Chlorine 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:

Zinc

(Zn)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Minimal Construct of CDC7-DBF4 Bound to XL413, PDB code: 6ya6:
Jump to Chlorine binding site number: 1; 2;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl601 b:13.0 occ:1.00 CL A:0SX601 0.0 13.0 1.0 CAM A:0SX601 1.8 10.0 1.0 CAC A:0SX601 2.7 10.1 1.0 CAE A:0SX601 2.7 11.3 1.0 CD1 A:TYR136 3.4 15.4 1.0 O A:LEU137 3.5 14.0 1.0 N A:LEU137 3.6 13.4 1.0 CD1 A:LEU184 3.7 13.3 1.0 CE1 A:HIS139 3.8 20.3 1.0 CE1 A:TYR136 3.8 16.7 1.0 ND1 A:HIS139 4.0 19.2 1.0 CAQ A:0SX601 4.0 9.6 1.0 CD1 A:ILE64 4.0 19.5 1.0 CAD A:0SX601 4.0 12.3 1.0 CA A:TYR136 4.1 16.1 1.0 CG A:TYR136 4.2 16.0 1.0 CB A:ALA88 4.2 9.9 1.0 C A:LEU137 4.3 11.3 1.0 C A:TYR136 4.4 14.8 1.0 CA A:LEU137 4.5 14.1 1.0 CAP A:0SX601 4.5 11.3 1.0 CB A:TYR136 4.6 14.9 1.0 O A:HOH922 4.6 27.9 1.0 O A:PRO135 4.7 15.1 1.0 CB A:LEU137 4.8 15.2 1.0 CD2 A:LEU184 4.8 15.9 1.0 CZ A:TYR136 4.9 16.1 1.0 CG A:LEU184 4.9 13.7 1.0 NE2 A:HIS139 5.0 18.9 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl402 b:30.0 occ:1.00 NH1 B:ARG214 3.2 19.3 1.0 O A:HOH1043 3.2 35.9 1.0 NH2 B:ARG214 3.8 24.1 1.0 CE A:LYS358 3.8 32.4 1.0 CZ B:ARG214 3.9 20.5 1.0 CG2 A:THR356 4.0 17.8 1.0 CB A:THR356 4.1 14.1 1.0 NZ A:LYS358 4.3 37.2 1.0 O A:HOH934 4.5 33.4 1.0 O A:HOH740 4.6 31.0 1.0 CD A:LYS358 4.6 21.6 1.0 O A:HOH1064 4.7 38.2 1.0 OD1 A:ASP357 4.7 19.6 1.0 OG1 A:THR356 4.8 14.9 1.0 CG A:LYS358 4.9 17.7 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