Zinc in PDB 4f99: Human CDC7 Kinase in Complex with DBF4 and Nucleotide

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

The structure of Human CDC7 Kinase in Complex with DBF4 and Nucleotide, PDB code: 4f99 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)	59.52 / 2.33
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.480, 61.480, 237.410, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.1

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

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Human CDC7 Kinase in Complex with DBF4 and Nucleotide (pdb code 4f99). 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 Nucleotide, PDB code: 4f99:

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


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 Nucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:64.5 occ:1.00 NE2 B:HIS309 2.1 69.7 1.0 ND1 B:HIS315 2.2 67.3 1.0 SG B:CYS296 2.3 66.5 1.0 SG B:CYS299 2.3 73.0 1.0 CE1 B:HIS309 2.6 66.2 1.0 CG B:HIS315 3.1 66.7 1.0 CE1 B:HIS315 3.1 67.4 1.0 CB B:CYS299 3.3 73.0 1.0 CB B:CYS296 3.3 71.0 1.0 CD2 B:HIS309 3.4 70.2 1.0 CB B:HIS315 3.4 63.0 1.0 N B:CYS299 3.8 72.7 1.0 ND1 B:HIS309 3.8 64.8 1.0 CA B:HIS315 4.0 62.5 1.0 CA B:CYS299 4.2 73.7 1.0 NE2 B:HIS315 4.2 69.0 1.0 CG B:HIS309 4.2 68.7 1.0 CD2 B:HIS315 4.3 69.5 1.0 CB B:CYS298 4.3 63.1 1.0 C B:CYS298 4.7 70.7 1.0 N B:HIS315 4.7 61.1 1.0 CA B:CYS296 4.8 69.7 1.0 CA B:CYS298 4.9 66.2 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