Zinc in PDB 4f9c: Human CDC7 Kinase in Complex with DBF4 and XL413

All present enzymatic activity of Human CDC7 Kinase in Complex with DBF4 and XL413:
2.7.11.1;

The structure of Human CDC7 Kinase in Complex with DBF4 and XL413, PDB code: 4f9c was solved by S.Hughes, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.74 / 2.08
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.270, 61.270, 238.940, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.9

The structure of Human CDC7 Kinase in Complex with DBF4 and XL413 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Human CDC7 Kinase in Complex with DBF4 and XL413 (pdb code 4f9c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Human CDC7 Kinase in Complex with DBF4 and XL413, PDB code: 4f9c:

Zinc binding site 1 out of 1 in the Human CDC7 Kinase in Complex with DBF4 and XL413


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human CDC7 Kinase in Complex with DBF4 and XL413 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:56.1 occ:1.00 NE2 B:HIS309 2.2 64.3 1.0 ND1 B:HIS315 2.2 63.4 1.0 SG B:CYS299 2.3 66.2 1.0 SG B:CYS296 2.4 58.7 1.0 CE1 B:HIS309 2.8 64.2 1.0 CE1 B:HIS315 3.1 64.5 1.0 CG B:HIS315 3.2 66.0 1.0 CD2 B:HIS309 3.3 67.0 1.0 CB B:CYS299 3.3 62.7 1.0 CB B:CYS296 3.4 58.9 1.0 CB B:HIS315 3.5 64.9 1.0 N B:CYS299 3.8 60.9 1.0 ND1 B:HIS309 4.0 63.8 1.0 CA B:HIS315 4.0 65.5 1.0 CA B:CYS299 4.2 64.3 1.0 CG B:HIS309 4.2 64.7 1.0 NE2 B:HIS315 4.3 66.2 1.0 CB B:CYS298 4.3 53.7 1.0 CD2 B:HIS315 4.3 66.1 1.0 N B:HIS315 4.7 64.9 1.0 C B:CYS298 4.7 58.6 1.0 CA B:CYS296 4.8 59.7 1.0 CA B:CYS298 4.9 55.8 1.0 O B:HIS309 4.9 61.3 1.0

S.Hughes, F.Elustondo, A.Di Fonzo, F.G.Leroux, A.C.Wong, A.P.Snijders, S.J.Matthews, P.Cherepanov. Crystal Structure of Human CDC7 Kinase in Complex with Its Activator DBF4. Nat.Struct.Mol.Biol. V. 19 1101 2012.
ISSN: ISSN 1545-9993
PubMed: 23064647
DOI: 10.1038/NSMB.2404