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Zinc in PDB 5pi3: Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 16)

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 16), PDB code: 5pi3 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 / 1.29
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.414, 71.414, 150.356, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 17.8

Other elements in 5pi3:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 16) 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 16) (pdb code 5pi3). 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 16), PDB code: 5pi3:

Zinc binding site 1 out of 1 in 5pi3

Go back to Zinc Binding Sites List in 5pi3
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 16)


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 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.4
occ:0.92
NE2 A:HIS244 2.1 12.8 1.0
SG A:CYS310 2.3 19.7 1.0
SG A:CYS312 2.3 18.9 1.0
SG A:CYS238 2.4 17.9 1.0
CE1 A:HIS244 3.1 13.8 1.0
CD2 A:HIS244 3.1 15.0 1.0
CB A:CYS238 3.2 19.1 1.0
CB A:CYS312 3.4 21.2 1.0
CB A:CYS310 3.5 20.8 1.0
N A:CYS312 3.9 23.6 1.0
CA A:CYS310 4.1 19.8 1.0
CA A:CYS312 4.2 23.4 1.0
ND1 A:HIS244 4.2 14.8 1.0
CG A:HIS244 4.2 13.7 1.0
CB A:GLU314 4.3 30.0 1.0
O A:HOH636 4.3 27.7 1.0
N A:GLU314 4.4 27.2 1.0
CA A:CYS238 4.5 20.0 1.0
N A:SER311 4.6 23.3 1.0
C A:CYS312 4.7 22.3 1.0
C A:CYS310 4.7 22.1 1.0
N A:GLY313 4.7 25.9 1.0
N A:ALA315 4.7 27.1 1.0
O A:HOH833 4.7 31.7 1.0
O A:ALA240 4.7 14.9 1.0
CA A:PHE241 4.8 13.5 1.0
CA A:GLU314 4.8 31.5 1.0
C A:ALA240 5.0 14.7 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: Wed Dec 16 06:40:07 2020

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