Atomistry » Nickel » PDB 5ph2-5pi5 » 5phk
Atomistry »
  Nickel »
    PDB 5ph2-5pi5 »
      5phk »

Nickel in PDB 5phk: Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09720A

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09720A, PDB code: 5phk 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) 29.44 / 1.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.502, 71.502, 150.880, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 16.4

Other elements in 5phk:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09720A also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09720A (pdb code 5phk). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09720A, PDB code: 5phk:

Nickel binding site 1 out of 1 in 5phk

Go back to Nickel Binding Sites List in 5phk
Nickel binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09720A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D in Complex with N09720A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:11.8
occ:0.81
OE1 A:GLU194 2.0 11.7 1.0
O2' A:OGA403 2.1 14.5 0.8
O1 A:OGA403 2.1 12.6 0.8
O A:HOH645 2.2 17.9 1.0
NE2 A:HIS280 2.2 11.6 1.0
NE2 A:HIS192 2.2 13.2 1.0
C2 A:OGA403 2.8 14.8 0.8
C1 A:OGA403 2.9 13.4 0.8
CE1 A:HIS280 3.0 11.7 1.0
CD A:GLU194 3.1 10.3 1.0
CE1 A:HIS192 3.1 13.1 1.0
CD2 A:HIS280 3.3 10.6 1.0
CD2 A:HIS192 3.3 12.4 1.0
OE2 A:GLU194 3.5 12.1 1.0
O2 A:OGA403 4.1 13.9 0.8
N1 A:OGA403 4.1 16.5 0.8
ND1 A:HIS280 4.2 9.5 1.0
ND1 A:HIS192 4.2 11.9 1.0
OG A:SER200 4.2 9.3 0.8
CG A:HIS280 4.4 8.5 1.0
CG A:HIS192 4.4 10.8 1.0
CG A:GLU194 4.4 9.8 1.0
O1 A:EDO411 4.4 18.4 0.4
O1 A:EDO411 4.7 38.8 0.6
O A:HOH837 4.8 49.3 1.0
CB A:SER200 4.8 10.6 0.2
OG A:SER200 4.8 11.5 0.2
C4 A:OGA403 4.8 18.3 0.8
CB A:SER200 4.8 9.5 0.8
C1 A:EDO411 4.9 20.1 0.4

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 01:42:51 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy