Zinc in PDB 6ya7: CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate

All present enzymatic activity of CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate:
2.7.11.1; 3.6.4.12;

The structure of CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate, PDB code: 6ya7 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)	60.20 / 1.67
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.280, 62.280, 234.790, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 18.5

The binding sites of Zinc atom in the CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate (pdb code 6ya7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate, PDB code: 6ya7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:15.7 occ:0.92 SG A:CYS353 2.3 17.7 1.0 SG A:CYS360 2.3 16.3 1.0 SG A:CYS351 2.4 18.0 1.0 SG A:CYS363 2.4 15.6 1.0 CB A:CYS353 3.1 19.9 1.0 CB A:CYS360 3.2 17.6 1.0 CB A:CYS351 3.3 17.9 1.0 CB A:CYS363 3.4 15.2 1.0 N A:CYS360 3.5 15.4 1.0 N A:CYS363 3.8 14.7 1.0 CA A:CYS360 3.8 15.1 1.0 N A:CYS353 4.0 17.0 1.0 CA A:CYS353 4.2 16.8 1.0 C A:VAL359 4.2 13.9 1.0 CA A:CYS363 4.2 13.8 1.0 C A:CYS360 4.3 15.0 1.0 O A:CYS360 4.3 16.4 1.0 O A:HOH934 4.4 32.2 1.0 O B:HOH536 4.4 26.0 1.0 O A:HOH955 4.4 26.0 1.0 CA A:VAL359 4.6 14.4 1.0 CA A:CYS351 4.7 20.7 1.0 CB A:ILE362 4.7 16.2 1.0 O B:HOH532 4.8 19.4 1.0 O A:VAL359 4.9 15.4 1.0 C A:ILE362 4.9 16.4 1.0 C A:CYS351 4.9 18.8 1.0 N A:ILE362 4.9 15.6 1.0 N A:ASP352 5.0 18.2 1.0

Zinc binding site 2 out of 4 in the CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:17.3 occ:0.69 O1A A:ADP604 1.8 28.4 1.0 OD2 A:ASP196 2.0 23.2 1.0 OD1 A:ASN182 2.1 15.6 1.0 S1G C:7O540 2.3 28.1 1.0 O A:HOH722 2.5 29.0 1.0 CG A:ASP196 2.9 21.1 1.0 CG A:ASN182 3.0 15.3 1.0 O1B A:ADP604 3.0 91.1 1.0 PA A:ADP604 3.1 23.4 1.0 C1S C:7O540 3.1 28.6 1.0 CB A:ASP196 3.2 12.8 1.0 O3B A:ADP604 3.2 93.8 1.0 ND2 A:ASN182 3.3 14.8 1.0 PB A:ADP604 3.5 85.8 1.0 O3A A:ADP604 3.6 51.2 1.0 O2A A:ADP604 3.8 21.9 1.0 OD1 A:ASP196 4.1 20.4 1.0 O5' A:ADP604 4.2 22.9 1.0 CB A:ASN182 4.4 11.5 1.0 O A:HOH701 4.4 85.2 1.0 C2S C:7O540 4.6 29.3 1.0 CA A:ASP196 4.7 13.1 1.0 C5' A:ADP604 4.7 20.9 1.0 O A:SER181 4.8 18.0 1.0 OD2 A:ASP177 4.8 19.6 1.0 CA A:ASN182 4.8 10.2 1.0 CE A:LYS179 4.9 14.3 1.0 OG A:SER181 5.0 22.1 1.0 O2B A:ADP604 5.0 96.0 1.0 O A:HOH757 5.0 28.2 1.0

Zinc binding site 3 out of 4 in the CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:61.6 occ:0.78 CE B:MET239 2.2 72.3 1.0 SG A:CYS449 2.2 37.0 1.0 CB A:CYS449 3.4 32.5 1.0 O A:LYS451 3.5 29.4 1.0 SD B:MET239 3.6 74.1 1.0 CG2 A:VAL453 4.1 23.7 1.0 CE A:MET428 4.3 32.0 1.0 CB A:SER433 4.5 17.3 1.0 CG1 A:VAL453 4.5 36.4 1.0 CB A:MET428 4.5 12.9 1.0 C A:LYS451 4.6 27.2 1.0 SD A:MET428 4.7 25.9 1.0 CA A:CYS449 4.8 17.5 1.0 CG2 B:VAL220 4.9 18.2 1.0 CB A:VAL453 5.0 32.0 1.0

Zinc binding site 4 out of 4 in the CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of CDC7-DBF4 Bound to An MCM2-S40 Derived Bivalent Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:19.6 occ:1.00 NE2 B:HIS309 2.1 19.9 1.0 ND1 B:HIS315 2.1 17.1 1.0 SG B:CYS296 2.3 15.8 1.0 SG B:CYS299 2.3 20.2 1.0 CE1 B:HIS309 3.0 23.9 1.0 CE1 B:HIS315 3.0 17.9 1.0 CD2 B:HIS309 3.1 17.4 1.0 CG B:HIS315 3.1 17.2 1.0 CB B:CYS296 3.2 15.4 1.0 CB B:CYS299 3.3 23.3 1.0 CB B:HIS315 3.5 17.8 1.0 N B:CYS299 3.8 19.1 1.0 CA B:HIS315 4.0 16.9 1.0 ND1 B:HIS309 4.1 23.3 1.0 CA B:CYS299 4.2 18.7 1.0 NE2 B:HIS315 4.2 15.5 1.0 CG B:HIS309 4.2 23.4 1.0 CD2 B:HIS315 4.2 15.2 1.0 CB B:CYS298 4.4 14.8 1.0 CA B:CYS296 4.6 17.6 1.0 C B:CYS298 4.8 19.4 1.0 N B:HIS315 4.8 20.6 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