5 99.4 1.0 C2' P:U35 4.5 99.4 1.0 CG A:ASP485 4.5 89.6 1.0 N A:ASP483 4.5 95.8 1.0 C A:ASP481 4.5 91.1 1.0 N A:PHE482 4.8 83.8 1.0 O A:ASP483 4.8 95.8 1.0 CA A:ASP485 4.9 89.6 1.0 CA A:ASP483 4.9 95.8 1.0 N A:ASP485 4.9 89.6 1.0 O5' P:U35 5.0 99.4 1.0

Magnesium binding site 2 out of 2 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range: probe atom residue distance (Å) B Occ O:Mg3002 b:207.3 occ:1.00 O2B O:ADP3001 2.0 213.0 1.0 OG1 O:THR1364 2.1 205.5 1.0 CG O:LYS1363 2.7 210.1 1.0 CD O:LYS1363 3.2 210.1 1.0 N O:THR1364 3.2 205.5 1.0 CB O:THR1364 3.3 205.5 1.0 PB O:ADP3001 3.4 213.0 1.0 CE O:LYS1363 3.6 210.1 1.0 O2A O:ADP3001 3.6 213.0 1.0 CA O:THR1364 3.6 205.5 1.0 CB O:LYS1363 3.9 210.1 1.0 F1 O:BEF3003 3.9 224.7 1.0 O1B O:ADP3001 3.9 213.0 1.0 OE2 O:GLU1591 4.0 213.1 1.0 C O:LYS1363 4.0 210.1 1.0 OD1 O:ASP1590 4.1 212.9 1.0 OD2 O:ASP1590 4.1 212.9 1.0 O3A O:ADP3001 4.3 213.0 1.0 CG2 O:THR1364 4.4 205.5 1.0 PA O:ADP3001 4.4 213.0 1.0 O3B O:ADP3001 4.4 213.0 1.0 CA O:LYS1363 4.5 210.1 1.0 CG O:ASP1590 4.5 212.9 1.0 NZ O:LYS1363 4.6 210.1 1.0 BE O:BEF3003 4.8 224.7 1.0 O O:LYS1363 4.8 210.1 1.0 O1A O:ADP3001 4.9 213.0 1.0 N O:LYS1363 4.9 210.1 1.0 O O:GLY1785 4.9 232.1 1.0

S.Rengachari, T.Hainthaler, C.Oberthuer, M.Lidschreiber, P.Cramer. Mechanism of Polyadenylation-Independent Rna Polymerase II Termination. Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
PubMed: 39424994
DOI: 10.1038/S41594-024-01409-0