Magnesium in PDB 2bcq: Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp

Enzymatic activity of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp

All present enzymatic activity of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp, PDB code: 2bcq was solved by M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	41.74 / 1.65
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	56.044, 62.539, 139.644, 90.00, 90.00, 90.00
*R / R_free (%)*	20.1 / 23

Other elements in 2bcq:

The structure of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp (pdb code 2bcq). 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 in Complex with A Dna Duplex Containing An Unpaired Dtmp, PDB code: 2bcq:

Magnesium binding site 1 out of 1 in 2bcq

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Magnesium Binding Sites List in 2bcq

Magnesium binding site 1 out of 1 in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp

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 in Complex with A Dna Duplex Containing An Unpaired Dtmp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg713 b:21.0 occ:1.00	OD2	A:ASP429	2.3	17.2	1.0
	OP1	P:DG7	2.4	18.9	1.0
	O12	A:PPV738	2.4	29.4	1.0
	O	A:ASP427	2.6	25.0	1.0
	O31	A:PPV738	2.7	29.2	1.0
	O22	A:PPV738	2.9	31.4	1.0
	P2	A:PPV738	3.0	25.8	1.0
	CG	A:ASP429	3.2	18.4	1.0
	CB	A:ASP427	3.4	22.6	1.0
	OD1	A:ASP429	3.4	15.9	1.0
	C	A:ASP427	3.5	22.6	1.0
	P1	A:PPV738	3.6	30.3	1.0
	P	P:DG7	3.6	17.3	1.0
	OPP	A:PPV738	3.6	30.3	1.0
	O	A:HOH2834	3.7	23.1	1.0
	O11	A:PPV738	3.8	28.7	1.0
	N	A:ASP427	3.8	22.6	1.0
	CA	A:ASP427	3.8	22.0	1.0
	C5'	P:DG7	3.9	16.1	1.0
	O5'	P:DG7	3.9	16.5	1.0
	O	A:HOH2903	4.0	34.9	1.0
	OP2	P:DG7	4.3	19.2	1.0
	CA	A:GLY416	4.5	19.0	1.0
	O32	A:PPV738	4.5	32.9	1.0
	N	A:SER417	4.6	19.0	1.0
	CB	A:ASP429	4.6	17.2	1.0
	CG	A:ASP427	4.7	22.4	1.0
	OG	A:SER417	4.7	20.2	1.0
	N	A:VAL428	4.7	18.6	1.0
	O3'	P:DC6	4.8	17.5	1.0
	N	A:ASP429	4.9	15.7	1.0
	C	A:GLY426	5.0	21.5	1.0

Reference:

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel. Structural Analysis of Strand Misalignment During Dna Synthesis By A Human Dna Polymerase Cell(Cambridge,Mass.) V. 124 331 2006.
ISSN: ISSN 0092-8674
PubMed: 16439207
DOI: 10.1016/J.CELL.2005.10.039

Page generated: Tue Aug 13 21:50:00 2024

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