Zinc in PDB 6ya6: Minimal Construct of CDC7-DBF4 Bound to XL413

All present enzymatic activity of Minimal Construct of CDC7-DBF4 Bound to XL413:
2.7.11.1;

The structure of Minimal Construct of CDC7-DBF4 Bound to XL413, PDB code: 6ya6 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)	42.85 / 1.44
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.640, 61.640, 233.910, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.3

The structure of Minimal Construct of CDC7-DBF4 Bound to XL413 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Minimal Construct of CDC7-DBF4 Bound to XL413 (pdb code 6ya6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Minimal Construct of CDC7-DBF4 Bound to XL413, PDB code: 6ya6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Minimal Construct of CDC7-DBF4 Bound to XL413


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Minimal Construct of CDC7-DBF4 Bound to XL413 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:13.0 occ:1.00 SG A:CYS353 2.3 12.6 1.0 SG A:CYS351 2.3 13.4 1.0 SG A:CYS360 2.3 12.2 1.0 SG A:CYS363 2.4 11.8 1.0 CB A:CYS353 3.1 12.7 1.0 CB A:CYS360 3.3 10.5 1.0 CB A:CYS351 3.3 16.2 1.0 CB A:CYS363 3.4 10.3 1.0 N A:CYS360 3.5 11.0 1.0 N A:CYS363 3.8 10.7 1.0 CA A:CYS360 3.8 10.5 1.0 N A:CYS353 4.0 11.4 1.0 CA A:CYS353 4.1 13.5 1.0 CA A:CYS363 4.2 11.2 1.0 C A:VAL359 4.2 11.1 1.0 O A:CYS360 4.3 12.0 1.0 C A:CYS360 4.3 11.1 1.0 O B:HOH524 4.4 14.9 1.0 O A:HOH1016 4.5 21.8 1.0 CA A:CYS351 4.7 13.4 1.0 CA A:VAL359 4.7 13.7 1.0 O A:HOH805 4.7 12.9 1.0 CB A:ILE362 4.8 14.3 1.0 N A:ASP352 4.9 15.0 1.0 C A:CYS351 4.9 14.1 1.0 C A:ILE362 4.9 13.2 1.0 N A:ILE362 4.9 11.8 1.0 O A:VAL359 4.9 12.5 1.0

Zinc binding site 2 out of 2 in the Minimal Construct of CDC7-DBF4 Bound to XL413


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Minimal Construct of CDC7-DBF4 Bound to XL413 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:23.9 occ:1.00 NE2 B:HIS309 2.0 27.4 1.0 ND1 B:HIS315 2.0 19.9 1.0 SG B:CYS296 2.3 21.8 1.0 SG B:CYS299 2.3 24.5 1.0 CE1 B:HIS309 2.9 31.9 1.0 CG B:HIS315 3.0 17.4 1.0 CE1 B:HIS315 3.0 19.1 1.0 CD2 B:HIS309 3.1 27.6 1.0 CB B:CYS296 3.2 22.5 1.0 CB B:HIS315 3.3 18.7 1.0 CB B:CYS299 3.3 23.4 1.0 N B:CYS299 3.9 21.4 1.0 CA B:HIS315 3.9 18.9 1.0 ND1 B:HIS309 4.0 32.0 1.0 NE2 B:HIS315 4.1 18.4 1.0 CD2 B:HIS315 4.1 19.4 1.0 CG B:HIS309 4.2 31.8 1.0 CA B:CYS299 4.3 24.8 1.0 CB B:CYS298 4.4 19.6 1.0 CA B:CYS296 4.6 24.9 1.0 N B:HIS315 4.7 23.4 1.0 C B:CYS298 4.9 27.4 1.0 CG2 A:THR95 5.0 21.5 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