Magnesium in PDB 7eh2: Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer

Enzymatic activity of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer

All present enzymatic activity of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer, PDB code: 7eh2 was solved by L.Li, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	97.82 / 3.34
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	184.85, 104.2, 296.65, 90, 98.42, 90
*R / R_free (%)*	20.1 / 24.8

Other elements in 7eh2:

The structure of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer (pdb code 7eh2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer, PDB code: 7eh2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7eh2

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Magnesium Binding Sites List in 7eh2

Magnesium binding site 1 out of 3 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mg2003 b:54.3 occ:1.00	O3'	I:G2	1.8	60.2	0.8
	OD1	D:ASP739	2.0	63.0	1.0
	OD1	D:ASP741	2.1	56.0	1.0
	OD1	D:ASP743	2.1	59.8	1.0
	CG	D:ASP739	2.8	60.8	1.0
	OD2	D:ASP739	2.9	65.9	1.0
	CG	D:ASP743	3.0	54.3	1.0
	CG	D:ASP741	3.0	57.9	1.0
	OD2	D:ASP743	3.1	54.5	1.0
	OD2	D:ASP741	3.2	65.8	1.0
	C3'	I:G2	3.2	63.6	0.8
	C4'	I:G2	3.8	69.6	0.8
	O2'	I:G2	3.9	65.0	0.8
	C2'	I:G2	4.1	68.3	0.8
	CB	D:ASP739	4.2	48.2	1.0
	C5'	I:G2	4.2	72.3	0.8
	CB	D:ASP743	4.4	53.0	1.0
	CB	D:ASP741	4.4	58.6	1.0
	N	D:ASP741	4.5	58.6	1.0
	N	D:ASP739	4.5	51.8	1.0
	NH2	D:ARG704	4.5	60.2	1.0
	N	D:ASP743	4.6	59.2	1.0
	C	D:ASP739	4.6	52.8	1.0
	CA	D:ASP739	4.7	50.8	1.0
	CA	D:ASP741	4.8	58.9	1.0
	O	D:ASP739	4.8	58.9	1.0
	C	D:ASP741	4.8	61.2	1.0
	CA	D:ASP743	4.8	57.6	1.0

Magnesium binding site 2 out of 3 in 7eh2

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Magnesium Binding Sites List in 7eh2

Magnesium binding site 2 out of 3 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
L:Mg401 b:77.4 occ:1.00	OD2	L:ASP168	2.2	86.5	1.0
	O	N:LYS840	2.4	82.9	1.0
	CG	L:ASP168	3.2	82.8	1.0
	OD1	L:ASP168	3.4	82.4	1.0
	C	N:LYS840	3.6	82.8	1.0
	OE2	L:GLU154	3.8	101.5	1.0
	N	N:VAL842	4.3	80.3	1.0
	CA	N:TYR841	4.3	81.1	1.0
	OE1	L:GLU154	4.4	113.9	1.0
	N	N:TYR841	4.4	87.4	1.0
	CD	L:GLU154	4.5	114.8	1.0
	CB	L:ASP168	4.5	77.1	1.0
	O	N:LEU839	4.6	79.1	1.0
	CA	N:LYS840	4.6	83.0	1.0
	OE1	L:GLU64	4.7	117.9	1.0
	C	N:TYR841	4.8	82.5	1.0
	NZ	L:LYS83	4.8	83.6	1.0
	OE2	L:GLU64	5.0	121.2	1.0

Magnesium binding site 3 out of 3 in 7eh2

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Magnesium Binding Sites List in 7eh2

Magnesium binding site 3 out of 3 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
N:Mg1603 b:61.0 occ:1.00	O3'	R:G2	1.8	71.0	0.8
	OD1	N:ASP739	2.0	69.4	1.0
	OD1	N:ASP741	2.1	64.9	1.0
	OD1	N:ASP743	2.1	66.5	1.0
	CG	N:ASP743	2.9	64.2	1.0
	CG	N:ASP739	2.9	69.2	1.0
	CG	N:ASP741	2.9	67.1	1.0
	OD2	N:ASP743	3.0	65.5	1.0
	OD2	N:ASP741	3.1	69.4	1.0
	OD2	N:ASP739	3.2	70.0	1.0
	C3'	R:G2	3.2	74.3	0.8
	C4'	R:G2	4.0	76.0	0.8
	O2'	R:G2	4.0	76.8	0.8
	C2'	R:G2	4.1	78.8	0.8
	CB	N:ASP739	4.3	56.4	1.0
	NH2	N:ARG704	4.3	64.6	1.0
	CB	N:ASP743	4.3	63.5	1.0
	CB	N:ASP741	4.4	62.6	1.0
	N	N:ASP739	4.4	63.3	1.0
	C5'	R:G2	4.4	75.4	0.8
	N	N:ASP741	4.5	65.5	1.0
	C	N:ASP739	4.6	62.9	1.0
	O	N:ASP739	4.6	65.5	1.0
	N	N:ASP743	4.7	65.8	1.0
	CA	N:ASP739	4.7	58.4	1.0
	CA	N:ASP741	4.8	62.1	1.0
	CA	N:ASP743	4.9	69.9	1.0
	C	N:ASP741	4.9	65.5	1.0

Reference:

K.S.Skalenko, L.Li, Y.Zhang, I.O.Vvedenskaya, J.T.Winkelman, A.L.Cope, D.M.Taylor, P.Shah, R.H.Ebright, J.B.Kinney, Y.Zhang, B.E.Nickels. Promoter-Sequence Determinants and Structural Basis of Primer-Dependent Transcription Initiation in Escherichia Coli . Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 34187896
DOI: 10.1073/PNAS.2106388118

Page generated: Wed Oct 2 20:43:32 2024

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