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Magnesium in PDB 7o4i: Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Initial Transcription Bubble

Enzymatic activity of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Initial Transcription Bubble

All present enzymatic activity of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Initial Transcription Bubble:
2.7.7.6; 3.6.4.12;

Other elements in 7o4i:

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

Zinc (Zn) 17 atoms
Fluorine (F) 3 atoms
Iron (Fe) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Initial Transcription Bubble (pdb code 7o4i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Initial Transcription Bubble, PDB code: 7o4i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7o4i

Go back to Magnesium Binding Sites List in 7o4i
Magnesium binding site 1 out of 2 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Initial Transcription Bubble


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Initial Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Mg902

b:172.6
occ:1.00
F1 7:BEF901 2.0 201.8 1.0
O3B 7:ADP903 2.0 201.2 1.0
PB 7:ADP903 3.2 201.2 1.0
BE 7:BEF901 3.3 201.8 1.0
O1B 7:ADP903 3.5 201.2 1.0
OD2 7:ASP488 3.9 206.3 1.0
F2 7:BEF901 4.1 201.8 1.0
NE1 7:TRP420 4.1 203.0 1.0
OG1 7:THR393 4.1 202.2 1.0
OD1 7:ASP488 4.1 206.3 1.0
O2B 7:ADP903 4.2 201.2 1.0
O1A 7:ADP903 4.2 201.2 1.0
OG 7:SER661 4.3 203.7 1.0
O3A 7:ADP903 4.3 201.2 1.0
CG 7:ASP488 4.4 206.3 1.0
F3 7:BEF901 4.4 201.8 1.0
CA 7:SER661 4.6 203.7 1.0
CZ2 7:TRP420 4.6 203.0 1.0
CE 7:LYS392 4.6 201.8 1.0
CE2 7:TRP420 4.6 203.0 1.0
PA 7:ADP903 4.7 201.2 1.0
CB 7:SER661 4.8 203.7 1.0
O2A 7:ADP903 4.8 201.2 1.0
OE2 7:GLU489 4.9 205.8 1.0
CB 7:LYS392 5.0 201.8 1.0

Magnesium binding site 2 out of 2 in 7o4i

Go back to Magnesium Binding Sites List in 7o4i
Magnesium binding site 2 out of 2 in the Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Initial Transcription Bubble


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast Rna Polymerase II Transcription Pre-Initiation Complex with Initial Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1803

b:37.1
occ:1.00
OD2 A:ASP483 2.0 31.5 1.0
OD1 A:ASP483 2.2 31.5 1.0
CG A:ASP483 2.4 31.5 1.0
OD1 A:ASP481 2.4 32.1 1.0
OD1 A:ASP485 2.5 29.0 1.0
OD2 A:ASP481 3.1 32.1 1.0
CG A:ASP481 3.1 32.1 1.0
CG A:ASP485 3.2 29.0 1.0
OD2 A:ASP485 3.3 29.0 1.0
CB A:ASP483 3.9 31.5 1.0
CB A:ASP481 4.5 32.1 1.0
N A:ASP483 4.6 31.5 1.0
CB A:ASP485 4.6 29.0 1.0
CA A:ASP483 4.7 31.5 1.0
N A:ASP485 4.9 29.0 1.0
C A:ASP483 4.9 31.5 1.0
N A:ASP481 4.9 32.1 1.0
O A:ASP481 5.0 32.1 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: Thu Oct 3 02:32:43 2024

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