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

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

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

Protein crystallography data

The structure of Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp, PDB code: 3lwm 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)*	47.45 / 2.19
*Space group*	P 3₁ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	109.592, 109.592, 91.037, 90.00, 90.00, 120.00
*R / R_free (%)*	18.3 / 22.8

Other elements in 3lwm:

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

Sodium

(Na)

4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp (pdb code 3lwm). 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 Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp, PDB code: 3lwm:

Magnesium binding site 1 out of 1 in 3lwm

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Magnesium Binding Sites List in 3lwm

Magnesium binding site 1 out of 1 in the Structure of the Large Fragment of Thermus Aquaticus Dna Polymerase I 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 the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex with A Blunt-Ended Dna and Ddatp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg835 b:55.6 occ:1.00	O2A	A:DDS1	2.1	57.5	1.0
	O	A:HOH166	2.1	45.2	1.0
	O	A:HOH46	2.3	41.4	1.0
	O3G	A:DDS1	2.3	46.2	1.0
	O1B	A:DDS1	2.4	52.7	1.0
	PA	A:DDS1	3.5	56.1	1.0
	O	A:HOH844	3.6	48.2	1.0
	PB	A:DDS1	3.7	52.0	1.0
	OD2	A:ASP610	3.7	58.6	1.0
	PG	A:DDS1	3.7	53.6	1.0
	O3A	A:DDS1	4.0	41.9	1.0
	C1	B:GOL1	4.0	81.4	1.0
	O5'	A:DDS1	4.1	60.5	1.0
	OD1	A:ASP610	4.2	62.2	1.0
	O3B	A:DDS1	4.2	34.5	1.0
	CG	A:ASP610	4.2	56.6	1.0
	O1G	A:DDS1	4.5	56.0	1.0
	O1A	A:DDS1	4.7	60.0	1.0
	N	A:GLN613	4.7	34.2	1.0
	C2	B:GOL1	4.7	79.7	1.0
	CA	A:SER612	4.7	36.0	1.0
	O2G	A:DDS1	4.8	58.5	1.0
	O	A:HOH63	4.8	31.4	1.0
	O	A:TYR611	4.9	34.4	1.0
	OE2	A:GLU820	4.9	76.8	1.0
	O2B	A:DDS1	5.0	39.3	1.0
	C3	B:GOL1	5.0	79.4	1.0

Reference:

S.Obeid, N.Blatter, R.Kranaster, A.Schnur, K.Diederichs, W.Welte, A.Marx. Replication Through An Abasic Dna Lesion: Structural Basis For Adenine Selectivity Embo J. V. 29 1738 2010.
ISSN: ISSN 0261-4189
PubMed: 20400942
DOI: 10.1038/EMBOJ.2010.64

Page generated: Wed Aug 14 18:41:10 2024

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