Magnesium 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:

Fluorine	(F)	3 atoms
Zinc	(Zn)	2 atoms

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

Magnesium binding site 1 out of 2 in the CDC7-DBF4 Bound to Adp-BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of CDC7-DBF4 Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:15.5 occ:1.00 O1A A:ADP601 2.0 13.9 1.0 F3 A:BEF603 2.0 16.6 1.0 O1B A:ADP601 2.1 13.7 1.0 O A:HOH827 2.1 14.4 1.0 OD2 A:ASP196 2.1 15.7 1.0 OD1 A:ASN182 2.1 13.2 1.0 BE A:BEF603 2.4 20.2 1.0 CG A:ASN182 3.0 14.1 1.0 CG A:ASP196 3.2 16.4 1.0 PB A:ADP601 3.2 18.6 1.0 PA A:ADP601 3.2 16.0 1.0 ND2 A:ASN182 3.3 13.6 1.0 F2 A:BEF603 3.4 19.8 1.0 O3A A:ADP601 3.5 15.6 1.0 CB A:ASP196 3.7 14.8 1.0 F1 A:BEF603 3.7 20.0 1.0 O3B A:ADP601 3.7 17.3 1.0 MG A:MG604 3.8 16.7 1.0 O A:HOH883 3.8 24.0 1.0 OD1 A:ASP196 4.2 16.1 1.0 O2A A:ADP601 4.3 14.3 1.0 O5' A:ADP601 4.3 16.0 1.0 O3' A:ADP601 4.4 18.7 1.0 C5' A:ADP601 4.4 14.3 1.0 CB A:ASN182 4.4 14.4 1.0 O2B A:ADP601 4.5 21.1 1.0 OG A:SER181 4.5 21.3 1.0 CE A:LYS179 4.6 17.2 1.0 O A:HOH749 4.6 24.1 1.0 OD2 A:ASP177 4.6 17.1 1.0 O A:HOH807 4.7 28.8 1.0 O A:HOH808 4.7 17.1 1.0 O A:SER181 4.7 14.5 1.0 CA A:ASN182 4.8 12.8 1.0 C3' A:ADP601 4.8 14.9 1.0 NZ A:LYS179 4.9 27.5 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of CDC7-DBF4 Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:16.7 occ:1.00 F1 A:BEF603 1.8 20.0 1.0 O A:HOH808 2.1 17.1 1.0 OD1 A:ASP196 2.1 16.1 1.0 OD2 A:ASP196 2.1 15.7 1.0 O3B A:ADP601 2.1 17.3 1.0 O A:HOH870 2.1 18.8 1.0 CG A:ASP196 2.4 16.4 1.0 BE A:BEF603 2.6 20.2 1.0 PB A:ADP601 3.2 18.6 1.0 O1B A:ADP601 3.4 13.7 1.0 F3 A:BEF603 3.6 16.6 1.0 O A:HOH930 3.7 34.2 1.0 MG A:MG602 3.8 15.5 1.0 F2 A:BEF603 3.8 19.8 1.0 CB A:ASP196 3.9 14.8 1.0 OD2 A:ASP177 4.1 17.1 1.0 O A:HOH864 4.1 20.9 1.0 NZ A:LYS90 4.2 14.9 1.0 O3A A:ADP601 4.2 15.6 1.0 O2B A:ADP601 4.3 21.1 1.0 N A:GLY198 4.5 15.7 1.0 O A:HOH749 4.6 24.1 1.0 CA A:GLY198 4.6 18.5 1.0 O A:HOH800 4.6 14.7 1.0 O1A A:ADP601 4.6 13.9 1.0 O A:ASP196 4.7 14.8 1.0 O A:HOH901 4.7 22.2 1.0 CA A:ASP196 4.7 16.4 1.0 CG A:LEU199 4.8 21.8 1.0 C A:ASP196 4.8 16.4 1.0 PA A:ADP601 4.8 16.0 1.0 N A:LEU199 4.9 14.5 1.0 O A:HOH799 4.9 28.1 1.0 ND2 A:ASN182 4.9 13.6 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