Magnesium in PDB 4f5p: Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog

Enzymatic activity of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog

All present enzymatic activity of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog:
2.7.7.7;

Protein crystallography data

The structure of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog, PDB code: 4f5p was solved by B.D.Freudenthal, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	22.11 / 1.85
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	54.380, 79.240, 54.880, 90.00, 105.49, 90.00
*R / R_free (%)*	20.3 / 24.5

Other elements in 4f5p:

The structure of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog (pdb code 4f5p). 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 Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog, PDB code: 4f5p:

Magnesium binding site 1 out of 1 in 4f5p

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Magnesium Binding Sites List in 4f5p

Magnesium binding site 1 out of 1 in the Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Open Ternary Mismatch Complex of R283K Dna Polymerase Beta with A Datp Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg401 b:45.5 occ:1.00	OD1	A:ASP190	2.1	31.1	1.0
	O	A:HOH652	2.1	34.7	1.0
	O1A	A:F2A404	2.1	55.2	1.0
	O2B	A:F2A404	2.2	63.5	1.0
	OD1	A:ASP192	2.2	49.5	1.0
	O3G	A:F2A404	2.3	39.9	1.0
	CG	A:ASP190	3.2	37.2	1.0
	PA	A:F2A404	3.4	75.0	1.0
	CG	A:ASP192	3.4	48.4	1.0
	PB	A:F2A404	3.6	55.6	1.0
	PG	A:F2A404	3.7	53.7	1.0
	OD2	A:ASP190	3.7	37.4	1.0
	C3A	A:F2A404	3.7	58.3	1.0
	O	A:ASP190	3.7	26.7	1.0
	O	A:HOH703	3.8	47.7	1.0
	OD2	A:ASP192	4.0	49.2	1.0
	O3B	A:F2A404	4.1	58.6	1.0
	C	A:ASP190	4.2	28.2	1.0
	O	A:HOH518	4.3	28.8	1.0
	O2G	A:F2A404	4.3	46.5	1.0
	N	A:ASP190	4.4	23.5	1.0
	O2A	A:F2A404	4.4	65.7	1.0
	CB	A:ASP190	4.5	23.9	1.0
	O5'	A:F2A404	4.5	71.8	1.0
	CB	A:ASP192	4.5	37.2	1.0
	C5'	A:F2A404	4.6	64.3	1.0
	CA	A:ASP190	4.6	21.8	1.0
	CA	A:GLY179	4.6	31.1	1.0
	O1G	A:F2A404	4.8	50.8	1.0
	N	A:ASP192	4.8	22.6	1.0
	O	A:HOH692	4.8	46.0	1.0
	N	A:MET191	4.8	24.2	1.0
	O1B	A:F2A404	4.9	65.0	1.0
	N	A:SER180	5.0	37.3	1.0

Reference:

B.D.Freudenthal, W.A.Beard, S.H.Wilson. Structures of Dntp Intermediate States During Dna Polymerase Active Site Assembly. Structure V. 20 1829 2012.
ISSN: ISSN 0969-2126
PubMed: 22959623
DOI: 10.1016/J.STR.2012.08.008

Page generated: Fri Aug 16 14:43:11 2024

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