Atomistry » Nickel » PDB 3a1f-3ds9 » 3njy
Atomistry »
  Nickel »
    PDB 3a1f-3ds9 »
      3njy »

Nickel in PDB 3njy: Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline

Protein crystallography data

The structure of Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline, PDB code: 3njy was solved by O.N.F.King, I.J.Clifton, M.Wang, D.J.Maloney, A.Jadhav, U.Oppermann, T.D.Heightman, A.Simeonov, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.68 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.550, 148.990, 56.910, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.6

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline (pdb code 3njy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline, PDB code: 3njy:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3njy

Go back to Nickel Binding Sites List in 3njy
Nickel binding site 1 out of 2 in the Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni501

b:50.2
occ:1.00
OAC A:8XQ360 2.2 36.5 1.0
OE2 A:GLU190 2.2 39.5 1.0
NAI A:8XQ360 2.3 48.7 1.0
O A:HOH508 2.3 45.4 1.0
NE2 A:HIS188 2.4 35.3 1.0
OE1 A:GLU190 2.7 31.7 1.0
CD A:GLU190 2.8 32.1 1.0
CAK A:8XQ360 2.9 40.9 1.0
CAN A:8XQ360 3.0 45.7 1.0
CAE A:8XQ360 3.3 49.1 1.0
CE1 A:HIS188 3.3 33.4 1.0
CD2 A:HIS188 3.3 33.0 1.0
NE2 A:HIS276 3.6 32.8 1.0
O A:HOH440 3.6 38.9 1.0
CAF A:8XQ360 4.3 41.4 1.0
CG A:GLU190 4.3 24.4 1.0
CE1 A:HIS276 4.3 33.4 1.0
CAM A:8XQ360 4.3 47.4 1.0
O A:HOH504 4.3 63.4 1.0
NZ A:LYS241 4.4 71.8 1.0
ND1 A:HIS188 4.4 30.3 1.0
O A:HOH381 4.5 32.7 1.0
CG A:HIS188 4.5 26.6 1.0
CAD A:8XQ360 4.6 48.4 1.0
CD2 A:HIS276 4.6 31.8 1.0
O A:HOH461 4.8 53.3 1.0
CE A:LYS241 4.8 63.4 1.0
CA A:GLU190 4.9 22.9 1.0
CAH A:8XQ360 5.0 47.9 1.0

Nickel binding site 2 out of 2 in 3njy

Go back to Nickel Binding Sites List in 3njy
Nickel binding site 2 out of 2 in the Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of JMJD2A Complexed with 5-Carboxy-8- Hydroxyquinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni501

b:46.5
occ:1.00
OAC B:8XQ360 2.0 30.3 1.0
NE2 B:HIS188 2.1 30.9 1.0
OE2 B:GLU190 2.2 45.3 1.0
NAI B:8XQ360 2.4 45.3 1.0
CAK B:8XQ360 2.8 36.0 1.0
O B:HOH466 2.9 47.2 1.0
CD B:GLU190 2.9 40.4 1.0
OE1 B:GLU190 2.9 40.2 1.0
CAN B:8XQ360 3.0 44.1 1.0
CE1 B:HIS188 3.1 32.0 1.0
CD2 B:HIS188 3.1 29.7 1.0
CAE B:8XQ360 3.4 45.2 1.0
NE2 B:HIS276 3.7 36.8 1.0
O B:HOH489 3.8 63.3 1.0
O B:HOH488 3.9 44.3 1.0
CAF B:8XQ360 4.1 35.6 1.0
ND1 B:HIS188 4.2 31.7 1.0
CE1 B:HIS276 4.3 35.0 1.0
CG B:HIS188 4.3 28.3 1.0
CG B:GLU190 4.3 34.7 1.0
CAM B:8XQ360 4.4 47.0 1.0
CAD B:8XQ360 4.7 45.1 1.0
O B:HOH406 4.8 36.2 1.0
CA B:GLU190 4.8 33.6 1.0
CD2 B:HIS276 4.8 35.5 1.0
NZ B:LYS241 4.9 64.3 1.0

Reference:

O.N.F.King, X.S.Li, M.Sakurai, A.Kawamura, N.R.Rose, S.S.Ng, A.M.Quinn, G.Rai, B.T.Mott, P.Beswick, R.J.Klose, U.Oppermann, A.Jadhav, T.D.Heightman, D.J.Maloney, C.J.Schofield, A.Simeonov. Quantitative High-Throughput Screening Identifies 8-Hydroxyquinolines As Cell-Active Histone Demethylase Inhibitors Plos One V. 5 E1553 2010.
ISSN: ESSN 1932-6203
PubMed: 21124847
DOI: 10.1371/JOURNAL.PONE.0015535
Page generated: Fri Sep 25 08:30:44 2020
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy