Magnesium in PDB 5xog: Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1

Enzymatic activity of Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1

All present enzymatic activity of Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1, PDB code: 5xog was solved by H.Ehara, M.Shirouzu, S.Sekine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	49.55 / 3.00
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	155.250, 159.910, 268.930, 90.00, 90.00, 90.00
*R / R_free (%)*	19.5 / 22.5

Other elements in 5xog:

The structure of Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1 also contains other interesting chemical elements:

Zinc

(Zn)

9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1 (pdb code 5xog). 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 Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1, PDB code: 5xog:

Magnesium binding site 1 out of 1 in 5xog

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Magnesium Binding Sites List in 5xog

Magnesium binding site 1 out of 1 in the Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rna Polymerase II Elongation Complex Bound with SPT5 KOW5 and ELF1 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1803 b:46.0 occ:1.00	O3'	P:U10	2.1	58.3	1.0
	OD1	A:ASP482	2.1	56.1	1.0
	OD1	A:ASP486	2.2	56.0	1.0
	OD1	A:ASP484	2.3	55.1	1.0
	OD2	A:ASP484	2.8	66.5	1.0
	CG	A:ASP484	2.8	56.7	1.0
	CG	A:ASP482	2.9	54.6	1.0
	O1A	A:APC1804	2.9	88.2	1.0
	OD2	A:ASP482	2.9	77.4	1.0
	CG	A:ASP486	3.1	55.7	1.0
	OD2	A:ASP486	3.3	58.8	1.0
	C3'	P:U10	3.4	50.7	1.0
	O2'	P:U10	3.6	57.3	1.0
	C4'	P:U10	3.9	49.6	1.0
	C2'	P:U10	4.0	54.3	1.0
	PA	A:APC1804	4.2	0.4	1.0
	CB	A:ASP484	4.3	53.4	1.0
	O5'	A:APC1804	4.3	76.4	1.0
	CB	A:ASP482	4.3	43.2	1.0
	CB	A:ASP486	4.5	45.9	1.0
	N	A:ASP484	4.5	44.5	1.0
	C5'	P:U10	4.5	47.5	1.0
	N	A:ASP482	4.7	38.6	1.0
	O	A:ASP482	4.7	56.1	1.0
	C	A:ASP482	4.7	44.4	1.0
	N	A:ASP486	4.7	52.8	1.0
	CA	A:ASP482	4.8	44.8	1.0
	CA	A:ASP484	4.8	43.6	1.0

Reference:

H.Ehara, T.Yokoyama, H.Shigematsu, S.Yokoyama, M.Shirouzu, S.I.Sekine. Structure of the Complete Elongation Complex of Rna Polymerase II with Basal Factors Science V. 357 921 2017.
ISSN: ESSN 1095-9203
PubMed: 28775211
DOI: 10.1126/SCIENCE.AAN8552

Page generated: Tue Aug 12 23:54:15 2025

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