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Zinc in PDB 9fzb: Human P53 Dna-Binding Domain Bound to Darpin C10-H82R

Protein crystallography data

The structure of Human P53 Dna-Binding Domain Bound to Darpin C10-H82R, PDB code: 9fzb was solved by B.Yuksel, D.I.Balourdas, P.Muenick, S.Knapp, V.Doetsch, A.C.Joerger, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.00 / 1.44
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.713, 94.011, 53.17, 90, 110.11, 90
R / Rfree (%) 15.4 / 18.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Human P53 Dna-Binding Domain Bound to Darpin C10-H82R (pdb code 9fzb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Human P53 Dna-Binding Domain Bound to Darpin C10-H82R, PDB code: 9fzb:

Zinc binding site 1 out of 1 in 9fzb

Go back to Zinc Binding Sites List in 9fzb
Zinc binding site 1 out of 1 in the Human P53 Dna-Binding Domain Bound to Darpin C10-H82R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human P53 Dna-Binding Domain Bound to Darpin C10-H82R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:22.6
occ:1.00
ND1 A:HIS179 2.0 23.0 1.0
SG A:CYS238 2.3 21.8 1.0
SG A:CYS176 2.3 23.0 1.0
SG A:CYS242 2.3 22.3 1.0
CE1 A:HIS179 3.0 24.2 1.0
CG A:HIS179 3.1 24.0 1.0
CB A:CYS242 3.2 22.1 1.0
CB A:CYS238 3.3 19.9 1.0
CB A:CYS176 3.4 23.1 1.0
CB A:HIS179 3.5 22.7 1.0
CA A:CYS238 3.8 19.2 1.0
N A:CYS176 3.9 21.2 1.0
NE2 A:HIS179 4.1 25.8 1.0
O A:HOH594 4.1 44.2 1.0
CD2 A:HIS179 4.2 25.4 1.0
CA A:CYS176 4.3 22.5 1.0
N A:ASN239 4.5 20.1 1.0
N A:HIS179 4.5 25.6 1.0
CA A:CYS242 4.6 21.8 1.0
O A:HOH494 4.6 24.6 1.0
CA A:HIS179 4.6 24.6 1.0
O A:MET237 4.7 22.9 1.0
C A:CYS238 4.7 19.7 1.0
O A:CYS176 4.9 22.3 1.0
C A:CYS176 4.9 22.5 1.0
N A:CYS238 5.0 18.4 1.0

Reference:

P.Munick, A.Strubel, D.I.Balourdas, J.S.Funk, M.Mernberger, C.Osterburg, B.Dreier, J.V.Schaefer, M.Tuppi, B.Yuksel, B.Schafer, S.Knapp, A.Pluckthun, T.Stiewe, A.C.Joerger, V.Dotsch. Darpin-Induced Reactivation of P53 in Hpv-Positive Cells. Nat.Struct.Mol.Biol. 2025.
ISSN: ESSN 1545-9985
PubMed: 39789211
DOI: 10.1038/S41594-024-01456-7
Page generated: Fri Aug 22 17:44:50 2025

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