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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 6ya7

Go back to Zinc Binding Sites List in 6ya7
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 6ya7

Go back to Zinc Binding Sites List in 6ya7
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 6ya7

Go back to Zinc Binding Sites List in 6ya7
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 6ya7

Go back to Zinc Binding Sites List in 6ya7
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

Reference:

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
Page generated: Wed Dec 16 13:15:36 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy