Fluorine in PDB 8buo: Structure of DDB1 Bound to DS24-Engaged CDK12-Cyclin K

All present enzymatic activity of Structure of DDB1 Bound to DS24-Engaged CDK12-Cyclin K:
2.7.11.22; 2.7.11.23;

The structure of Structure of DDB1 Bound to DS24-Engaged CDK12-Cyclin K, PDB code: 8buo was solved by Z.Kozicka, G.Kempf, G.Petzold, N.H.Thoma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.19 / 3.58
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	249.8, 249.8, 218.078, 90, 90, 120
R / Rfree (%)	17.7 / 21.9

The binding sites of Fluorine atom in the Structure of DDB1 Bound to DS24-Engaged CDK12-Cyclin K (pdb code 8buo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of DDB1 Bound to DS24-Engaged CDK12-Cyclin K, PDB code: 8buo:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of DDB1 Bound to DS24-Engaged CDK12-Cyclin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of DDB1 Bound to DS24-Engaged CDK12-Cyclin K within 5.0Å range: probe atom residue distance (Å) B Occ B:F1101 b:202.7 occ:1.00 F1 B:RLC1101 0.0 202.7 1.0 C7 B:RLC1101 1.4 192.7 1.0 HH B:TYR815 2.0 192.9 0.0 C6 B:RLC1101 2.3 176.7 1.0 C8 B:RLC1101 2.4 178.0 1.0 N1 B:RLC1101 2.4 182.8 1.0 OH B:TYR815 2.5 160.4 1.0 H81 B:RLC1101 2.5 214.1 0.0 C2 B:RLC1101 2.8 172.5 1.0 HD11 A:ILE909 3.0 192.5 0.0 HG22 B:ILE733 3.4 191.1 0.0 C11 B:RLC1101 3.6 158.8 1.0 O B:ASP817 3.6 158.9 1.0 C1 B:RLC1101 3.6 175.4 1.0 C9 B:RLC1101 3.6 164.3 1.0 HG21 B:ILE733 3.6 191.1 0.0 CZ B:TYR815 3.7 166.7 1.0 HD13 A:ILE909 3.8 192.5 0.0 CD1 A:ILE909 3.8 160.0 1.0 H11 B:RLC1101 3.9 211.0 0.0 HE1 B:TYR815 3.9 194.7 0.0 CG2 B:ILE733 4.0 158.8 1.0 C10 B:RLC1101 4.1 165.6 1.0 CE1 B:TYR815 4.2 161.8 1.0 C3 B:RLC1101 4.2 161.5 1.0 HD2 B:LYS743 4.2 171.8 0.0 HZ2 B:LYS743 4.3 187.6 0.0 HD12 A:ILE909 4.3 192.5 0.0 H111 B:RLC1101 4.4 191.1 0.0 HE A:ARG928 4.5 211.3 0.0 HH21 A:ARG928 4.5 211.2 0.0 HB B:ILE733 4.6 180.3 0.0 HG23 B:ILE733 4.7 191.1 0.0 C B:ASP817 4.7 162.0 1.0 CE2 B:TYR815 4.7 173.6 1.0 H31 B:RLC1101 4.7 194.3 0.0 HA B:ASP817 4.8 204.8 0.0 HG12 A:ILE909 4.8 189.2 0.0 C5 B:RLC1101 4.8 175.5 1.0 HE2 B:TYR815 4.8 208.9 0.0 C12 B:RLC1101 4.9 147.3 1.0 CG1 A:ILE909 4.9 157.3 1.0 O B:MET816 4.9 158.0 1.0 HA B:HIS818 4.9 169.9 0.0 H122 B:RLC1101 4.9 177.3 0.0 CB B:ILE733 4.9 149.9 1.0

Fluorine binding site 2 out of 3 in the Structure of DDB1 Bound to DS24-Engaged CDK12-Cyclin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of DDB1 Bound to DS24-Engaged CDK12-Cyclin K within 5.0Å range: probe atom residue distance (Å) B Occ E:F1101 b:194.8 occ:1.00 F1 E:RLC1101 0.0 194.8 1.0 C7 E:RLC1101 1.4 186.3 1.0 HH E:TYR815 1.9 185.6 0.0 C8 E:RLC1101 2.3 179.0 1.0 C6 E:RLC1101 2.4 172.8 1.0 OH E:TYR815 2.4 154.3 1.0 N1 E:RLC1101 2.4 169.8 1.0 H81 E:RLC1101 2.5 215.3 0.0 HD11 D:ILE909 2.7 176.9 0.0 C2 E:RLC1101 2.8 163.3 1.0 HE1 E:TYR815 3.6 178.2 0.0 CZ E:TYR815 3.6 159.3 1.0 CD1 D:ILE909 3.6 147.0 1.0 C11 E:RLC1101 3.6 157.8 1.0 C9 E:RLC1101 3.6 164.7 1.0 C1 E:RLC1101 3.7 163.1 1.0 HD13 D:ILE909 3.7 176.9 0.0 O E:ASP817 3.8 143.2 1.0 HZ2 E:LYS743 3.9 167.6 0.0 H11 E:RLC1101 3.9 196.3 0.0 HG21 E:ILE733 3.9 180.4 0.0 CE1 E:TYR815 4.0 148.1 1.0 C10 E:RLC1101 4.1 160.9 1.0 HD2 E:LYS743 4.1 161.3 0.0 HD12 D:ILE909 4.1 176.9 0.0 C3 E:RLC1101 4.2 142.3 1.0 H111 E:RLC1101 4.4 189.9 0.0 HG22 E:ILE733 4.4 180.4 0.0 HG12 D:ILE909 4.5 154.9 0.0 CG1 D:ILE909 4.6 128.7 1.0 CG2 E:ILE733 4.6 149.9 1.0 HE D:ARG928 4.7 176.9 0.0 H31 E:RLC1101 4.7 171.3 0.0 CE2 E:TYR815 4.7 168.2 1.0 NZ E:LYS743 4.8 139.2 1.0 OD1 D:ASN907 4.8 143.6 1.0 C5 E:RLC1101 4.8 172.0 1.0 HA E:ASP817 4.8 184.3 0.0 HG13 D:ILE909 4.8 154.9 0.0 C E:ASP817 4.8 142.3 1.0 HE2 E:TYR815 4.8 202.4 0.0 HH21 D:ARG928 4.9 183.6 0.0 C12 E:RLC1101 4.9 151.4 1.0 HZ3 E:LYS743 4.9 167.6 0.0 CD E:LYS743 5.0 134.0 1.0 H121 E:RLC1101 5.0 182.2 0.0

Fluorine binding site 3 out of 3 in the Structure of DDB1 Bound to DS24-Engaged CDK12-Cyclin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of DDB1 Bound to DS24-Engaged CDK12-Cyclin K within 5.0Å range: probe atom residue distance (Å) B Occ H:F1101 b:179.8 occ:1.00 F1 H:RLC1101 0.0 179.8 1.0 C7 H:RLC1101 1.4 167.8 1.0 HH H:TYR815 2.1 176.2 0.0 C8 H:RLC1101 2.3 156.1 1.0 C6 H:RLC1101 2.4 160.9 1.0 N1 H:RLC1101 2.4 168.2 1.0 H81 H:RLC1101 2.5 187.8 0.0 HD11 G:ILE909 2.6 178.5 0.0 OH H:TYR815 2.7 146.4 1.0 C2 H:RLC1101 2.8 157.1 1.0 CD1 G:ILE909 3.4 148.3 1.0 HD13 G:ILE909 3.5 178.5 0.0 C11 H:RLC1101 3.6 150.0 1.0 C9 H:RLC1101 3.6 157.8 1.0 C1 H:RLC1101 3.6 163.9 1.0 O H:ASP817 3.7 135.7 1.0 HD12 G:ILE909 3.8 178.5 0.0 HE1 H:TYR815 3.8 177.5 0.0 CZ H:TYR815 3.9 157.2 1.0 H11 H:RLC1101 3.9 197.2 0.0 HG22 H:ILE733 4.0 163.1 0.0 C10 H:RLC1101 4.1 157.4 1.0 HG21 H:ILE733 4.1 163.1 0.0 HZ2 H:LYS743 4.2 176.1 0.0 C3 H:RLC1101 4.2 145.0 1.0 HE G:ARG928 4.2 179.9 0.0 CE1 H:TYR815 4.2 147.5 1.0 HH21 G:ARG928 4.3 182.0 0.0 HD2 H:LYS743 4.3 168.6 0.0 H111 H:RLC1101 4.4 180.4 0.0 CG2 H:ILE733 4.5 135.5 1.0 HG12 G:ILE909 4.6 164.2 0.0 CG1 G:ILE909 4.6 136.4 1.0 H31 H:RLC1101 4.7 174.5 0.0 NH2 G:ARG928 4.7 151.2 1.0 NE G:ARG928 4.7 149.5 1.0 HG13 G:ILE909 4.8 164.2 0.0 C5 H:RLC1101 4.8 163.4 1.0 HB H:ILE733 4.8 176.0 0.0 HA H:HIS818 4.9 158.2 0.0 C12 H:RLC1101 4.9 156.9 1.0 C H:ASP817 4.9 132.1 1.0 H121 H:RLC1101 4.9 188.7 0.0 HG3 G:ARG928 5.0 165.5 0.0 CE2 H:TYR815 5.0 160.8 1.0

Z.Kozicka, G.Kempf, G.Petzold, N.H.Thoma. Structure of DDB1 Bound to DS17-Engaged CDK12-Cyclin K To Be Published.