Fluorine in PDB 3taf: 5-Fluorocytosine Paired with Ddgmp in RB69 GP43

All present enzymatic activity of 5-Fluorocytosine Paired with Ddgmp in RB69 GP43:
2.7.7.7;

The structure of 5-Fluorocytosine Paired with Ddgmp in RB69 GP43, PDB code: 3taf was solved by K.E.Zahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.99 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	132.984, 123.242, 169.347, 90.00, 96.96, 90.00
R / Rfree (%)	23.2 / 28

The binding sites of Fluorine atom in the 5-Fluorocytosine Paired with Ddgmp in RB69 GP43 (pdb code 3taf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the 5-Fluorocytosine Paired with Ddgmp in RB69 GP43, PDB code: 3taf:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the 5-Fluorocytosine Paired with Ddgmp in RB69 GP43


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 5-Fluorocytosine Paired with Ddgmp in RB69 GP43 within 5.0Å range: probe atom residue distance (Å) B Occ E:F3 b:93.4 occ:1.00 F E:C373 0.0 93.4 1.0 C5 E:C373 1.3 91.7 1.0 C6 E:C373 2.3 90.4 1.0 C4 E:C373 2.4 92.1 1.0 N4 E:C373 2.8 93.4 1.0 O4 E:SO419 3.2 0.6 1.0 O3 E:SO419 3.3 0.3 1.0 C2 E:DC2 3.5 0.6 1.0 N1 E:C373 3.6 88.2 1.0 N3 E:C373 3.6 92.7 1.0 O2 E:DC2 3.6 0.6 1.0 N3 E:DC2 3.8 0.8 1.0 C2' E:DC2 3.8 0.2 1.0 S E:SO419 3.9 0.1 1.0 N1 E:DC2 3.9 0.7 1.0 O1P E:C373 3.9 91.2 1.0 C2 E:C373 4.1 91.1 1.0 C4 E:DC2 4.3 0.5 1.0 O5' E:C373 4.4 90.2 1.0 C1' E:DC2 4.4 0.6 1.0 C6 E:DC2 4.5 0.6 1.0 C3' E:DC2 4.5 99.4 1.0 C5 E:DC2 4.7 0.5 1.0 P E:C373 4.7 92.4 1.0 C1' E:C373 4.8 84.6 1.0 O2 E:SO419 4.8 0.4 1.0 N7 E:DG4 4.8 70.1 1.0 O4' E:C373 4.8 82.7 1.0 O1 E:SO419 5.0 0.4 1.0

Fluorine binding site 2 out of 4 in the 5-Fluorocytosine Paired with Ddgmp in RB69 GP43


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 5-Fluorocytosine Paired with Ddgmp in RB69 GP43 within 5.0Å range: probe atom residue distance (Å) B Occ G:F3 b:40.0 occ:1.00 F G:C373 0.0 40.0 1.0 C5 G:C373 1.3 38.4 1.0 C6 G:C373 2.3 37.9 1.0 C4 G:C373 2.4 37.8 1.0 N4 G:C373 2.8 37.6 1.0 O2 G:DC2 3.4 56.3 1.0 C2 G:DC2 3.5 58.0 1.0 N1 G:C373 3.6 37.3 1.0 C1' G:DC2 3.6 55.4 1.0 O2 G:SO419 3.6 93.9 1.0 N1 G:DC2 3.6 57.0 1.0 N3 G:C373 3.6 37.9 1.0 C2' G:DC2 3.6 54.9 1.0 C2 G:C373 4.1 37.7 1.0 O1 G:SO419 4.2 94.9 1.0 N3 G:DC2 4.3 60.8 1.0 O1P G:C373 4.3 46.5 1.0 C6 G:DC2 4.4 58.4 1.0 S G:SO419 4.5 96.5 1.0 O5' G:C373 4.6 43.5 1.0 C1' G:C373 4.8 38.0 1.0 O4' G:C373 4.8 39.5 1.0 C4 G:DC2 4.9 62.8 1.0 O G:HOH38 5.0 48.4 1.0 O4' G:DC2 5.0 54.5 1.0 N7 G:DG4 5.0 33.5 1.0 P G:C373 5.0 45.8 1.0

Fluorine binding site 3 out of 4 in the 5-Fluorocytosine Paired with Ddgmp in RB69 GP43


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 5-Fluorocytosine Paired with Ddgmp in RB69 GP43 within 5.0Å range: probe atom residue distance (Å) B Occ I:F3 b:64.1 occ:1.00 F I:C373 0.0 64.1 1.0 C5 I:C373 1.3 60.5 1.0 C6 I:C373 2.3 59.9 1.0 C4 I:C373 2.4 59.4 1.0 N4 I:C373 2.8 59.1 1.0 O3 I:SO419 3.1 87.0 1.0 N1 I:C373 3.6 58.8 1.0 N3 I:C373 3.6 59.4 1.0 C2' I:DC2 3.8 72.5 1.0 O1P I:C373 3.8 62.8 1.0 C2 I:DC2 3.9 78.1 1.0 N1 I:DC2 4.0 77.0 1.0 C2 I:C373 4.1 59.8 1.0 N3 I:DC2 4.1 80.5 1.0 O2 I:DC2 4.1 76.8 1.0 O4 I:SO419 4.2 86.5 1.0 S I:SO419 4.2 88.3 1.0 O5' I:C373 4.4 61.2 1.0 C6 I:DC2 4.4 78.8 1.0 C4 I:DC2 4.5 82.2 1.0 C1' I:DC2 4.5 74.2 1.0 C3' I:DC2 4.5 70.5 1.0 N7 I:DG4 4.5 46.5 1.0 C5 I:DC2 4.6 81.5 1.0 P I:C373 4.7 62.6 1.0 C1' I:C373 4.8 57.4 1.0 O6 I:DG4 4.8 44.6 1.0 O4' I:C373 4.9 57.2 1.0 O1 I:SO419 4.9 88.3 1.0

Fluorine binding site 4 out of 4 in the 5-Fluorocytosine Paired with Ddgmp in RB69 GP43


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 5-Fluorocytosine Paired with Ddgmp in RB69 GP43 within 5.0Å range: probe atom residue distance (Å) B Occ K:F3 b:0.2 occ:1.00 F K:C373 0.0 0.2 1.0 C5 K:C373 1.3 0.4 1.0 C6 K:C373 2.3 0.6 1.0 C4 K:C373 2.4 0.7 1.0 O1 K:SO419 2.7 1.0 1.0 N4 K:C373 2.8 0.3 1.0 O1P K:C373 3.2 0.5 1.0 N1 K:C373 3.6 0.8 1.0 N3 K:C373 3.6 0.6 1.0 C2' K:DC2 3.8 0.2 1.0 S K:SO419 3.8 0.7 1.0 O2 K:SO419 3.8 1.0 1.0 C3' K:DC2 3.8 0.6 1.0 N1 K:DC2 4.0 0.7 1.0 C2 K:DC2 4.1 0.1 1.0 C2 K:C373 4.1 0.2 1.0 C6 K:DC2 4.1 0.8 1.0 P K:C373 4.2 0.8 1.0 O5' K:C373 4.2 0.8 1.0 N3 K:DC2 4.3 0.7 1.0 C5 K:DC2 4.3 0.2 1.0 O4 K:SO419 4.4 0.6 1.0 C4 K:DC2 4.4 0.9 1.0 O3' K:DC2 4.4 0.6 1.0 C1' K:DC2 4.5 0.2 1.0 O2 K:DC2 4.5 0.2 1.0 C1' K:C373 4.8 1.0 1.0 O4' K:C373 4.8 0.6 1.0

K.E.Zahn, A.Averill, S.S.Wallace, S.Doublie. The Miscoding Potential of 5-Hydroxycytosine Arises Due to Template Instability in the Replicative Polymerase Active Site. Biochemistry V. 50 10350 2011.
ISSN: ISSN 0006-2960
PubMed: 22026756
DOI: 10.1021/BI201219S