Zinc 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
Magnesium	(Mg)	2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CDC7-DBF4 Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:20.1 occ:1.00 SG A:CYS351 2.3 18.9 1.0 SG A:CYS360 2.3 17.5 1.0 SG A:CYS353 2.3 18.8 1.0 SG A:CYS363 2.4 18.5 1.0 CB A:CYS353 3.1 15.5 1.0 CB A:CYS360 3.3 20.8 1.0 CB A:CYS363 3.3 17.1 1.0 CB A:CYS351 3.3 21.5 1.0 N A:CYS360 3.4 16.1 1.0 N A:CYS363 3.7 16.5 1.0 CA A:CYS360 3.8 17.2 1.0 N A:CYS353 4.0 22.4 1.0 O A:HOH918 4.1 34.6 1.0 CA A:CYS363 4.1 15.3 1.0 C A:VAL359 4.1 16.1 1.0 CA A:CYS353 4.2 18.1 1.0 C A:CYS360 4.3 15.9 1.0 O A:CYS360 4.3 14.7 1.0 O A:HOH913 4.5 34.7 1.0 CA A:VAL359 4.6 17.8 1.0 O B:HOH516 4.6 23.4 1.0 O A:HOH771 4.7 20.8 1.0 CA A:CYS351 4.7 24.0 1.0 CB A:ILE362 4.8 20.4 1.0 C A:ILE362 4.9 19.0 1.0 O A:VAL359 4.9 17.3 1.0 N A:ASP352 4.9 25.2 1.0 C A:CYS351 4.9 24.6 1.0 N A:ILE362 5.0 16.9 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of CDC7-DBF4 Bound to Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:31.4 occ:1.00 NE2 B:HIS309 2.0 33.6 1.0 ND1 B:HIS315 2.1 28.6 1.0 SG B:CYS296 2.2 33.8 1.0 SG B:CYS299 2.4 35.7 1.0 CE1 B:HIS309 2.9 40.5 1.0 CE1 B:HIS315 3.0 28.6 1.0 CG B:HIS315 3.1 28.3 1.0 CD2 B:HIS309 3.1 35.1 1.0 CB B:CYS296 3.2 36.9 1.0 CB B:CYS299 3.3 41.5 1.0 CB B:HIS315 3.4 32.6 1.0 N B:CYS299 3.8 33.0 1.0 CA B:HIS315 4.0 29.0 1.0 ND1 B:HIS309 4.1 36.9 1.0 NE2 B:HIS315 4.1 27.8 1.0 CG B:HIS309 4.2 35.7 1.0 CA B:CYS299 4.2 39.1 1.0 CD2 B:HIS315 4.2 29.3 1.0 CB B:CYS298 4.4 28.1 1.0 CA B:CYS296 4.6 38.6 1.0 C B:CYS298 4.7 36.9 1.0 N B:HIS315 4.7 32.6 1.0 CA B:CYS298 5.0 32.6 1.0 CG2 A:THR95 5.0 31.9 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