Zinc in PDB 4f9b: Human CDC7 Kinase in Complex with DBF4 and PHA767491

All present enzymatic activity of Human CDC7 Kinase in Complex with DBF4 and PHA767491:
2.7.11.1;

The structure of Human CDC7 Kinase in Complex with DBF4 and PHA767491, PDB code: 4f9b 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)	59.54 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.920, 67.880, 238.160, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 23.9

The binding sites of Zinc atom in the Human CDC7 Kinase in Complex with DBF4 and PHA767491 (pdb code 4f9b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human CDC7 Kinase in Complex with DBF4 and PHA767491, PDB code: 4f9b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human CDC7 Kinase in Complex with DBF4 and PHA767491


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 PHA767491 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:71.9 occ:1.00 ND1 B:HIS315 2.1 59.5 1.0 NE2 B:HIS309 2.1 87.2 1.0 SG B:CYS299 2.3 84.0 1.0 SG B:CYS296 2.3 63.4 1.0 CG B:HIS315 2.9 69.5 1.0 CE1 B:HIS309 3.0 96.1 1.0 CB B:HIS315 3.1 74.5 1.0 CD2 B:HIS309 3.2 88.3 1.0 CE1 B:HIS315 3.2 65.5 1.0 CB B:CYS299 3.3 77.3 1.0 CB B:CYS296 3.4 68.4 1.0 CA B:HIS315 3.8 73.1 1.0 N B:CYS299 3.9 75.2 1.0 ND1 B:HIS309 4.1 92.9 1.0 CD2 B:HIS315 4.2 69.0 1.0 CA B:CYS299 4.2 75.4 1.0 CG B:HIS309 4.3 89.8 1.0 NE2 B:HIS315 4.3 67.3 1.0 CB B:CYS298 4.4 62.7 1.0 N B:HIS315 4.5 75.1 1.0 CA B:CYS296 4.8 70.2 1.0 CG2 A:THR95 4.8 58.0 1.0 C B:CYS298 4.9 73.5 1.0 C B:HIS315 5.0 75.0 1.0

Zinc binding site 2 out of 2 in the Human CDC7 Kinase in Complex with DBF4 and PHA767491


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human CDC7 Kinase in Complex with DBF4 and PHA767491 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:81.8 occ:1.00 NE2 D:HIS309 2.1 79.8 1.0 ND1 D:HIS315 2.2 89.4 1.0 SG D:CYS299 2.3 96.2 1.0 SG D:CYS296 2.3 74.5 1.0 CE1 D:HIS309 2.7 84.7 1.0 CG D:HIS315 3.1 98.0 1.0 CE1 D:HIS315 3.2 91.1 1.0 CB D:HIS315 3.3 98.3 1.0 CD2 D:HIS309 3.4 82.9 1.0 CB D:CYS299 3.4 99.0 1.0 CB D:CYS296 3.4 73.6 1.0 N D:CYS299 3.8 0.9 1.0 CA D:HIS315 3.9 0.8 1.0 ND1 D:HIS309 4.0 84.6 1.0 CA D:CYS299 4.2 0.5 1.0 CD2 D:HIS315 4.3 96.4 1.0 CB D:CYS298 4.3 86.0 1.0 NE2 D:HIS315 4.3 93.7 1.0 CG D:HIS309 4.3 82.1 1.0 N D:HIS315 4.6 0.1 1.0 C D:CYS298 4.8 89.7 1.0 CA D:CYS296 4.8 76.4 1.0 CA D:CYS298 4.9 85.1 1.0 O D:HIS309 4.9 77.3 1.0 N D:CYS298 5.0 79.7 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