Fluorine in PDB 6ya8: CDC7-DBF4 Bound to Adp-BEF3

All present enzymatic activity of CDC7-DBF4 Bound to Adp-BEF3:
2.7.11.1;

The structure of CDC7-DBF4 Bound to Adp-BEF3, PDB code: 6ya8 was solved by S.D.Dick, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.86 / 1.79
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.150, 61.150, 235.440, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.7

The structure of CDC7-DBF4 Bound to Adp-BEF3 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the CDC7-DBF4 Bound to Adp-BEF3 (pdb code 6ya8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the CDC7-DBF4 Bound to Adp-BEF3, PDB code: 6ya8:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the CDC7-DBF4 Bound to Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of CDC7-DBF4 Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:20.0 occ:1.00 F1 A:BEF603 0.0 20.0 1.0 BE A:BEF603 1.6 20.2 1.0 MG A:MG604 1.8 16.7 1.0 F2 A:BEF603 2.3 19.8 1.0 O A:HOH808 2.6 17.1 1.0 O A:HOH930 2.7 34.2 1.0 F3 A:BEF603 2.8 16.6 1.0 O3B A:ADP601 2.9 17.3 1.0 O A:HOH749 2.9 24.1 1.0 OD2 A:ASP196 2.9 15.7 1.0 O1B A:ADP601 3.0 13.7 1.0 O A:HOH901 3.1 22.2 1.0 O A:HOH870 3.2 18.8 1.0 OD2 A:ASP177 3.3 17.1 1.0 PB A:ADP601 3.3 18.6 1.0 MG A:MG602 3.7 15.5 1.0 CG A:ASP196 3.8 16.4 1.0 OD1 A:ASP196 3.8 16.1 1.0 O A:HOH799 4.1 28.1 1.0 O2B A:ADP601 4.1 21.1 1.0 O A:HOH883 4.2 24.0 1.0 CG A:ASP177 4.5 17.4 1.0 CD1 A:LEU199 4.6 24.9 1.0 CG A:LEU199 4.7 21.8 1.0 O3A A:ADP601 4.7 15.6 1.0 O A:HOH925 4.8 31.3 1.0 ND2 A:ASN182 4.9 13.6 1.0

Fluorine binding site 2 out of 3 in the CDC7-DBF4 Bound to Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of CDC7-DBF4 Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:19.8 occ:1.00 F2 A:BEF603 0.0 19.8 1.0 BE A:BEF603 1.5 20.2 1.0 O A:HOH901 1.9 22.2 1.0 O A:HOH883 2.0 24.0 1.0 O A:HOH749 2.2 24.1 1.0 F1 A:BEF603 2.3 20.0 1.0 F3 A:BEF603 2.3 16.6 1.0 O1B A:ADP601 2.3 13.7 1.0 MG A:MG602 3.4 15.5 1.0 PB A:ADP601 3.4 18.6 1.0 O A:HOH911 3.5 47.5 1.0 O A:HOH860 3.7 31.3 1.0 O2B A:ADP601 3.8 21.1 1.0 MG A:MG604 3.8 16.7 1.0 OD2 A:ASP196 3.9 15.7 1.0 O A:HOH827 3.9 14.4 1.0 O3B A:ADP601 3.9 17.3 1.0 NZ A:LYS179 4.0 27.5 1.0 O A:HOH799 4.0 28.1 1.0 O A:HOH930 4.0 34.2 1.0 OD2 A:ASP177 4.0 17.1 1.0 O A:HOH807 4.0 28.8 1.0 O A:HOH925 4.4 31.3 1.0 CE A:LYS179 4.6 17.2 1.0 O A:HOH808 4.6 17.1 1.0 O A:HOH702 4.7 33.9 1.0 O3A A:ADP601 4.8 15.6 1.0 O1A A:ADP601 4.9 13.9 1.0

Fluorine binding site 3 out of 3 in the CDC7-DBF4 Bound to Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of CDC7-DBF4 Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:16.6 occ:1.00 F3 A:BEF603 0.0 16.6 1.0 BE A:BEF603 1.6 20.2 1.0 MG A:MG602 2.0 15.5 1.0 F2 A:BEF603 2.3 19.8 1.0 OD2 A:ASP196 2.7 15.7 1.0 O1B A:ADP601 2.7 13.7 1.0 O A:HOH749 2.7 24.1 1.0 F1 A:BEF603 2.8 20.0 1.0 ND2 A:ASN182 2.9 13.6 1.0 OD2 A:ASP177 2.9 17.1 1.0 O A:HOH827 3.0 14.4 1.0 O A:HOH883 3.0 24.0 1.0 OD1 A:ASN182 3.1 13.2 1.0 CE A:LYS179 3.3 17.2 1.0 CG A:ASN182 3.4 14.1 1.0 NZ A:LYS179 3.4 27.5 1.0 MG A:MG604 3.6 16.7 1.0 O A:HOH808 3.9 17.1 1.0 CG A:ASP196 3.9 16.4 1.0 CG A:ASP177 3.9 17.4 1.0 O1A A:ADP601 4.0 13.9 1.0 PB A:ADP601 4.0 18.6 1.0 O A:HOH901 4.1 22.2 1.0 O3B A:ADP601 4.3 17.3 1.0 OD1 A:ASP177 4.4 18.9 1.0 O A:HOH702 4.5 33.9 1.0 OG A:SER181 4.5 21.3 1.0 OD1 A:ASP196 4.7 16.1 1.0 CD A:LYS179 4.7 17.6 1.0 CB A:ASP196 4.8 14.8 1.0 CB A:ASN182 4.8 14.4 1.0 O3A A:ADP601 4.9 15.6 1.0 CB A:ASP177 4.9 14.8 1.0 O A:HOH911 5.0 47.5 1.0

S.D.Dick, S.Federico, S.M.Hughes, V.E.Pye, N.O'reilly, P.Cherepanov. Structural Basis For the Activation and Target Site Specificity of CDC7 Kinase Structure 2020.
ISSN: ISSN 0969-2126