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Zinc in PDB 2geq: Crystal Structure of A P53 Core Dimer Bound to Dna

Protein crystallography data

The structure of Crystal Structure of A P53 Core Dimer Bound to Dna, PDB code: 2geq was solved by W.C.Ho, M.X.Fitzgerald, R.Marmorstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.15 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.755, 94.290, 119.822, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 23.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A P53 Core Dimer Bound to Dna (pdb code 2geq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A P53 Core Dimer Bound to Dna, PDB code: 2geq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2geq

Go back to Zinc Binding Sites List in 2geq
Zinc binding site 1 out of 2 in the Crystal Structure of A P53 Core Dimer Bound to 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 A P53 Core Dimer Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:24.4
occ:1.00
ND1 A:HIS176 2.1 29.2 1.0
SG A:CYS239 2.3 30.4 1.0
SG A:CYS173 2.3 23.5 1.0
SG A:CYS235 2.5 30.2 1.0
CB A:CYS239 3.0 29.8 1.0
CE1 A:HIS176 3.0 27.8 1.0
CG A:HIS176 3.1 29.4 1.0
CB A:CYS173 3.4 22.5 1.0
CB A:CYS235 3.5 21.8 1.0
CB A:HIS176 3.5 29.4 1.0
CA A:CYS235 3.9 21.8 1.0
N A:CYS173 4.1 22.4 1.0
NE2 A:HIS176 4.1 27.2 1.0
CD2 A:HIS176 4.2 26.4 1.0
CA A:CYS173 4.3 23.2 1.0
N A:HIS176 4.3 29.2 1.0
CA A:CYS239 4.4 29.6 1.0
N A:ASN236 4.4 23.6 1.0
CA A:HIS176 4.6 31.4 1.0
O A:MET234 4.6 22.1 1.0
C A:CYS235 4.7 23.0 1.0
O A:CYS173 4.9 22.3 1.0
SD B:MET240 4.9 46.2 1.0
O A:HOH341 4.9 35.9 1.0
C A:CYS173 4.9 24.6 1.0

Zinc binding site 2 out of 2 in 2geq

Go back to Zinc Binding Sites List in 2geq
Zinc binding site 2 out of 2 in the Crystal Structure of A P53 Core Dimer Bound to 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 A P53 Core Dimer Bound to Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:28.9
occ:1.00
ND1 B:HIS176 2.1 26.2 1.0
SG B:CYS239 2.1 25.1 1.0
SG B:CYS173 2.3 24.4 1.0
SG B:CYS235 2.5 29.5 1.0
CE1 B:HIS176 3.0 27.7 1.0
CB B:CYS239 3.1 26.4 1.0
CG B:HIS176 3.1 27.7 1.0
CB B:CYS173 3.4 23.8 1.0
CB B:HIS176 3.5 28.7 1.0
CB B:CYS235 3.6 23.4 1.0
CA B:CYS235 4.0 22.3 1.0
N B:CYS173 4.0 20.0 1.0
NE2 B:HIS176 4.1 26.9 1.0
CD2 B:HIS176 4.2 26.2 1.0
CA B:CYS173 4.3 21.6 1.0
CA B:CYS239 4.4 25.9 1.0
N B:ASN236 4.4 22.8 1.0
N B:HIS176 4.5 28.7 1.0
O B:HOH340 4.5 54.8 1.0
O B:HOH352 4.6 41.4 1.0
O B:MET234 4.6 18.6 1.0
CA B:HIS176 4.7 30.9 1.0
C B:CYS235 4.7 22.8 1.0
O B:CYS173 4.8 23.1 1.0
C B:CYS173 4.9 22.8 1.0

Reference:

W.C.Ho, M.X.Fitzgerald, R.Marmorstein. Structure of the P53 Core Domain Dimer Bound to Dna. J.Biol.Chem. V. 281 20494 2006.
ISSN: ISSN 0021-9258
PubMed: 16717092
DOI: 10.1074/JBC.M603634200
Page generated: Wed Dec 16 03:29:25 2020

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