Atomistry » Zinc » PDB 5a0s-5a8a » 5a3p
Atomistry »
  Zinc »
    PDB 5a0s-5a8a »
      5a3p »

Zinc in PDB 5a3p: Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B).

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B)., PDB code: 5a3p was solved by R.Nowak, V.Srikannathasan, C.Johansson, C.Gileadi, C.Tallant, K.Kupinska, C.Strain-Damerell, A.Szykowska, F.Von Delft, N.A.Burgess-Brown, C.H.Arrowsmith, C.Bountra, A.M.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.56 / 2.01
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 141.788, 141.788, 152.272, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 22.4

Other elements in 5a3p:

The structure of Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B). also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B). (pdb code 5a3p). 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 the Catalytic Domain of Human PLU1 (JARID1B)., PDB code: 5a3p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5a3p

Go back to Zinc Binding Sites List in 5a3p
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B).


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 the Catalytic Domain of Human PLU1 (JARID1B). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1755

b:26.5
occ:1.00
ND1 A:HIS718 2.1 34.7 1.0
SG A:CYS692 2.1 24.8 1.0
SG A:CYS715 2.3 25.0 1.0
SG A:CYS695 2.4 25.8 1.0
CE1 A:HIS718 2.9 33.2 1.0
CB A:CYS692 3.1 23.5 1.0
CG A:HIS718 3.2 34.3 1.0
CB A:CYS695 3.4 25.1 1.0
CB A:CYS715 3.5 22.8 1.0
CB A:HIS718 3.7 29.1 1.0
N A:CYS695 3.8 27.6 1.0
N A:CYS715 3.9 23.5 1.0
NE2 A:HIS718 4.1 35.0 1.0
CA A:CYS695 4.2 29.2 1.0
CA A:CYS715 4.2 22.8 1.0
CD2 A:HIS718 4.3 36.6 1.0
CG2 A:THR697 4.4 26.9 1.0
N A:HIS718 4.6 29.3 1.0
CA A:CYS692 4.6 26.1 1.0
CB A:LYS694 4.6 30.7 1.0
O A:CYS715 4.7 23.6 1.0
C A:CYS715 4.7 23.1 1.0
CD A:ARG619 4.7 35.0 1.0
CB A:HIS717 4.8 29.3 1.0
CA A:HIS718 4.8 32.4 1.0
C A:CYS695 4.9 28.1 1.0
C A:LYS694 4.9 37.5 1.0

Zinc binding site 2 out of 2 in 5a3p

Go back to Zinc Binding Sites List in 5a3p
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human PLU1 (JARID1B).


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 the Catalytic Domain of Human PLU1 (JARID1B). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1756

b:52.5
occ:1.00
SG A:CYS723 2.3 39.0 1.0
CB A:CYS708 2.5 46.1 1.0
SG A:CYS706 2.5 36.4 1.0
SG A:CYS708 2.6 62.1 1.0
SG A:CYS725 2.7 44.4 1.0
CB A:CYS725 3.1 37.5 1.0
CB A:CYS723 3.3 37.4 1.0
CB A:CYS706 3.5 33.4 1.0
CA A:CYS708 3.8 47.0 1.0
N A:CYS725 4.0 40.5 1.0
N A:CYS708 4.1 41.2 1.0
CA A:CYS725 4.2 36.6 1.0
CE1 A:TYR730 4.3 37.1 1.0
C A:CYS708 4.4 49.1 1.0
N A:LYS709 4.5 44.6 1.0
CA A:CYS723 4.7 34.2 1.0
CG A:LYS709 4.7 49.4 1.0
CA A:CYS706 4.8 30.4 1.0
N A:SER724 4.8 40.8 1.0
C A:CYS723 4.9 36.1 1.0
C A:CYS706 4.9 34.3 1.0

Reference:

C.Johansson, S.Velupillai, A.Tumber, A.Szykowska, E.S.Hookway, R.P.Nowak, C.Strain-Damerell, C.Gileadi, M.Philpott, N.Burgess-Brown, N.Wu, J.Kopec, A.Nuzzi, H.Steuber, U.Egner, V.Badock, S.Munro, N.B.Lathangue, S.Westaway, J.Brown, N.Athanasou, R.Prinjha, P.E.Brennan, U.Oppermann. Structural Analysis of Human KDM5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. V. 12 539 2016.
ISSN: ISSN 1552-4450
PubMed: 27214403
DOI: 10.1038/NCHEMBIO.2087
Page generated: Wed Dec 16 06:01:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy