Calcium in PDB 6mr8: D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog

Enzymatic activity of D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog

All present enzymatic activity of D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog:
2.7.7.7;

Protein crystallography data

The structure of D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog, PDB code: 6mr8 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)*	24.80 / 1.90
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	55.015, 80.282, 55.564, 90.00, 110.46, 90.00
*R / R_free (%)*	19.6 / 23.9

Other elements in 6mr8:

The structure of D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog also contains other interesting chemical elements:

Sodium

(Na)

5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog (pdb code 6mr8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog, PDB code: 6mr8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6mr8

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Calcium Binding Sites List in 6mr8

Calcium binding site 1 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine 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 D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca406 b:45.1 occ:0.85	O	A:HOH512	2.2	34.5	1.0
	O1A	A:GKS401	2.3	50.9	0.8
	OD2	A:ASP192	2.3	31.7	0.5
	OD1	A:ASP190	2.5	28.3	1.0
	O	A:HOH662	2.7	33.6	1.0
	PA	A:GKS401	3.1	57.4	0.8
	O2A	A:GKS401	3.2	53.6	0.8
	CG	A:ASP192	3.2	26.6	0.5
	O1B	A:GKS401	3.2	48.1	0.8
	CA	A:CA407	3.2	64.5	0.8
	CG	A:ASP190	3.3	30.8	1.0
	OD1	A:ASP192	3.4	33.0	0.5
	O	A:HOH537	3.4	44.0	1.0
	OD2	A:ASP190	3.5	34.8	1.0
	O2G	A:GKS401	3.8	42.6	0.8
	O	A:HOH564	3.8	41.6	1.0
	O3A	A:GKS401	3.9	53.8	0.8
	PB	A:GKS401	4.2	55.3	0.8
	O	A:HOH597	4.3	36.8	1.0
	O5'	A:GKS401	4.4	53.1	0.8
	O	A:HOH689	4.5	45.8	1.0
	CB	A:ASP192	4.6	28.0	0.5
	CB	A:ASP192	4.7	28.1	0.5
	O	A:ASP190	4.7	23.1	1.0
	CA	A:GLY179	4.7	30.1	1.0
	PG	A:GKS401	4.8	59.2	0.8
	CB	A:ASP190	4.8	20.5	1.0
	O3B	A:GKS401	4.8	59.3	0.8
	OD1	A:ASP192	4.9	33.0	0.5
	C	A:ASP190	4.9	22.9	1.0

Calcium binding site 2 out of 3 in 6mr8

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Calcium Binding Sites List in 6mr8

Calcium binding site 2 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine 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 D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca407 b:64.5 occ:0.85	O3A	A:GKS401	2.6	53.8	0.8
	O1G	A:GKS401	2.7	57.7	0.8
	O	A:HOH537	2.7	44.0	1.0
	O2A	A:GKS401	2.7	53.6	0.8
	O	A:HOH689	2.8	45.8	1.0
	PA	A:GKS401	2.9	57.4	0.8
	O3B	A:GKS401	3.1	59.3	0.8
	O	P:HOH235	3.1	42.7	0.5
	O	A:HOH703	3.1	30.0	1.0
	PG	A:GKS401	3.2	59.2	0.8
	CA	A:CA406	3.2	45.1	0.8
	PB	A:GKS401	3.3	55.3	0.8
	O2G	A:GKS401	3.4	42.6	0.8
	O1A	A:GKS401	3.5	50.9	0.8
	O1B	A:GKS401	3.6	48.1	0.8
	O	A:HOH501	3.6	30.0	1.0
	O	P:HOH235	4.0	37.3	0.5
	N2	A:GKS401	4.2	57.0	0.8
	O	A:HOH512	4.2	34.5	1.0
	OD2	A:ASP190	4.4	34.8	1.0
	O5'	A:GKS401	4.5	53.1	0.8
	OD1	A:ASP190	4.6	28.3	1.0
	O2B	A:GKS401	4.6	48.3	0.8
	O3G	A:GKS401	4.7	50.4	0.8
	CG	A:ASP190	4.8	30.8	1.0
	O	A:HOH662	4.9	33.6	1.0

Calcium binding site 3 out of 3 in 6mr8

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Calcium Binding Sites List in 6mr8

Calcium binding site 3 out of 3 in the D276G Dna Polymerase Beta Substrate Complex with Templating Adenine 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 D276G Dna Polymerase Beta Substrate Complex with Templating Adenine and Incoming Fapy-Dgtp Analog within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ca408 b:25.0 occ:1.00	O	A:HOH666	2.3	23.7	1.0
	O	A:HOH717	2.4	25.7	1.0
	OD1	A:ASP145	2.5	19.1	1.0
	O	A:HOH677	2.5	28.7	1.0
	OD2	A:ASP145	2.6	21.0	1.0
	O	A:HOH550	2.7	25.3	1.0
	CG	A:ASP145	2.9	22.7	1.0
	O	A:HOH720	3.3	32.2	1.0
	O	A:HOH718	3.6	32.0	1.0
	O	A:HOH613	4.3	22.7	1.0
	O	A:HOH639	4.3	19.1	1.0
	O	A:HOH524	4.4	39.2	1.0
	CB	A:ASP145	4.4	19.4	1.0
	ND1	A:HIS252	4.4	24.0	1.0
	OE1	A:GLU249	4.5	36.7	1.0
	CA	A:PRO251	4.5	24.4	1.0
	O	A:HOH634	4.6	32.8	1.0
	O	A:HOH746	4.8	43.2	1.0
	N	A:HIS252	4.9	23.2	1.0
	O	A:TYR250	4.9	26.6	1.0
	CE1	A:HIS252	5.0	29.6	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 16:09:28 2025

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