Fluorine in PDB 7nw0: Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna

All present enzymatic activity of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna:
2.3.1.48; 2.7.7.6; 3.6.4.12;

The structure of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna also contains other interesting chemical elements:

Zinc	(Zn)	15 atoms
Iron	(Fe)	4 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Fluorine atom in the Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna (pdb code 7nw0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna, PDB code: 7nw0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna within 5.0Å range: probe atom residue distance (Å) B Occ 7:F903 b:56.2 occ:1.00 F1 7:BEF903 0.0 56.2 1.0 BE 7:BEF903 1.5 56.2 1.0 MG 7:MG902 2.2 55.0 1.0 F3 7:BEF903 2.6 56.2 1.0 F2 7:BEF903 2.7 56.2 1.0 O3B 7:ADP901 2.7 53.0 1.0 O1B 7:ADP901 2.9 53.0 1.0 PB 7:ADP901 3.3 53.0 1.0 CA 7:SER614 4.0 51.8 1.0 CE 7:LYS346 4.0 54.7 1.0 OE2 7:GLU442 4.0 60.2 1.0 NH2 7:ARG645 4.2 53.1 1.0 OD1 7:ASP441 4.3 67.7 1.0 O2B 7:ADP901 4.4 53.0 1.0 N 7:SER614 4.4 51.8 1.0 OD2 7:ASP441 4.4 67.7 1.0 OG 7:SER614 4.4 51.8 1.0 O3A 7:ADP901 4.6 53.0 1.0 O2A 7:ADP901 4.6 53.0 1.0 CB 7:SER614 4.7 51.8 1.0 NZ 7:LYS346 4.7 54.7 1.0 CG 7:ASP441 4.8 67.7 1.0 CD 7:GLU442 5.0 60.2 1.0 NH1 7:ARG642 5.0 53.5 1.0

Fluorine binding site 2 out of 3 in the Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna within 5.0Å range: probe atom residue distance (Å) B Occ 7:F903 b:56.2 occ:1.00 F2 7:BEF903 0.0 56.2 1.0 BE 7:BEF903 1.6 56.2 1.0 F3 7:BEF903 2.6 56.2 1.0 F1 7:BEF903 2.7 56.2 1.0 O3B 7:ADP901 2.7 53.0 1.0 NZ 7:LYS346 2.8 54.7 1.0 CE 7:LYS346 2.8 54.7 1.0 PB 7:ADP901 3.6 53.0 1.0 CA 7:CYS342 3.7 54.7 1.0 O2B 7:ADP901 3.8 53.0 1.0 SG 7:CYS342 3.8 54.7 1.0 CB 7:ALA468 3.8 49.1 1.0 CB 7:CYS342 4.0 54.7 1.0 O1B 7:ADP901 4.0 53.0 1.0 CD 7:LYS346 4.3 54.7 1.0 N 7:GLY343 4.4 54.6 1.0 NH2 7:ARG642 4.4 53.5 1.0 MG 7:MG902 4.4 55.0 1.0 OE1 7:GLN638 4.5 43.3 1.0 N 7:CYS342 4.5 54.7 1.0 NH2 7:ARG645 4.6 53.1 1.0 C 7:CYS342 4.6 54.7 1.0 N 7:ALA468 4.7 49.1 1.0 O 7:PRO341 4.9 44.7 1.0 CA 7:ALA468 4.9 49.1 1.0

Fluorine binding site 3 out of 3 in the Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Rna Polymerase II Pre-Initiation Complex with Open Promoter Dna within 5.0Å range: probe atom residue distance (Å) B Occ 7:F903 b:56.2 occ:1.00 F3 7:BEF903 0.0 56.2 1.0 BE 7:BEF903 1.5 56.2 1.0 NH2 7:ARG645 2.5 53.1 1.0 O3B 7:ADP901 2.6 53.0 1.0 F2 7:BEF903 2.6 56.2 1.0 F1 7:BEF903 2.6 56.2 1.0 NH1 7:ARG642 2.8 53.5 1.0 NH2 7:ARG642 3.1 53.5 1.0 CZ 7:ARG642 3.3 53.5 1.0 CZ 7:ARG645 3.4 53.1 1.0 NH1 7:ARG645 3.6 53.1 1.0 N 7:SER614 3.7 51.8 1.0 CA 7:SER614 3.9 51.8 1.0 PB 7:ADP901 4.0 53.0 1.0 MG 7:MG902 4.3 55.0 1.0 CB 7:CYS342 4.4 54.7 1.0 C 7:SER614 4.5 51.8 1.0 O1B 7:ADP901 4.6 53.0 1.0 OE1 7:GLN638 4.6 43.3 1.0 SG 7:CYS342 4.6 54.7 1.0 NE 7:ARG645 4.6 53.1 1.0 N 7:GLY343 4.6 54.6 1.0 NE 7:ARG642 4.6 53.5 1.0 CA 7:CYS342 4.7 54.7 1.0 N 7:PHE615 4.7 49.3 1.0 O3A 7:ADP901 4.9 53.0 1.0 O2B 7:ADP901 4.9 53.0 1.0 C 7:THR613 4.9 51.6 1.0 O 7:PHE615 4.9 49.3 1.0

S.Aibara, S.Schilbach, P.Cramer. Structures of Mammalian Rna Polymerase II Pre-Initiation Complexes. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 33902107
DOI: 10.1038/S41586-021-03554-8