Magnesium in PDB 8red: Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex

Enzymatic activity of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex

All present enzymatic activity of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex:
2.7.7.6;

Other elements in 8red:

The structure of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex (pdb code 8red). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex, PDB code: 8red:

Magnesium binding site 1 out of 1 in 8red

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Magnesium Binding Sites List in 8red

Magnesium binding site 1 out of 1 in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 8NT Complex within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mg1501 b:9.9 occ:1.00	O3'	R:U6	2.2	23.2	1.0
	OD1	D:ASP462	2.5	13.7	1.0
	OD1	D:ASP464	2.7	25.3	1.0
	OD2	D:ASP462	2.7	13.7	1.0
	CG	D:ASP462	2.9	13.7	1.0
	CB	D:ASP460	3.2	19.4	1.0
	O	D:ASP460	3.5	19.4	1.0
	C3'	R:U6	3.6	24.4	1.0
	CG	D:ASP464	3.7	25.3	1.0
	OD2	D:ASP464	3.9	25.3	1.0
	CA	D:ASP460	4.0	19.4	1.0
	C4'	R:U6	4.0	16.7	1.0
	C	D:ASP460	4.1	19.4	1.0
	O2'	R:U6	4.1	19.7	1.0
	N	D:ASP460	4.1	19.4	1.0
	CB	D:ASP462	4.4	13.7	1.0
	CG	D:ASP460	4.4	19.4	1.0
	C2'	R:U6	4.4	17.1	1.0
	C5'	R:U6	4.6	22.2	1.0
	N	D:ASP462	4.7	13.7	1.0
	OD1	D:ASP460	4.7	19.4	1.0
	NH2	D:ARG425	4.9	13.1	1.0
	CB	D:ASP464	5.0	25.3	1.0

Reference:

F.Gao, F.Ye, B.Zhang, N.Cronin, M.Buck, X.Zhang. Structural Basis of Sigma 54 Displacement and Promoter Escape in Bacterial Transcription. Proc.Natl.Acad.Sci.Usa V. 121 70120 2024.
ISSN: ESSN 1091-6490
PubMed: 38170755
DOI: 10.1073/PNAS.2309670120

Page generated: Fri Aug 15 13:57:57 2025

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