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Zinc in PDB 2wbu: Crystal Structure of the Zinc Finger Domain of KLF4 Bound to Its Target Dna

Protein crystallography data

The structure of Crystal Structure of the Zinc Finger Domain of KLF4 Bound to Its Target Dna, PDB code: 2wbu was solved by A.Schuetz, G.Zocher, D.Carstanjen, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.93 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 50.275, 50.275, 131.027, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 27.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Zinc Finger Domain of KLF4 Bound to Its Target Dna (pdb code 2wbu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Zinc Finger Domain of KLF4 Bound to Its Target Dna, PDB code: 2wbu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2wbu

Go back to Zinc Binding Sites List in 2wbu
Zinc binding site 1 out of 3 in the Crystal Structure of the Zinc Finger Domain of KLF4 Bound to Its Target Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Zinc Finger Domain of KLF4 Bound to Its Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1484

b:34.6
occ:1.00
NE2 A:HIS478 1.8 20.5 1.0
NE2 A:HIS482 2.1 24.2 1.0
SG A:CYS465 2.1 18.4 1.0
SG A:CYS462 2.1 12.1 1.0
CE1 A:HIS478 2.6 21.1 1.0
CD2 A:HIS478 3.0 17.6 1.0
CD2 A:HIS482 3.0 21.3 1.0
CE1 A:HIS482 3.1 22.2 1.0
CB A:CYS462 3.2 14.8 1.0
CB A:CYS465 3.4 17.2 1.0
N A:CYS465 3.6 16.7 1.0
ND1 A:HIS478 3.8 20.2 1.0
CG A:HIS478 4.0 17.9 1.0
CA A:CYS465 4.0 17.4 1.0
C A:LYS464 4.1 15.9 1.0
CG A:HIS482 4.2 22.7 1.0
ND1 A:HIS482 4.2 21.0 1.0
CB A:LYS464 4.5 15.2 1.0
CA A:CYS462 4.6 14.8 1.0
CA A:LYS464 4.7 15.0 1.0
C A:CYS465 4.7 18.6 1.0
O A:LYS464 4.7 15.2 1.0
N A:LYS464 4.7 14.6 1.0
CB A:ARG467 5.0 20.6 1.0
O A:CYS465 5.0 18.9 1.0

Zinc binding site 2 out of 3 in 2wbu

Go back to Zinc Binding Sites List in 2wbu
Zinc binding site 2 out of 3 in the Crystal Structure of the Zinc Finger Domain of KLF4 Bound to Its Target Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Zinc Finger Domain of KLF4 Bound to Its Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1485

b:32.3
occ:1.00
NE2 A:HIS454 2.1 17.7 1.0
SG A:CYS432 2.1 11.7 1.0
SG A:CYS437 2.2 13.3 1.0
NE2 A:HIS450 2.2 19.7 1.0
CD2 A:HIS450 2.9 16.2 1.0
CD2 A:HIS454 3.0 16.1 1.0
CE1 A:HIS454 3.1 17.1 1.0
CB A:CYS437 3.2 14.1 1.0
CB A:CYS432 3.2 13.2 1.0
CE1 A:HIS450 3.4 18.3 1.0
CB A:TRP434 3.8 15.6 1.0
CG A:HIS450 4.1 17.8 1.0
CG A:HIS454 4.1 18.1 1.0
ND1 A:HIS454 4.2 17.2 1.0
ND1 A:HIS450 4.3 18.7 1.0
O A:HOH2001 4.4 25.6 1.0
CB A:TRP439 4.4 18.7 1.0
CG A:TRP434 4.6 15.7 1.0
CA A:CYS437 4.6 14.7 1.0
CA A:CYS432 4.7 13.8 1.0
N A:TRP439 4.9 17.8 1.0
CD1 A:TRP439 5.0 21.1 1.0
N A:TRP434 5.0 15.7 1.0

Zinc binding site 3 out of 3 in 2wbu

Go back to Zinc Binding Sites List in 2wbu
Zinc binding site 3 out of 3 in the Crystal Structure of the Zinc Finger Domain of KLF4 Bound to Its Target Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Zinc Finger Domain of KLF4 Bound to Its Target Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1486

b:40.7
occ:1.00
NE2 A:HIS420 2.0 23.7 1.0
NE2 A:HIS424 2.1 28.0 1.0
SG A:CYS402 2.1 25.3 1.0
SG A:CYS407 2.2 31.7 1.0
CB A:CYS407 2.8 33.5 1.0
CD2 A:HIS424 3.0 24.1 1.0
CE1 A:HIS420 3.0 24.6 1.0
CD2 A:HIS420 3.0 21.8 1.0
CB A:CYS402 3.2 31.0 1.0
CE1 A:HIS424 3.2 27.1 1.0
ND1 A:HIS420 4.1 23.0 1.0
CG A:HIS420 4.1 24.6 1.0
CG A:HIS424 4.2 23.8 1.0
ND1 A:HIS424 4.2 25.6 1.0
O A:CYS402 4.3 33.6 1.0
CA A:CYS407 4.3 34.0 1.0
CA A:CYS402 4.5 31.7 1.0
CD A:LYS409 4.5 34.8 1.0
CB A:LYS409 4.6 32.7 1.0
C A:CYS402 4.7 32.6 1.0
CB A:TYR404 4.7 34.4 1.0
O A:TYR404 4.9 35.7 1.0
OG1 A:THR423 5.0 23.9 1.0

Reference:

A.Schuetz, D.Nana, C.Rose, G.Zocher, M.Milanovic, J.Koenigsmann, R.Blasig, U.Heinemann, D.Carstanjen. The Structure of the KLF4 Dna-Binding Domain Links to Self-Renewal and Macrophage Differentiation. Cell.Mol.Life Sci. V. 68 3121 2011.
ISSN: ISSN 1420-682X
PubMed: 21290164
DOI: 10.1007/S00018-010-0618-X
Page generated: Wed Dec 16 03:57:20 2020

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