Magnesium in PDB 8bdr: Early Transcription Elongation State of Influenza B/Mem Polymerase Backtracked Due to Double Incoproation of Nucleotide Analogue T1106 and with Singly Incoporated T1106 at the U +1 Position

Enzymatic activity of Early Transcription Elongation State of Influenza B/Mem Polymerase Backtracked Due to Double Incoproation of Nucleotide Analogue T1106 and with Singly Incoporated T1106 at the U +1 Position

All present enzymatic activity of Early Transcription Elongation State of Influenza B/Mem Polymerase Backtracked Due to Double Incoproation of Nucleotide Analogue T1106 and with Singly Incoporated T1106 at the U +1 Position:
2.7.7.48;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Early Transcription Elongation State of Influenza B/Mem Polymerase Backtracked Due to Double Incoproation of Nucleotide Analogue T1106 and with Singly Incoporated T1106 at the U +1 Position (pdb code 8bdr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Early Transcription Elongation State of Influenza B/Mem Polymerase Backtracked Due to Double Incoproation of Nucleotide Analogue T1106 and with Singly Incoporated T1106 at the U +1 Position, PDB code: 8bdr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8bdr

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Magnesium Binding Sites List in 8bdr

Magnesium binding site 1 out of 2 in the Early Transcription Elongation State of Influenza B/Mem Polymerase Backtracked Due to Double Incoproation of Nucleotide Analogue T1106 and with Singly Incoporated T1106 at the U +1 Position

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Early Transcription Elongation State of Influenza B/Mem Polymerase Backtracked Due to Double Incoproation of Nucleotide Analogue T1106 and with Singly Incoporated T1106 at the U +1 Position within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg801 b:41.3 occ:1.00	OD2	B:ASP444	2.0	30.8	1.0
	OD1	B:ASP444	2.0	40.6	1.0
	CG	B:ASP444	2.2	32.6	1.0
	O17	M:K1F17	2.9	45.7	1.0
	HB2	B:ASP305	3.0	24.2	1.0
	O3'	M:C16	3.1	42.7	1.0
	HB3	B:ASP305	3.2	24.2	1.0
	H5	M:K1F17	3.5	40.9	1.0
	CB	B:ASP305	3.6	29.2	1.0
	P14	M:K1F17	3.6	50.8	1.0
	CB	B:ASP444	3.7	21.5	1.0
	HO2'	M:C16	3.8	41.2	1.0
	HB2	B:ASP445	3.8	26.1	1.0
	HA	B:ASP445	3.9	25.7	1.0
	C	B:ASP444	3.9	32.1	1.0
	N	B:ASP445	4.0	29.0	1.0
	H	B:ASN306	4.0	25.6	1.0
	HA	B:ASP305	4.0	23.4	1.0
	H4'	M:C16	4.1	41.2	1.0
	O	B:ASP444	4.1	29.7	1.0
	HB2	B:ASP444	4.1	27.9	1.0
	H6	M:K1F17	4.2	41.4	1.0
	C12	M:K1F17	4.2	41.8	1.0
	H	B:ASP445	4.2	27.4	1.0
	HB3	B:ASP444	4.2	28.8	1.0
	CA	B:ASP445	4.2	18.2	1.0
	C3'	M:C16	4.3	39.8	1.0
	CB	B:ASP445	4.3	24.2	1.0
	CA	B:ASP305	4.4	24.5	1.0
	CG	B:ASP445	4.4	38.1	1.0
	CA	B:ASP444	4.4	20.1	1.0
	O13	M:K1F17	4.4	44.0	1.0
	O2'	M:C16	4.5	46.3	1.0
	H5''	M:C16	4.5	41.9	1.0
	C4'	M:C16	4.6	41.4	1.0
	OD2	B:ASP445	4.7	37.4	1.0
	H	B:ASP444	4.7	28.4	1.0
	N	B:ASN306	4.7	24.3	1.0
	OD1	B:ASP445	4.7	36.1	1.0
	CG	B:ASP305	4.7	35.2	1.0
	O1	M:K1F17	4.8	43.8	1.0
	OD2	B:ASP305	4.9	34.3	1.0
	O	B:ASN306	5.0	38.1	1.0
	H3'	M:C16	5.0	41.5	1.0

Magnesium binding site 2 out of 2 in 8bdr

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Magnesium Binding Sites List in 8bdr

Magnesium binding site 2 out of 2 in the Early Transcription Elongation State of Influenza B/Mem Polymerase Backtracked Due to Double Incoproation of Nucleotide Analogue T1106 and with Singly Incoporated T1106 at the U +1 Position

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Early Transcription Elongation State of Influenza B/Mem Polymerase Backtracked Due to Double Incoproation of Nucleotide Analogue T1106 and with Singly Incoporated T1106 at the U +1 Position within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg802 b:33.9 occ:1.00	OD1	B:ASP445	1.9	36.1	1.0
	CG	B:ASP445	2.8	38.1	1.0
	OD2	B:ASP445	3.0	37.4	1.0
	HG23	B:THR303	3.2	22.1	1.0
	O	B:GLY304	3.3	23.5	1.0
	HA	B:PHE491	3.6	23.7	1.0
	HG22	B:THR303	3.7	22.6	1.0
	H	B:THR492	3.7	26.0	1.0
	HB3	B:ASP305	3.7	24.2	1.0
	CG2	B:THR303	3.8	25.2	1.0
	C	B:GLY304	3.9	17.0	1.0
	OE1	B:GLU490	4.0	28.1	1.0
	H	B:GLY304	4.0	21.2	1.0
	H	B:PHE446	4.0	23.9	1.0
	OE2	B:GLU490	4.0	33.3	1.0
	O	B:GLU490	4.0	29.6	1.0
	HA	B:ASP445	4.1	25.7	1.0
	HG21	B:THR303	4.2	22.5	1.0
	CB	B:ASP445	4.2	24.2	1.0
	CD	B:GLU490	4.2	33.2	1.0
	N	B:GLY304	4.3	18.5	1.0
	N	B:ASP305	4.4	18.6	1.0
	O	B:PHE446	4.5	27.5	1.0
	N	B:THR492	4.5	25.9	1.0
	HA	B:ASP305	4.5	23.4	1.0
	CA	B:PHE491	4.5	21.9	1.0
	CB	B:ASP305	4.5	29.2	1.0
	CA	B:GLY304	4.6	17.6	1.0
	HB3	B:ASP445	4.6	26.1	1.0
	CA	B:ASP445	4.7	18.2	1.0
	N	B:PHE446	4.7	22.4	1.0
	C	B:GLU490	4.7	23.0	1.0
	HD1	B:PHE491	4.7	23.0	1.0
	CA	B:ASP305	4.7	24.5	1.0
	HB2	B:ASP445	4.8	26.1	1.0
	C	B:THR303	4.8	26.2	1.0
	H	B:SER493	4.8	24.1	1.0
	HA2	B:GLY304	4.9	21.3	1.0
	N	B:PHE491	4.9	15.1	1.0
	HA	B:THR303	4.9	22.1	1.0
	H	B:ASP305	4.9	22.9	1.0
	CG	B:ASP305	5.0	35.2	1.0

Reference:

T.Kouba, S.Cusack. Direct Observation of Backtracking By Influenza A and B Polymerases Upon Consecutive Incorporation of Nucleoside Analogue T1106 Cell Rep 2022.
ISSN: ESSN 2211-1247
DOI: 10.1016/J.CELREP.2022.111901

Page generated: Thu Oct 3 19:20:32 2024

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