Magnesium in PDB 3po4: Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp

Enzymatic activity of Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp

All present enzymatic activity of Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp:
2.7.7.7;

Protein crystallography data

The structure of Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp, PDB code: 3po4 was solved by A.Marx, K.Diederichs, S.Obeid, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	48.20 / 1.80
*Space group*	P 3₁ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	113.525, 113.525, 91.238, 90.00, 90.00, 120.00
*R / R_free (%)*	16.4 / 19.4

Other elements in 3po4:

The structure of Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp (pdb code 3po4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp, PDB code: 3po4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3po4

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Magnesium Binding Sites List in 3po4

Magnesium binding site 1 out of 3 in the Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1 b:36.3 occ:1.00	O2A	A:DDS835	2.0	66.0	1.0
	O2B	A:DDS835	2.1	32.5	1.0
	O	A:HOH842	2.1	30.7	1.0
	O	A:HOH851	2.1	48.0	1.0
	O	A:HOH19	2.1	37.2	1.0
	O3G	A:DDS835	2.1	41.7	1.0
	O	A:HOH1021	2.1	61.8	1.0
	PB	A:DDS835	3.1	34.5	1.0
	PA	A:DDS835	3.2	51.8	1.0
	PG	A:DDS835	3.2	39.6	1.0
	O3A	A:DDS835	3.6	0.2	1.0
	O3B	A:DDS835	3.6	34.7	1.0
	O	A:HOH1022	3.7	63.3	1.0
	O2G	A:DDS835	3.8	44.3	1.0
	OD2	A:ASP610	3.8	39.1	0.6
	O1A	A:DDS835	3.9	58.5	1.0
	O	A:HOH250	4.1	51.5	1.0
	O	A:HOH96	4.1	28.7	1.0
	OE1	A:GLU820	4.2	54.3	1.0
	O	A:HOH1009	4.3	37.6	1.0
	N	A:GLN613	4.3	24.6	1.0
	O1B	A:DDS835	4.5	27.0	1.0
	O5'	A:DDS835	4.5	52.6	1.0
	O1G	A:DDS835	4.5	45.8	1.0
	O	A:HOH1023	4.5	60.4	1.0
	CA	A:SER612	4.7	26.4	1.0
	O	A:TYR611	4.7	28.9	1.0
	O	A:HOH1007	4.7	44.3	1.0
	C5'	A:DDS835	4.7	66.9	1.0

Magnesium binding site 2 out of 3 in 3po4

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Magnesium Binding Sites List in 3po4

Magnesium binding site 2 out of 3 in the Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg1 b:36.8 occ:1.00	O	B:HOH501	2.1	26.1	1.0
	O	C:HOH543	2.1	53.9	1.0
	O	B:HOH503	2.1	35.4	1.0
	O	B:HOH502	2.1	29.5	1.0
	O	B:HOH504	2.1	29.9	1.0
	O	B:HOH505	2.1	42.5	1.0
	O6	B:DG108	4.1	23.6	1.0
	O	B:HOH99	4.2	27.3	1.0
	O	C:HOH308	4.2	39.0	1.0
	O	C:HOH31	4.3	26.4	1.0
	O	B:HOH410	4.3	40.2	1.0
	O	B:HOH506	4.3	35.6	1.0
	N7	B:DG107	4.3	24.3	1.0
	O6	B:DG107	4.3	24.0	1.0
	N4	C:DC209	4.6	24.4	1.0
	O	B:HOH306	4.7	42.0	1.0
	C5	B:DC106	4.9	33.3	1.0

Magnesium binding site 3 out of 3 in 3po4

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Magnesium Binding Sites List in 3po4

Magnesium binding site 3 out of 3 in the Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in Complex with A Blunt-Ended Dna and Ddatp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg113 b:34.6 occ:1.00	O	A:HOH1009	2.0	37.6	1.0
	O	B:HOH538	2.1	39.1	1.0
	O	A:HOH1007	2.1	44.3	1.0
	O	B:HOH531	2.1	39.7	1.0
	O	A:HOH1008	2.1	31.4	1.0
	OP2	B:2DA112	2.3	27.7	1.0
	O	A:HOH1022	3.2	63.3	1.0
	O	A:HOH1020	3.4	45.4	1.0
	P	B:2DA112	3.6	26.7	1.0
	O	A:HOH1021	3.7	61.8	1.0
	OE1	A:GLU786	3.8	39.1	1.0
	OD1	A:ASP610	3.8	57.3	0.4
	C5'	B:2DA112	3.9	25.5	1.0
	O5'	B:2DA112	4.0	25.3	1.0
	O	B:HOH81	4.2	34.1	1.0
	OD1	A:ASP785	4.3	26.2	1.0
	O	A:HOH1023	4.4	60.4	1.0
	O2A	A:DDS835	4.4	66.0	1.0
	OD2	A:ASP785	4.4	35.8	1.0
	OP1	B:2DA112	4.4	25.3	1.0
	O3'	B:DC111	4.6	23.8	1.0
	NZ	A:LYS831	4.7	72.3	1.0
	CD	A:GLU786	4.8	56.5	1.0
	CG	A:ASP785	4.9	29.5	1.0
	C5'	A:DDS835	5.0	66.9	1.0
	OD2	A:ASP610	5.0	39.1	0.6

Reference:

S.Obeid, A.Schnur, C.Gloeckner, N.Blatter, W.Welte, K.Diederichs, A.Marx. Learning From Directed Evolution: Thermus Aquaticus Dna Polymerase Mutants with Translesion Synthesis Activity. Chembiochem V. 12 1574 2011.
ISSN: ISSN 1439-4227
PubMed: 21480455
DOI: 10.1002/CBIC.201000783

Page generated: Thu Aug 15 09:40:51 2024

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