Calcium in PDB 6dia: Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

Enzymatic activity of Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog, PDB code: 6dia was solved by B.D.Freudenthal, M.R.Smith, 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)*	22.57 / 1.97
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	54.947, 80.584, 55.314, 90.00, 109.94, 90.00
*R / R_free (%)*	19.6 / 24.6

Other elements in 6dia:

The structure of Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog (pdb code 6dia). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog, PDB code: 6dia:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6dia

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Calcium Binding Sites List in 6dia

Calcium binding site 1 out of 3 in the Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

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 Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca403 b:34.9 occ:1.00	O1A	A:GKS401	2.3	32.1	1.0
	OD2	A:ASP192	2.4	36.3	1.0
	O	A:HOH512	2.4	29.0	1.0
	OD1	A:ASP190	2.5	27.1	1.0
	O3G	A:GKS401	2.6	38.2	1.0
	O2B	A:GKS401	2.6	31.9	1.0
	O	A:HOH649	2.7	29.3	1.0
	OD1	A:ASP192	2.8	39.6	1.0
	CG	A:ASP192	3.0	33.8	1.0
	CG	A:ASP190	3.4	30.7	1.0
	PA	A:GKS401	3.5	40.6	1.0
	OD2	A:ASP190	3.7	38.1	1.0
	PB	A:GKS401	3.7	39.5	1.0
	O3A	A:GKS401	3.7	40.3	1.0
	N2	A:GKS401	3.8	32.2	1.0
	PG	A:GKS401	3.8	41.9	1.0
	O	A:HOH519	4.1	48.5	1.0
	O2G	A:GKS401	4.1	45.8	1.0
	O3B	A:GKS401	4.1	46.9	1.0
	O	A:HOH507	4.2	34.8	1.0
	O2A	A:GKS401	4.3	43.9	1.0
	O	A:HOH584	4.4	30.4	1.0
	CB	A:ASP192	4.5	27.2	1.0
	O3'	P:DC10	4.6	32.2	1.0
	NA	P:NA101	4.6	46.3	1.0
	O	A:ASP190	4.6	22.9	1.0
	O	A:HOH520	4.7	39.2	1.0
	O5'	A:GKS401	4.7	40.9	1.0
	CA	A:GLY179	4.8	28.0	1.0
	O	A:HOH598	4.8	28.7	1.0
	CB	A:ASP190	4.8	18.8	1.0
	C	A:ASP190	4.9	20.6	1.0
	C2	A:GKS401	5.0	42.6	1.0
	N	A:ASP190	5.0	23.3	1.0

Calcium binding site 2 out of 3 in 6dia

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Calcium Binding Sites List in 6dia

Calcium binding site 2 out of 3 in the Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca404 b:34.9 occ:1.00	O	A:HOH720	2.3	33.5	1.0
	O	A:HOH652	2.3	25.9	1.0
	OD1	A:ASP145	2.5	21.0	1.0
	OD2	A:ASP145	2.6	23.0	1.0
	O	A:HOH576	2.6	28.6	1.0
	O	A:HOH679	2.6	32.4	1.0
	CG	A:ASP145	2.9	26.1	1.0
	O	A:HOH712	3.6	38.3	1.0
	O	A:HOH710	3.9	35.6	1.0
	O	A:HOH642	4.3	22.0	1.0
	CB	A:ASP145	4.4	18.9	1.0
	O	A:HOH681	4.5	40.5	1.0
	CA	A:PRO251	4.6	27.8	1.0
	ND1	A:HIS252	4.6	32.7	1.0
	OE1	A:GLU249	4.7	44.2	1.0
	N	A:HIS252	4.9	26.1	1.0

Calcium binding site 3 out of 3 in 6dia

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Calcium Binding Sites List in 6dia

Calcium binding site 3 out of 3 in the Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog

Mono view

Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming Fapy-Dgtp Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
T:Ca101 b:51.2 occ:1.00	O	T:HOH208	2.3	26.2	1.0
	O	A:HOH522	2.3	35.2	1.0
	O	A:HOH505	2.3	35.7	1.0
	O	T:HOH219	2.4	35.6	1.0
	O	A:HOH517	2.5	43.1	1.0
	O	A:HOH530	2.6	30.5	1.0
	O2	T:DC6	2.9	31.4	1.0
	OE1	A:GLU295	3.6	40.5	1.0
	C2	T:DC6	4.0	29.4	1.0
	O4'	T:DG7	4.0	23.4	1.0
	O	T:HOH256	4.3	35.2	1.0
	N3	T:DG7	4.3	22.6	1.0
	N3	T:DC6	4.5	28.7	1.0
	OH	A:TYR271	4.5	39.2	1.0
	O4'	T:DC8	4.5	22.9	1.0
	C4'	T:DG7	4.5	29.0	1.0
	CD	A:GLU295	4.7	38.9	1.0
	O	A:HOH577	4.7	37.6	1.0
	N2	T:DG7	4.8	23.7	1.0
	C1'	T:DG7	4.8	25.4	1.0
	C5'	T:DC8	4.9	28.6	1.0
	C2	T:DG7	4.9	24.1	1.0
	OH	A:TYR296	4.9	33.9	1.0
	C4'	T:DC8	5.0	29.1	1.0

Reference:

M.R.Smith, D.D.Shock, W.A.Beard, M.M.Greenberg, B.D.Freudenthal, S.H.Wilson. A Guardian Residue Hinders Insertion of A Fapy•Dgtp Analog By Modulating the Open-Closed Dna Polymerase Transition. Nucleic Acids Res. V. 47 3197 2019.
ISSN: ESSN 1362-4962
PubMed: 30649431
DOI: 10.1093/NAR/GKZ002

Page generated: Wed Jul 9 13:26:03 2025

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