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Zinc in PDB 5pk5: Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 90)

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 90), PDB code: 5pk5 was solved by N.M.Pearce, T.Krojer, R.Talon, A.R.Bradley, M.Fairhead, R.Sethi, N.Wright, E.Maclean, P.Collins, J.Brandao-Neto, A.Douangamath, Z.Renjie, A.Dias, M.Vollmar, J.Ng, A.Szykowska, N.Burgess-Brown, P.E.Brennan, O.Cox, U.Oppermann, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.39 / 1.39
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.407, 71.407, 150.239, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 17.7

Other elements in 5pk5:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 90) also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 90) (pdb code 5pk5). 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 Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 90), PDB code: 5pk5:

Zinc binding site 1 out of 1 in 5pk5

Go back to Zinc Binding Sites List in 5pk5
Zinc binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 90)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 90) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:17.0
occ:0.92
NE2 A:HIS244 2.1 13.7 1.0
SG A:CYS310 2.3 20.7 1.0
SG A:CYS312 2.3 19.6 1.0
SG A:CYS238 2.4 18.7 1.0
CE1 A:HIS244 3.1 15.1 1.0
CD2 A:HIS244 3.1 15.2 1.0
CB A:CYS238 3.1 19.2 1.0
CB A:CYS312 3.4 22.4 1.0
CB A:CYS310 3.4 19.6 1.0
N A:CYS312 3.9 26.7 1.0
CA A:CYS310 4.0 19.6 1.0
CA A:CYS312 4.1 25.0 1.0
ND1 A:HIS244 4.2 16.2 1.0
CG A:HIS244 4.2 14.6 1.0
CB A:GLU314 4.3 31.9 1.0
N A:GLU314 4.4 30.4 1.0
O A:HOH544 4.4 36.2 1.0
CA A:CYS238 4.5 21.2 1.0
N A:GLY313 4.6 29.7 1.0
C A:CYS312 4.6 24.7 1.0
C A:CYS310 4.6 24.4 1.0
N A:SER311 4.7 27.9 1.0
O A:HOH830 4.7 30.9 1.0
N A:ALA315 4.7 30.2 1.0
O A:ALA240 4.7 15.6 1.0
CA A:PHE241 4.8 14.3 1.0
CA A:GLU314 4.8 33.1 1.0
C A:ALA240 5.0 16.1 1.0

Reference:

N.M.Pearce, T.Krojer, A.R.Bradley, P.Collins, R.P.Nowak, R.Talon, B.D.Marsden, S.Kelm, J.Shi, C.M.Deane, F.Von Delft. A Multi-Crystal Method For Extracting Obscured Crystallographic States From Conventionally Uninterpretable Electron Density. Nat Commun V. 8 15123 2017.
ISSN: ESSN 2041-1723
PubMed: 28436492
DOI: 10.1038/NCOMMS15123
Page generated: Mon Oct 28 02:18:31 2024

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