Calcium in PDB 4ubb: Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S

Enzymatic activity of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S

All present enzymatic activity of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S, PDB code: 4ubb was solved by B.D.Freudenthal, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	31.90 / 1.90
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	50.798, 79.849, 55.625, 90.00, 107.58, 90.00
*R / R_free (%)*	18.1 / 22.8

Other elements in 4ubb:

The structure of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S (pdb code 4ubb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S, PDB code: 4ubb:

Calcium binding site 1 out of 1 in 4ubb

Go back to

Calcium Binding Sites List in 4ubb

Calcium binding site 1 out of 1 in the Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
P:Ca102 b:51.4 occ:0.60	O	P:HOH214	0.3	45.1	0.4
	MG	P:MG101	2.0	28.3	0.4
	O	A:HOH716	2.2	50.5	1.0
	O	A:HOH681	2.4	40.5	0.6
	O	P:HOH208	2.4	38.2	0.6
	O	A:HOH588	2.5	30.2	1.0
	O1A	A:8DG401	2.5	16.0	0.6
	OP2	P:8OG11	2.8	23.9	0.4
	O	A:HOH717	2.9	47.7	0.4
	O	A:HOH708	3.2	36.8	0.5
	PA	A:8DG401	3.8	16.2	0.6
	OP2	P:DC10	4.2	31.4	0.5
	OP2	P:DC10	4.2	31.8	0.5
	P	P:8OG11	4.2	24.7	0.4
	O3A	A:8DG401	4.2	23.1	0.6
	O12	A:PPV404	4.3	19.5	0.4
	O	P:HOH203	4.4	32.2	1.0
	O2G	A:8DG401	4.4	21.5	0.6
	O	A:HOH667	4.5	38.0	1.0
	O	P:HOH202	4.5	31.4	1.0
	O8	P:8OG11	4.6	18.9	0.4
	O2A	A:8DG401	4.8	18.5	0.6
	O5'	A:8DG401	4.8	19.9	0.6
	O8	A:8DG401	4.8	23.2	0.6
	O3B	A:8DG401	4.8	21.2	0.6
	O5'	P:8OG11	4.9	18.3	0.4
	OP1	P:8OG11	4.9	17.4	0.4

Reference:

B.D.Freudenthal, W.A.Beard, L.Perera, D.D.Shock, T.Kim, T.Schlick, S.H.Wilson. Uncovering the Polymerase-Induced Cytotoxicty of An Oxidized Nucleotide Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13886

Page generated: Wed Jul 9 02:17:05 2025

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