Magnesium in PDB 4b9u: Structure of the High Fidelity Dna Polymerase I with An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair in the Post-Insertion Site.

Enzymatic activity of Structure of the High Fidelity Dna Polymerase I with An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair in the Post-Insertion Site.

All present enzymatic activity of Structure of the High Fidelity Dna Polymerase I with An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair in the Post-Insertion Site.:
2.7.7.7;

Protein crystallography data

The structure of Structure of the High Fidelity Dna Polymerase I with An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair in the Post-Insertion Site., PDB code: 4b9u was solved by T.H.Gehrke, U.Lischke, S.Arnold, S.Schneider, T.Carell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	50.00 / 2.10
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	88.748, 93.853, 105.648, 90.00, 90.00, 90.00
*R / R_free (%)*	19.143 / 22.356

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the High Fidelity Dna Polymerase I with An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair in the Post-Insertion Site. (pdb code 4b9u). 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 Structure of the High Fidelity Dna Polymerase I with An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair in the Post-Insertion Site., PDB code: 4b9u:

Magnesium binding site 1 out of 1 in 4b9u

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Magnesium Binding Sites List in 4b9u

Magnesium binding site 1 out of 1 in the Structure of the High Fidelity Dna Polymerase I with An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair in the Post-Insertion Site.

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the High Fidelity Dna Polymerase I with An Oxidative Formamidopyrimidine-Dg Dna Lesion -Da Basepair in the Post-Insertion Site. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1882 b:44.8 occ:1.00	O	A:TYR654	2.6	22.1	1.0
	OD2	A:ASP653	2.7	33.8	1.0
	OD2	A:ASP830	3.0	31.5	1.0
	O1	A:SO41880	3.1	25.2	0.5
	O3	A:SO41880	3.5	25.4	0.5
	CG	A:ASP653	3.7	28.3	1.0
	O	A:HOH2119	3.7	25.9	1.0
	C	A:TYR654	3.7	21.1	1.0
	S	A:SO41880	3.8	31.2	0.5
	CG	A:ASP830	3.9	28.2	1.0
	CB	A:ASP653	4.0	23.3	1.0
	OD1	A:ASP830	4.2	29.2	1.0
	CA	A:SER655	4.3	19.2	1.0
	O2	A:SO41880	4.3	26.0	0.5
	N	A:SER655	4.5	18.6	1.0
	N	A:TYR654	4.7	20.3	1.0
	N	A:GLN656	4.7	18.2	1.0
	C	A:ASP653	4.7	20.5	1.0
	OD1	A:ASP653	4.8	29.3	1.0
	CA	A:TYR654	4.8	20.2	1.0
	CA	A:ASP653	5.0	21.4	1.0

Reference:

T.H.Gehrke, U.Lischke, K.L.Gasteiger, S.Schneider, S.Arnold, H.C.Muller, D.S.Stephenson, H.Zipse, T.Carell. Unexpected Non-Hoogsteen-Based Mutagenicity Mechanism of Fapy-Dna Lesions. Nat.Chem.Biol. V. 9 455 2013.
ISSN: ISSN 1552-4450
PubMed: 23685671
DOI: 10.1038/NCHEMBIO.1254

Page generated: Mon Aug 11 06:53:58 2025

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