Magnesium in PDB 8sy7: E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Stp Base Pair in the Active Site

Enzymatic activity of E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Stp Base Pair in the Active Site

All present enzymatic activity of E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Stp Base Pair in the Active Site:
2.7.7.6;

Other elements in 8sy7:

The structure of E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Stp Base Pair in the Active Site also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Stp Base Pair in the Active Site (pdb code 8sy7). 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 E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Stp Base Pair in the Active Site, PDB code: 8sy7:

Magnesium binding site 1 out of 1 in 8sy7

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Magnesium Binding Sites List in 8sy7

Magnesium binding site 1 out of 1 in the E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Stp Base Pair in the Active Site

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Dna-Directed Rna Polymerase Transcription Elongation Complex Bound the Unnatural Db-Stp Base Pair in the Active Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
J:Mg1503 b:23.3 occ:1.00	OD1	J:ASP460	2.1	14.7	1.0
	OD1	J:ASP462	2.3	14.5	1.0
	O	J:ASP460	2.3	14.7	1.0
	CG	J:ASP464	2.3	9.9	1.0
	OD1	J:ASP464	2.3	9.9	1.0
	OD2	J:ASP464	2.4	9.9	1.0
	CG	J:ASP462	3.1	14.5	1.0
	C	J:ASP460	3.3	14.7	1.0
	CG	J:ASP460	3.4	14.7	1.0
	CB	J:ASP464	3.5	9.9	1.0
	O03	J:X0O1504	3.5	38.8	1.0
	N	J:ASP464	3.5	9.9	1.0
	N	J:ASP462	3.6	14.5	1.0
	OD2	J:ASP462	3.7	14.5	1.0
	N	J:ASP460	3.9	14.7	1.0
	CA	J:ASP464	3.9	9.9	1.0
	CA	J:ASP460	4.0	14.7	1.0
	C	J:ASP462	4.1	14.5	1.0
	N	J:GLY463	4.1	8.5	1.0
	CA	J:ASP462	4.1	14.5	1.0
	CB	J:ASP462	4.2	14.5	1.0
	OD2	J:ASP460	4.2	14.7	1.0
	CB	J:ASP460	4.2	14.7	1.0
	N	J:PHE461	4.3	13.9	1.0
	C3'	R:G9	4.3	32.0	1.0
	O2'	R:G9	4.4	32.0	1.0
	C	J:GLY463	4.4	8.5	1.0
	C4'	R:G9	4.5	32.0	1.0
	O	J:ASP462	4.6	14.5	1.0
	C	J:PHE461	4.6	13.9	1.0
	CA	J:PHE461	4.7	13.9	1.0
	CA	J:GLY463	4.7	8.5	1.0
	P01	J:X0O1504	4.8	38.8	1.0
	O02	J:X0O1504	4.9	38.8	1.0
	C2'	R:G9	5.0	32.0	1.0

Reference:

J.Oh, Z.Shan, S.Hoshika, J.Xu, J.Chong, S.A.Benner, D.Lyumkis, D.Wang. A Unified Watson-Crick Geometry Drives Transcription of Six-Letter Expanded Dna Alphabets By E. Coli Rna Polymerase. Nat Commun V. 14 8219 2023.
ISSN: ESSN 2041-1723
PubMed: 38086811
DOI: 10.1038/S41467-023-43735-9

Page generated: Fri Oct 4 20:16:59 2024

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