Magnesium in PDB 7m45: Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec

Enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec

All present enzymatic activity of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec, PDB code: 7m45 was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	24.02 / 1.89
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	56.018, 62.547, 140.01, 90, 90, 90
*R / R_free (%)*	20.5 / 24.2

Other elements in 7m45:

The structure of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec (pdb code 7m45). 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 Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec, PDB code: 7m45:

Magnesium binding site 1 out of 1 in 7m45

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Magnesium Binding Sites List in 7m45

Magnesium binding site 1 out of 1 in the Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg603 b:25.8 occ:1.00	O1A	A:TTP602	1.8	23.3	0.4
	OD1	A:ASP427	1.9	32.8	0.6
	O1B	A:TTP602	2.0	32.3	0.4
	O	A:HOH701	2.0	30.7	1.0
	OD2	A:ASP429	2.0	30.2	1.0
	OD1	A:ASP427	2.1	33.7	0.4
	OP1	P:DT7	2.2	22.7	0.6
	O2G	A:TTP602	2.2	39.8	0.4
	O21	A:PPV601	2.3	34.6	0.6
	O22	A:PPV601	2.4	40.2	0.6
	CG	A:ASP427	2.9	34.4	0.6
	CG	A:ASP429	3.0	32.9	1.0
	CG	A:ASP427	3.1	34.2	0.4
	PB	A:TTP602	3.1	36.2	0.4
	PA	A:TTP602	3.1	27.4	0.4
	PG	A:TTP602	3.2	42.9	0.4
	OD2	A:ASP427	3.3	34.4	0.6
	OD1	A:ASP429	3.3	28.4	1.0
	P1	A:PPV601	3.3	35.9	0.6
	O31	A:PPV601	3.3	38.6	0.6
	O3G	A:TTP602	3.4	41.6	0.4
	OD2	A:ASP427	3.4	35.1	0.4
	NA	A:NA606	3.5	30.5	1.0
	O3A	A:TTP602	3.5	36.2	0.4
	P2	A:PPV601	3.6	43.2	0.6
	P	P:DT7	3.6	26.5	0.6
	O3B	A:TTP602	3.6	39.7	0.4
	OPP	A:PPV601	3.9	40.2	0.6
	O32	A:PPV601	4.0	39.7	0.6
	O5'	A:TTP602	4.1	26.2	0.4
	C5'	A:TTP602	4.1	26.6	0.4
	C5'	P:DT7	4.1	27.1	0.6
	O	A:ASP427	4.1	22.9	0.6
	O2A	A:TTP602	4.1	27.2	0.4
	CB	A:ASP427	4.2	31.0	0.6
	O5'	P:DT7	4.2	25.0	0.6
	O	A:ASP427	4.2	22.5	0.4
	CB	A:ASP429	4.3	28.6	1.0
	C	A:ASP427	4.3	22.3	0.6
	C	A:ASP427	4.4	22.4	0.4
	O2B	A:TTP602	4.4	36.5	0.4
	CB	A:ASP427	4.4	30.7	0.4
	N	A:ASP427	4.4	25.1	0.4
	O	A:HOH775	4.4	28.1	0.6
	OP2	P:DT7	4.4	27.2	0.6
	CA	A:GLY416	4.5	30.0	1.0
	O1G	A:TTP602	4.5	43.0	0.4
	N	A:ASP427	4.6	25.6	0.6
	O3'	P:DC6	4.6	30.7	0.6
	N	A:SER417	4.6	28.7	1.0
	CA	A:ASP427	4.6	24.0	0.6
	CA	A:ASP427	4.6	24.3	0.4
	O	A:HOH818	4.6	26.2	0.6
	O	A:HOH754	4.6	28.4	1.0
	O11	A:PPV601	4.7	34.9	0.6
	OG	A:SER417	4.8	33.4	1.0
	O12	A:PPV601	4.9	43.6	0.6
	N	A:VAL428	4.9	23.8	1.0
	N	A:ASP429	4.9	23.7	1.0

Reference:

J.A.Jamsen, D.D.Shock, S.H.Wilson. Watching Right and Wrong Nucleotide Insertion Captures Hidden Polymerase Fidelity Checkpoints. Nat Commun V. 13 3193 2022.
ISSN: ESSN 2041-1723
PubMed: 35680862
DOI: 10.1038/S41467-022-30141-W

Page generated: Wed Oct 2 23:41:19 2024

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