Fluorine in PDB 7o75: Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna

Enzymatic activity of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna

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

Other elements in 7o75:

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

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna (pdb code 7o75). 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 with Open Promoter Dna, PDB code: 7o75:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7o75

Go back to Fluorine Binding Sites List in 7o75
Fluorine binding site 1 out of 3 in the Yeast Rna Polymerase II Transcription 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 Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
7:F901

b:104.6
occ:1.00
 F1 7:BEF901 0.0 104.6 1.0
BE 7:BEF901 1.5 104.6 1.0
MG 7:MG902 2.0 100.9 1.0
F3 7:BEF901 2.6 104.6 1.0
F2 7:BEF901 2.6 104.6 1.0
O1B 7:ADP903 2.7 108.2 1.0
O3B 7:ADP903 2.9 108.2 1.0
NH2 7:ARG692 3.1 101.5 1.0
PB 7:ADP903 3.3 108.2 1.0
CA 7:SER661 3.8 102.1 1.0
OE2 7:GLU489 4.3 94.1 1.0
OG 7:SER661 4.3 102.1 1.0
CZ 7:ARG692 4.3 101.5 1.0
N 7:SER661 4.3 102.1 1.0
O2B 7:ADP903 4.4 108.2 1.0
CB 7:SER661 4.4 102.1 1.0
O3A 7:ADP903 4.5 108.2 1.0
NZ 7:LYS392 4.5 101.7 1.0
O1A 7:ADP903 4.6 108.2 1.0
CE 7:LYS392 4.7 101.7 1.0
OD1 7:ASP488 4.7 95.7 1.0
NH2 7:ARG689 4.8 94.4 1.0
C 7:SER661 4.8 102.1 1.0
NH1 7:ARG689 4.9 94.4 1.0
CD 7:GLU489 4.9 94.1 1.0
NH1 7:ARG692 5.0 101.5 1.0

Fluorine binding site 2 out of 3 in 7o75

Go back to Fluorine Binding Sites List in 7o75
Fluorine binding site 2 out of 3 in the Yeast Rna Polymerase II Transcription 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 Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
7:F901

b:104.6
occ:1.00
 F2 7:BEF901 0.0 104.6 1.0
BE 7:BEF901 1.6 104.6 1.0
F3 7:BEF901 2.6 104.6 1.0
F1 7:BEF901 2.6 104.6 1.0
O1B 7:ADP903 2.7 108.2 1.0
NZ 7:LYS392 2.7 101.7 1.0
CE 7:LYS392 3.5 101.7 1.0
PB 7:ADP903 3.5 108.2 1.0
CB 7:ALA515 3.6 91.8 1.0
SG 7:CYS388 3.6 95.3 1.0
CA 7:CYS388 3.6 95.3 1.0
O2B 7:ADP903 3.7 108.2 1.0
CB 7:CYS388 3.9 95.3 1.0
O3B 7:ADP903 4.0 108.2 1.0
MG 7:MG902 4.2 100.9 1.0
N 7:GLY389 4.3 100.0 1.0
NH2 7:ARG689 4.3 94.4 1.0
N 7:CYS388 4.5 95.3 1.0
C 7:CYS388 4.5 95.3 1.0
N 7:ALA515 4.6 91.8 1.0
CA 7:ALA515 4.6 91.8 1.0
NH2 7:ARG692 4.7 101.5 1.0
NE2 7:GLN685 4.8 90.5 1.0
OE2 7:GLU489 4.9 94.1 1.0
O 7:PRO387 5.0 92.9 1.0
CD 7:LYS392 5.0 101.7 1.0
O3A 7:ADP903 5.0 108.2 1.0

Fluorine binding site 3 out of 3 in 7o75

Go back to Fluorine Binding Sites List in 7o75
Fluorine binding site 3 out of 3 in the Yeast Rna Polymerase II Transcription 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 Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
7:F901

b:104.6
occ:1.00
 F3 7:BEF901 0.0 104.6 1.0
BE 7:BEF901 1.5 104.6 1.0
NH2 7:ARG692 2.6 101.5 1.0
F2 7:BEF901 2.6 104.6 1.0
O1B 7:ADP903 2.6 108.2 1.0
F1 7:BEF901 2.6 104.6 1.0
NH2 7:ARG689 2.6 94.4 1.0
NH1 7:ARG689 3.3 94.4 1.0
CZ 7:ARG689 3.3 94.4 1.0
CZ 7:ARG692 3.4 101.5 1.0
NE 7:ARG692 3.6 101.5 1.0
CB 7:CYS388 3.9 95.3 1.0
SG 7:CYS388 4.0 95.3 1.0
PB 7:ADP903 4.0 108.2 1.0
N 7:GLY389 4.1 100.0 1.0
CA 7:CYS388 4.2 95.3 1.0
MG 7:MG902 4.4 100.9 1.0
NH1 7:ARG692 4.5 101.5 1.0
O3B 7:ADP903 4.6 108.2 1.0
C 7:CYS388 4.6 95.3 1.0
NE 7:ARG689 4.6 94.4 1.0
N 7:SER661 4.7 102.1 1.0
CA 7:SER661 4.8 102.1 1.0
O3A 7:ADP903 4.9 108.2 1.0
O 7:ILE662 4.9 102.5 1.0
O2B 7:ADP903 4.9 108.2 1.0
CD 7:ARG692 4.9 101.5 1.0
O 7:GLY688 5.0 90.1 1.0

Reference:

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
Page generated: Fri Aug 2 10:41:42 2024

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