Magnesium in PDB 6xll: Cryo-Em Structure of E. Coli Rnap-Promoter Initial Transcribing Complex with 5-Nt Rna Transcript (Rpitc-5NT)

Enzymatic activity of Cryo-Em Structure of E. Coli Rnap-Promoter Initial Transcribing Complex with 5-Nt Rna Transcript (Rpitc-5NT)

All present enzymatic activity of Cryo-Em Structure of E. Coli Rnap-Promoter Initial Transcribing Complex with 5-Nt Rna Transcript (Rpitc-5NT):
2.7.7.6;

Other elements in 6xll:

The structure of Cryo-Em Structure of E. Coli Rnap-Promoter Initial Transcribing Complex with 5-Nt Rna Transcript (Rpitc-5NT) 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 E. Coli Rnap-Promoter Initial Transcribing Complex with 5-Nt Rna Transcript (Rpitc-5NT) (pdb code 6xll). 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 E. Coli Rnap-Promoter Initial Transcribing Complex with 5-Nt Rna Transcript (Rpitc-5NT), PDB code: 6xll:

Magnesium binding site 1 out of 1 in 6xll

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Magnesium Binding Sites List in 6xll

Magnesium binding site 1 out of 1 in the Cryo-Em Structure of E. Coli Rnap-Promoter Initial Transcribing Complex with 5-Nt Rna Transcript (Rpitc-5NT)

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 E. Coli Rnap-Promoter Initial Transcribing Complex with 5-Nt Rna Transcript (Rpitc-5NT) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mg1501 b:65.5 occ:1.00	O3'	R:U5	1.8	81.0	1.0
	OD1	D:ASP460	2.0	61.3	1.0
	OD1	D:ASP462	2.0	61.4	1.0
	OD1	D:ASP464	2.1	63.0	1.0
	CG	D:ASP464	2.8	63.0	1.0
	OD2	D:ASP464	2.8	63.0	1.0
	CG	D:ASP460	3.0	61.3	1.0
	CG	D:ASP462	3.0	61.4	1.0
	C3'	R:U5	3.2	81.0	1.0
	OD2	D:ASP462	3.3	61.4	1.0
	OD2	D:ASP460	3.4	61.3	1.0
	O	D:ASP460	3.7	61.3	1.0
	O2'	R:U5	3.9	81.0	1.0
	C4'	R:U5	3.9	81.0	1.0
	C2'	R:U5	4.1	81.0	1.0
	CB	D:ASP464	4.2	63.0	1.0
	CB	D:ASP460	4.3	61.3	1.0
	N	D:ASP460	4.3	61.3	1.0
	C	D:ASP460	4.3	61.3	1.0
	C5'	R:U5	4.4	81.0	1.0
	CB	D:ASP462	4.4	61.4	1.0
	N	D:ASP462	4.4	61.4	1.0
	CA	D:ASP460	4.6	61.3	1.0
	N	D:ASP464	4.6	63.0	1.0
	C	D:ASP462	4.7	61.4	1.0
	CA	D:ASP462	4.7	61.4	1.0
	CA	D:ASP464	4.8	63.0	1.0
	O	D:ASP462	4.9	61.4	1.0
	O5'	R:U5	4.9	81.0	1.0

Reference:

Y.Yang, C.Liu, W.Shi, D.G.Schatz, Y.Hu, B.Liu. Structural Visualization of Bacterial Multidrug-Activated Transcription To Be Published.

Page generated: Tue Oct 1 23:35:19 2024

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