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Zinc 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
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 4ai9

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of JMJD2A Complexed with Daminozide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:39.4
occ:1.00
NE2 A:HIS240 2.3 34.6 1.0
SG A:CYS234 2.3 44.8 1.0
SG A:CYS306 2.4 34.8 1.0
SG A:CYS308 2.5 45.3 1.0
CE1 A:HIS240 3.2 33.8 1.0
CB A:CYS234 3.2 47.7 1.0
CD2 A:HIS240 3.3 32.0 1.0
N A:CYS308 3.4 54.1 1.0
CB A:CYS308 3.5 52.5 1.0
CB A:CYS306 3.5 39.7 1.0
N A:SER307 3.9 46.3 1.0
CA A:CYS306 3.9 41.5 1.0
CA A:CYS308 3.9 55.2 1.0
C A:CYS306 4.1 43.4 1.0
N A:ARG309 4.3 60.6 1.0
ND1 A:HIS240 4.3 34.2 1.0
C A:CYS308 4.4 58.0 1.0
CG A:HIS240 4.4 32.4 1.0
C A:SER307 4.5 53.5 1.0
CA A:CYS234 4.5 48.8 1.0
CG A:ARG309 4.5 64.9 1.0
O A:ALA236 4.6 35.3 1.0
O A:HOH2196 4.7 49.5 1.0
CA A:SER307 4.8 51.0 1.0
C A:ALA236 4.9 38.1 1.0
CD A:ARG309 4.9 65.7 1.0
CA A:PHE237 4.9 33.9 1.0
O A:CYS306 5.0 41.6 1.0

Zinc binding site 2 out of 2 in 4ai9

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of JMJD2A Complexed with Daminozide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:33.3
occ:1.00
NE2 B:HIS240 2.2 37.0 1.0
SG B:CYS306 2.3 36.9 1.0
SG B:CYS234 2.4 39.9 1.0
SG B:CYS308 2.5 42.9 1.0
CE1 B:HIS240 3.1 33.4 1.0
CD2 B:HIS240 3.2 32.4 1.0
CB B:CYS234 3.2 40.6 1.0
CB B:CYS306 3.5 37.1 1.0
N B:CYS308 3.5 47.6 1.0
CB B:CYS308 3.5 46.7 1.0
CA B:CYS306 3.9 38.3 1.0
CA B:CYS308 3.9 48.6 1.0
N B:SER307 4.0 41.6 1.0
C B:CYS306 4.2 40.0 1.0
N B:ARG309 4.2 55.6 1.0
ND1 B:HIS240 4.3 33.1 1.0
CG B:HIS240 4.3 30.4 1.0
CG B:ARG309 4.3 62.3 1.0
C B:CYS308 4.3 51.8 1.0
CA B:CYS234 4.5 42.4 1.0
C B:SER307 4.6 46.6 1.0
O B:HOH2258 4.7 49.2 1.0
O B:HOH2216 4.7 51.4 1.0
CD B:ARG309 4.8 62.7 1.0
O B:ALA236 4.8 30.3 1.0
CA B:SER307 4.9 44.2 1.0
CB B:ARG309 5.0 60.4 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: Wed Dec 16 05:03:13 2020

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