Chlorine in PDB 4ai9: JMJD2A Complexed with Daminozide

Protein crystallography data

The structure of JMJD2A Complexed with Daminozide, PDB code: 4ai9 was solved by R.Chowdhury, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.62 / 2.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.476, 149.752, 57.533, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 23.7

Other elements in 4ai9:

The structure of JMJD2A Complexed with Daminozide also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the JMJD2A Complexed with Daminozide (pdb code 4ai9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the JMJD2A Complexed with Daminozide, PDB code: 4ai9:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4ai9

Go back to Chlorine Binding Sites List in 4ai9
Chlorine binding site 1 out of 2 in the JMJD2A Complexed with Daminozide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of JMJD2A Complexed with Daminozide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:76.1
occ:1.00
N A:GLY229 3.2 49.6 1.0
CA A:PHE227 3.6 45.9 1.0
C A:PHE227 3.6 46.9 1.0
CA A:GLY229 3.7 49.6 1.0
N A:PRO228 3.8 48.1 1.0
N A:SER230 3.8 49.2 1.0
CD A:PRO228 3.9 47.9 1.0
CB A:PHE227 4.0 46.4 1.0
O A:PHE227 4.1 46.9 1.0
C A:PRO228 4.3 48.6 1.0
CG A:PRO228 4.3 47.6 1.0
C A:GLY229 4.3 49.7 1.0
OG A:SER230 4.4 49.4 1.0
CD1 A:PHE227 4.5 45.5 1.0
CA A:PRO228 4.5 48.1 1.0
CB A:SER230 4.8 47.1 1.0
CG A:PHE227 4.8 46.6 1.0
O A:PHE226 4.8 48.7 1.0
CA A:SER230 4.9 48.1 1.0
N A:PHE227 4.9 46.2 1.0

Chlorine binding site 2 out of 2 in 4ai9

Go back to Chlorine Binding Sites List in 4ai9
Chlorine binding site 2 out of 2 in the JMJD2A Complexed with Daminozide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of JMJD2A Complexed with Daminozide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:86.0
occ:1.00
CA B:PHE227 3.4 37.7 1.0
N B:GLY229 3.6 38.7 1.0
C B:PHE227 3.6 37.0 1.0
N B:SER230 3.7 40.2 1.0
CB B:PHE227 3.7 37.6 1.0
CD1 B:PHE227 3.9 38.3 1.0
N B:PRO228 4.0 37.3 1.0
CA B:GLY229 4.0 40.7 1.0
OG B:SER230 4.0 40.0 1.0
O B:PHE227 4.0 36.8 1.0
CG B:PHE227 4.3 37.8 1.0
CD B:PRO228 4.3 37.2 1.0
C B:GLY229 4.4 40.6 1.0
C B:PRO228 4.5 39.3 1.0
CB B:SER230 4.5 36.8 1.0
O B:PHE226 4.7 39.2 1.0
CA B:SER230 4.7 38.7 1.0
CG B:PRO228 4.7 35.2 1.0
N B:PHE227 4.8 37.9 1.0
CA B:PRO228 4.8 38.3 1.0

Reference:

N.R.Rose, E.C.Woon, A.Tumber, L.J.Walport, R.Chowdhury, X.S.Li, O.N.King, C.Lejeune, S.S.Ng, T.Krojer, M.C.Chan, A.M.Rydzik, R.J.Hopkinson, K.H.Che, M.Daniel, C.Strain-Damerell, C.Gileadi, G.Kochan, I.K.Leung, J.Dunford, K.K.Yeoh, P.J.Ratcliffe, N.Burgess-Brown, F.Von Delft, S.Muller, B.Marsden, P.E.Brennan, M.A.Mcdonough, U.Oppermann, R.J.Klose, C.J.Schofield, A.Kawamura. Plant Growth Regulator Daminozide Is A Selective Inhibitor of Human KDM2/7 Histone Demethylases. J. Med. Chem. V. 55 6639 2012.
ISSN: ISSN 1520-4804
PubMed: 22724510
DOI: 10.1021/JM300677J
Page generated: Sat Dec 12 10:23:38 2020

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