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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 / Rfree (%) 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

Go back to 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

Go back to 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

Go back to 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

Go back to 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: Mon Jul 14 21:33:42 2025

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