Fluorine in PDB 7o4j: Yeast Rna Polymerase II Transcription Pre-Initiation Complex (Consensus)

All present enzymatic activity of Yeast Rna Polymerase II Transcription Pre-Initiation Complex (Consensus):
2.7.7.6; 3.6.4.12;

The structure of Yeast Rna Polymerase II Transcription Pre-Initiation Complex (Consensus) also contains other interesting chemical elements:

Zinc	(Zn)	17 atoms
Magnesium	(Mg)	2 atoms
Iron	(Fe)	4 atoms

The binding sites of Fluorine atom in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex (Consensus) (pdb code 7o4j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex (Consensus), PDB code: 7o4j:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex (Consensus)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex (Consensus) within 5.0Å range: probe atom residue distance (Å) B Occ 7:F901 b:88.5 occ:1.00 F1 7:BEF901 0.0 88.5 1.0 BE 7:BEF901 1.5 88.5 1.0 MG 7:MG902 2.0 66.4 1.0 F3 7:BEF901 2.6 88.5 1.0 F2 7:BEF901 2.6 88.5 1.0 O3B 7:ADP903 2.7 89.2 1.0 O1B 7:ADP903 2.9 89.2 1.0 PB 7:ADP903 3.3 89.2 1.0 OE2 7:GLU489 3.4 86.6 1.0 CA 7:SER661 4.1 90.4 1.0 O2B 7:ADP903 4.3 89.2 1.0 N 7:SER661 4.4 90.4 1.0 CE 7:LYS392 4.5 86.5 1.0 CD 7:GLU489 4.5 86.6 1.0 O3A 7:ADP903 4.6 89.2 1.0 NZ 7:LYS392 4.6 86.5 1.0 OG 7:SER661 4.7 90.4 1.0 CB 7:SER661 4.7 90.4 1.0 NH2 7:ARG689 4.7 86.7 1.0 O1A 7:ADP903 4.8 89.2 1.0 OE1 7:GLU489 4.9 86.6 1.0 NH2 7:ARG692 4.9 89.4 1.0 NH1 7:ARG692 4.9 89.4 1.0 OD1 7:ASP488 5.0 86.1 1.0 NH1 7:ARG689 5.0 86.7 1.0

Fluorine binding site 2 out of 3 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex (Consensus)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex (Consensus) within 5.0Å range: probe atom residue distance (Å) B Occ 7:F901 b:88.5 occ:1.00 F2 7:BEF901 0.0 88.5 1.0 BE 7:BEF901 1.6 88.5 1.0 F3 7:BEF901 2.6 88.5 1.0 F1 7:BEF901 2.6 88.5 1.0 O3B 7:ADP903 2.7 89.2 1.0 NZ 7:LYS392 3.0 86.5 1.0 CA 7:CYS388 3.5 87.7 1.0 CE 7:LYS392 3.5 86.5 1.0 SG 7:CYS388 3.6 87.7 1.0 PB 7:ADP903 3.6 89.2 1.0 CB 7:ALA515 3.6 85.7 1.0 O2B 7:ADP903 3.7 89.2 1.0 CB 7:CYS388 3.8 87.7 1.0 N 7:GLY389 4.0 88.7 1.0 O1B 7:ADP903 4.1 89.2 1.0 C 7:CYS388 4.3 87.7 1.0 MG 7:MG902 4.3 66.4 1.0 NH2 7:ARG689 4.4 86.7 1.0 N 7:CYS388 4.4 87.7 1.0 N 7:ALA515 4.6 85.7 1.0 CA 7:ALA515 4.7 85.7 1.0 O 7:PRO387 4.7 87.8 1.0 OE2 7:GLU489 4.8 86.6 1.0 NH1 7:ARG692 4.9 89.4 1.0 C 7:PRO387 4.9 87.8 1.0 NE2 7:GLN685 5.0 87.9 1.0

Fluorine binding site 3 out of 3 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex (Consensus)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex (Consensus) within 5.0Å range: probe atom residue distance (Å) B Occ 7:F901 b:88.5 occ:1.00 F3 7:BEF901 0.0 88.5 1.0 BE 7:BEF901 1.5 88.5 1.0 F2 7:BEF901 2.6 88.5 1.0 O3B 7:ADP903 2.6 89.2 1.0 F1 7:BEF901 2.6 88.5 1.0 NH1 7:ARG692 2.6 89.4 1.0 NH2 7:ARG689 2.7 86.7 1.0 NH1 7:ARG689 3.3 86.7 1.0 CZ 7:ARG689 3.3 86.7 1.0 CZ 7:ARG692 3.5 89.4 1.0 NH2 7:ARG692 3.6 89.4 1.0 PB 7:ADP903 4.0 89.2 1.0 N 7:GLY389 4.2 88.7 1.0 CB 7:CYS388 4.2 87.7 1.0 MG 7:MG902 4.3 66.4 1.0 SG 7:CYS388 4.4 87.7 1.0 N 7:SER661 4.5 90.4 1.0 CA 7:CYS388 4.5 87.7 1.0 O1B 7:ADP903 4.5 89.2 1.0 NE 7:ARG689 4.6 86.7 1.0 CA 7:SER661 4.7 90.4 1.0 C 7:CYS388 4.7 87.7 1.0 NE 7:ARG692 4.8 89.4 1.0 O2B 7:ADP903 4.9 89.2 1.0 O3A 7:ADP903 4.9 89.2 1.0 O 7:GLY688 5.0 85.7 1.0

S.Schilbach, S.Aibara, C.Dienemann, F.Grabbe, P.Cramer. Structure of Rna Polymerase II Pre-Initiation Complex at 2.9 Angstrom Defines Initial Dna Opening Cell(Cambridge,Mass.) 2021.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2021.05.012