Fluorine in PDB 7o72: Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Closed Promoter Dna

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

All present enzymatic activity of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Closed Promoter Dna:
2.7.7.6; 3.6.4.12;

Other elements in 7o72:

The structure of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Closed 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 Closed Promoter Dna (pdb code 7o72). 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 Closed Promoter Dna, PDB code: 7o72:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7o72

Go back to Fluorine Binding Sites List in 7o72
Fluorine binding site 1 out of 3 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Closed 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 Closed Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
7:F901

b:215.9
occ:1.00
F1 7:BEF901 0.0 215.9 1.0
BE 7:BEF901 1.5 215.9 1.0
MG 7:MG902 2.0 155.1 1.0
F3 7:BEF901 2.6 215.9 1.0
F2 7:BEF901 2.7 215.9 1.0
O3B 7:ADP903 2.7 217.4 1.0
OE2 7:GLU489 2.8 219.1 1.0
O1B 7:ADP903 2.9 217.4 1.0
NZ 7:LYS392 3.2 214.0 1.0
PB 7:ADP903 3.3 217.4 1.0
CA 7:SER661 4.0 223.2 1.0
CD 7:GLU489 4.0 219.1 1.0
CE 7:LYS392 4.1 214.0 1.0
O2B 7:ADP903 4.2 217.4 1.0
CB 7:SER661 4.3 223.2 1.0
N 7:SER661 4.3 223.2 1.0
OG 7:SER661 4.5 223.2 1.0
O3A 7:ADP903 4.6 217.4 1.0
OG1 7:THR660 4.6 222.1 1.0
OE1 7:GLU489 4.6 219.1 1.0
NH2 7:ARG692 4.8 213.9 1.0
O1A 7:ADP903 4.9 217.4 1.0
OD2 7:ASP488 4.9 223.0 1.0

Fluorine binding site 2 out of 3 in 7o72

Go back to Fluorine Binding Sites List in 7o72
Fluorine binding site 2 out of 3 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Closed 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 Closed Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
7:F901

b:215.9
occ:1.00
F2 7:BEF901 0.0 215.9 1.0
BE 7:BEF901 1.6 215.9 1.0
F3 7:BEF901 2.6 215.9 1.0
F1 7:BEF901 2.7 215.9 1.0
NZ 7:LYS392 2.7 214.0 1.0
O3B 7:ADP903 2.7 217.4 1.0
CB 7:ALA515 3.4 213.3 1.0
CA 7:CYS388 3.5 212.2 1.0
PB 7:ADP903 3.6 217.4 1.0
CB 7:CYS388 3.7 212.2 1.0
SG 7:CYS388 3.8 212.2 1.0
O2B 7:ADP903 3.8 217.4 1.0
CE 7:LYS392 3.9 214.0 1.0
N 7:GLY389 4.0 212.4 1.0
OE2 7:GLU489 4.1 219.1 1.0
O1B 7:ADP903 4.2 217.4 1.0
C 7:CYS388 4.3 212.2 1.0
NH2 7:ARG692 4.3 213.9 1.0
NH2 7:ARG689 4.3 218.1 1.0
MG 7:MG902 4.4 155.1 1.0
OE1 7:GLN685 4.5 215.9 1.0
N 7:CYS388 4.5 212.2 1.0
CA 7:ALA515 4.6 213.3 1.0
N 7:ALA515 4.6 213.3 1.0
OG1 7:THR660 4.8 222.1 1.0
NE2 7:GLN685 4.8 215.9 1.0
O 7:PRO387 4.9 208.2 1.0
CD 7:LYS392 5.0 214.0 1.0
CD 7:GLN685 5.0 215.9 1.0
CD 7:GLU489 5.0 219.1 1.0
OE1 7:GLU489 5.0 219.1 1.0

Fluorine binding site 3 out of 3 in 7o72

Go back to Fluorine Binding Sites List in 7o72
Fluorine binding site 3 out of 3 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Closed 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 Closed Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
7:F901

b:215.9
occ:1.00
F3 7:BEF901 0.0 215.9 1.0
BE 7:BEF901 1.5 215.9 1.0
O3B 7:ADP903 2.6 217.4 1.0
F2 7:BEF901 2.6 215.9 1.0
NH2 7:ARG689 2.6 218.1 1.0
F1 7:BEF901 2.6 215.9 1.0
NH2 7:ARG692 2.7 213.9 1.0
NH1 7:ARG689 3.4 218.1 1.0
CZ 7:ARG689 3.4 218.1 1.0
N 7:SER661 3.6 223.2 1.0
CZ 7:ARG692 3.7 213.9 1.0
CA 7:SER661 3.9 223.2 1.0
PB 7:ADP903 4.0 217.4 1.0
NH1 7:ARG692 4.0 213.9 1.0
MG 7:MG902 4.2 155.1 1.0
OG1 7:THR660 4.2 222.1 1.0
N 7:GLY389 4.3 212.4 1.0
CB 7:CYS388 4.5 212.2 1.0
O1B 7:ADP903 4.5 217.4 1.0
NZ 7:LYS392 4.7 214.0 1.0
NE 7:ARG689 4.7 218.1 1.0
CA 7:CYS388 4.7 212.2 1.0
C 7:THR660 4.8 222.1 1.0
C 7:SER661 4.8 223.2 1.0
OE2 7:GLU489 4.8 219.1 1.0
O3A 7:ADP903 4.9 217.4 1.0
NE 7:ARG692 4.9 213.9 1.0
O2B 7:ADP903 4.9 217.4 1.0
C 7:CYS388 4.9 212.2 1.0
N 7:ILE662 4.9 221.0 1.0
CB 7:SER661 4.9 223.2 1.0
SG 7:CYS388 5.0 212.2 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: Sat Jul 10 14:36:25 2021

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