Fluorine in PDB 7nvv: Xpb-Containing Part of Tfiih in A Post-Translocated State (with Adp- BEF3)

All present enzymatic activity of Xpb-Containing Part of Tfiih in A Post-Translocated State (with Adp- BEF3):
3.6.4.12;

The structure of Xpb-Containing Part of Tfiih in A Post-Translocated State (with Adp- BEF3) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Xpb-Containing Part of Tfiih in A Post-Translocated State (with Adp- BEF3) (pdb code 7nvv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Xpb-Containing Part of Tfiih in A Post-Translocated State (with Adp- BEF3), PDB code: 7nvv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Xpb-Containing Part of Tfiih in A Post-Translocated State (with Adp- BEF3)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Xpb-Containing Part of Tfiih in A Post-Translocated State (with Adp- BEF3) within 5.0Å range: probe atom residue distance (Å) B Occ 7:F903 b:18.4 occ:1.00 F1 7:BEF903 0.0 18.4 1.0 BE 7:BEF903 1.5 18.4 1.0 MG 7:MG902 2.0 14.2 1.0 F3 7:BEF903 2.6 18.4 1.0 F2 7:BEF903 2.6 18.4 1.0 O3B 7:ADP901 2.7 17.6 1.0 O2B 7:ADP901 2.9 17.6 1.0 PB 7:ADP901 3.3 17.6 1.0 OE2 7:GLU442 3.7 21.5 1.0 CA 7:SER614 3.9 21.7 1.0 NH2 7:ARG645 4.0 18.9 1.0 CE 7:LYS346 4.1 15.7 1.0 N 7:SER614 4.2 21.7 1.0 O2A 7:ADP901 4.4 17.6 1.0 O3A 7:ADP901 4.4 17.6 1.0 O1B 7:ADP901 4.5 17.6 1.0 OG 7:SER614 4.5 21.7 1.0 NZ 7:LYS346 4.6 15.7 1.0 OD2 7:ASP441 4.7 19.8 1.0 CB 7:SER614 4.7 21.7 1.0 NH1 7:ARG642 4.7 19.2 1.0 CD 7:GLU442 4.8 21.5 1.0 OD1 7:ASP441 4.8 19.8 1.0 NH2 7:ARG642 4.8 19.2 1.0 C 7:SER614 4.8 21.7 1.0

Fluorine binding site 2 out of 3 in the Xpb-Containing Part of Tfiih in A Post-Translocated State (with Adp- BEF3)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Xpb-Containing Part of Tfiih in A Post-Translocated State (with Adp- BEF3) within 5.0Å range: probe atom residue distance (Å) B Occ 7:F903 b:18.4 occ:1.00 F2 7:BEF903 0.0 18.4 1.0 BE 7:BEF903 1.6 18.4 1.0 F3 7:BEF903 2.5 18.4 1.0 F1 7:BEF903 2.6 18.4 1.0 O3B 7:ADP901 2.7 17.6 1.0 NZ 7:LYS346 2.8 15.7 1.0 CE 7:LYS346 3.0 15.7 1.0 SG 7:CYS342 3.5 16.8 1.0 CA 7:CYS342 3.5 16.8 1.0 PB 7:ADP901 3.7 17.6 1.0 CB 7:CYS342 3.7 16.8 1.0 CB 7:ALA468 3.8 16.9 1.0 O2B 7:ADP901 4.0 17.6 1.0 O1B 7:ADP901 4.0 17.6 1.0 MG 7:MG902 4.2 14.2 1.0 NH2 7:ARG642 4.2 19.2 1.0 OE1 7:GLN638 4.3 20.4 1.0 N 7:GLY343 4.4 17.0 1.0 N 7:CYS342 4.4 16.8 1.0 CD 7:LYS346 4.5 15.7 1.0 C 7:CYS342 4.5 16.8 1.0 OE2 7:GLU442 4.7 21.5 1.0 N 7:ALA468 4.9 16.9 1.0 O 7:PRO341 4.9 16.6 1.0 NH2 7:ARG645 5.0 18.9 1.0 C 7:PRO341 5.0 16.6 1.0 CA 7:ALA468 5.0 16.9 1.0

Fluorine binding site 3 out of 3 in the Xpb-Containing Part of Tfiih in A Post-Translocated State (with Adp- BEF3)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Xpb-Containing Part of Tfiih in A Post-Translocated State (with Adp- BEF3) within 5.0Å range: probe atom residue distance (Å) B Occ 7:F903 b:18.4 occ:1.00 F3 7:BEF903 0.0 18.4 1.0 BE 7:BEF903 1.5 18.4 1.0 NH2 7:ARG642 2.5 19.2 1.0 F2 7:BEF903 2.5 18.4 1.0 F1 7:BEF903 2.6 18.4 1.0 O3B 7:ADP901 2.6 17.6 1.0 NH1 7:ARG642 2.8 19.2 1.0 CZ 7:ARG642 3.1 19.2 1.0 NH2 7:ARG645 3.1 18.9 1.0 NH1 7:ARG645 3.2 18.9 1.0 CZ 7:ARG645 3.6 18.9 1.0 CB 7:CYS342 3.9 16.8 1.0 N 7:SER614 4.1 21.7 1.0 PB 7:ADP901 4.1 17.6 1.0 SG 7:CYS342 4.2 16.8 1.0 N 7:GLY343 4.2 17.0 1.0 CA 7:CYS342 4.2 16.8 1.0 CA 7:SER614 4.3 21.7 1.0 MG 7:MG902 4.4 14.2 1.0 NE 7:ARG642 4.4 19.2 1.0 O2B 7:ADP901 4.6 17.6 1.0 OE1 7:GLN638 4.6 20.4 1.0 C 7:CYS342 4.7 16.8 1.0 NE 7:ARG645 4.8 18.9 1.0 C 7:SER614 4.9 21.7 1.0 O 7:GLY641 4.9 18.1 1.0 O3A 7:ADP901 4.9 17.6 1.0 N 7:PHE615 5.0 21.2 1.0 OE2 7:GLU442 5.0 21.5 1.0 NZ 7:LYS346 5.0 15.7 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