Fluorine in PDB 4f5r: Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit

Enzymatic activity of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit

All present enzymatic activity of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit:
2.7.7.7;

Protein crystallography data

The structure of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit, PDB code: 4f5r was solved by B.D.Freudenthal, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	21.36 / 2.20
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	55.028, 79.446, 102.090, 90.00, 96.96, 90.00
*R / R_free (%)*	21 / 27.8

Other elements in 4f5r:

The structure of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Sodium	(Na)	4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit (pdb code 4f5r). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit, PDB code: 4f5r:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4f5r

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Fluorine Binding Sites List in 4f5r

Fluorine binding site 1 out of 4 in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F402 b:43.6 occ:1.00	F1A	A:6CF402	0.0	43.6	1.0
	C3A	A:6CF402	1.3	48.1	1.0
	F2A	A:6CF402	2.2	42.1	1.0
	P1	A:6CF402	2.6	47.9	1.0
	P2	A:6CF402	2.6	62.1	1.0
	O5'	A:6CF402	3.0	48.3	1.0
	O1B	A:6CF402	3.0	54.9	1.0
	O3G	A:6CF402	3.0	54.9	1.0
	O1A	A:6CF402	3.3	41.5	1.0
	O	A:HOH564	3.3	30.2	1.0
	O3B	A:6CF402	3.3	52.8	1.0
	O	A:HOH624	3.4	34.7	1.0
	C5'	A:6CF402	3.4	38.4	1.0
	P3	A:6CF402	3.7	53.9	1.0
	O2A	A:6CF402	3.9	42.6	1.0
	O2B	A:6CF402	3.9	44.5	1.0
	O	A:HOH680	4.1	43.0	1.0
	O	A:HOH543	4.3	40.4	1.0
	O1G	A:6CF402	4.4	44.8	1.0
	N	A:SER180	4.7	29.0	1.0
	CA	A:GLY179	4.8	27.6	1.0
	C4'	A:6CF402	4.9	37.9	1.0
	O2G	A:6CF402	5.0	49.7	1.0

Fluorine binding site 2 out of 4 in 4f5r

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Fluorine Binding Sites List in 4f5r

Fluorine binding site 2 out of 4 in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F402 b:42.1 occ:1.00	F2A	A:6CF402	0.0	42.1	1.0
	C3A	A:6CF402	1.3	48.1	1.0
	F1A	A:6CF402	2.2	43.6	1.0
	P1	A:6CF402	2.6	47.9	1.0
	P2	A:6CF402	2.6	62.1	1.0
	O2A	A:6CF402	3.0	42.6	1.0
	N	A:SER180	3.1	29.0	1.0
	C5'	A:6CF402	3.1	38.4	1.0
	O3B	A:6CF402	3.2	52.8	1.0
	O5'	A:6CF402	3.2	48.3	1.0
	O2B	A:6CF402	3.3	44.5	1.0
	O	A:HOH624	3.3	34.7	1.0
	CA	A:GLY179	3.6	27.6	1.0
	NH1	A:ARG183	3.6	29.9	1.0
	C	A:GLY179	3.6	29.1	1.0
	O1A	A:6CF402	3.9	41.5	1.0
	O1B	A:6CF402	3.9	54.9	1.0
	CA	A:SER180	4.0	28.8	1.0
	CB	A:SER180	4.0	32.5	1.0
	O3G	A:6CF402	4.1	54.9	1.0
	P3	A:6CF402	4.2	53.9	1.0
	NH2	A:ARG183	4.3	30.0	1.0
	CZ	A:ARG183	4.4	31.9	1.0
	O	A:HOH564	4.4	30.2	1.0
	O	A:HOH543	4.6	40.4	1.0
	O	A:GLY179	4.6	29.7	1.0
	C4'	A:6CF402	4.6	37.9	1.0
	OG	A:SER180	4.7	26.9	1.0
	O	A:THR273	4.8	23.8	1.0
	N	A:GLY179	4.9	26.6	1.0

Fluorine binding site 3 out of 4 in 4f5r

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Fluorine Binding Sites List in 4f5r

Fluorine binding site 3 out of 4 in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:F404 b:31.1 occ:1.00	F1A	B:6CF404	0.0	31.1	1.0
	C3A	B:6CF404	1.3	34.8	1.0
	F2A	B:6CF404	2.2	35.4	1.0
	P1	B:6CF404	2.5	37.9	1.0
	P2	B:6CF404	2.6	29.6	1.0
	O1B	B:6CF404	2.8	38.6	1.0
	O	B:HOH514	2.8	34.0	1.0
	O5'	B:6CF404	2.9	34.0	1.0
	O2A	B:6CF404	3.2	28.6	1.0
	O3B	B:6CF404	3.6	41.2	1.0
	O2B	B:6CF404	3.8	30.5	1.0
	C5'	B:6CF404	3.8	27.0	1.0
	C3'	B:6CF404	3.8	32.8	1.0
	O1A	B:6CF404	3.9	27.2	1.0
	C6	B:6CF404	3.9	29.2	1.0
	C4'	B:6CF404	4.4	30.2	1.0
	C5	B:6CF404	4.4	34.1	1.0
	P3	B:6CF404	4.5	36.8	1.0
	O3'	B:6CF404	4.5	35.3	1.0
	C2'	B:6CF404	4.6	28.9	1.0
	O1G	B:6CF404	4.7	35.7	1.0
	N1	B:6CF404	4.8	30.9	1.0
	O4'	B:6CF404	4.8	29.8	1.0
	MN	B:MN402	4.9	29.6	1.0
	O3G	B:6CF404	4.9	28.6	1.0
	CB	B:ASP276	5.0	34.8	1.0
	C1'	B:6CF404	5.0	30.5	1.0

Fluorine binding site 4 out of 4 in 4f5r

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Fluorine Binding Sites List in 4f5r

Fluorine binding site 4 out of 4 in the Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Open and Closed Ternary Complex of R283K Dna Polymerase Beta with A Dctp Analog in the Same Asymmetric Unit within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:F404 b:35.4 occ:1.00	F2A	B:6CF404	0.0	35.4	1.0
	C3A	B:6CF404	1.3	34.8	1.0
	F1A	B:6CF404	2.2	31.1	1.0
	P1	B:6CF404	2.6	37.9	1.0
	P2	B:6CF404	2.6	29.6	1.0
	O1G	B:6CF404	2.8	35.7	1.0
	O3B	B:6CF404	2.8	41.2	1.0
	O2A	B:6CF404	3.0	28.6	1.0
	P3	B:6CF404	3.0	36.8	1.0
	O3G	B:6CF404	3.2	28.6	1.0
	O1A	B:6CF404	3.3	27.2	1.0
	O2B	B:6CF404	3.6	30.5	1.0
	O1B	B:6CF404	3.8	38.6	1.0
	O5'	B:6CF404	3.8	34.0	1.0
	MN	B:MN402	3.9	29.6	1.0
	O	B:HOH514	4.4	34.0	1.0
	O	B:HOH562	4.5	23.4	1.0
	O2G	B:6CF404	4.5	35.8	1.0
	C5'	B:6CF404	4.8	27.0	1.0
	OD1	B:ASP190	5.0	28.1	1.0

Reference:

B.D.Freudenthal, W.A.Beard, S.H.Wilson. Structures of Dntp Intermediate States During Dna Polymerase Active Site Assembly. Structure V. 20 1829 2012.
ISSN: ISSN 0969-2126
PubMed: 22959623
DOI: 10.1016/J.STR.2012.08.008

Page generated: Thu Aug 1 01:26:35 2024

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