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Nickel 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:

Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms

Nickel Binding Sites:

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

Nickel binding site 1 out of 2 in 4ai9

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


Mono view


Stereo pair view

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

b:42.5
occ:1.00
OE2 A:GLU190 2.1 39.2 1.0
NE2 A:HIS188 2.2 25.6 1.0
O01 A:DZA605 2.3 55.5 1.0
NE2 A:HIS276 2.3 31.5 1.0
N04 A:DZA605 2.3 61.7 1.0
O A:HOH2159 2.6 53.9 1.0
C05 A:DZA605 2.8 59.0 1.0
C02 A:DZA605 3.0 58.4 1.0
CE1 A:HIS188 3.0 27.8 1.0
N03 A:DZA605 3.0 60.2 1.0
CD A:GLU190 3.1 36.8 1.0
CE1 A:HIS276 3.2 29.7 1.0
C06 A:DZA605 3.2 63.1 1.0
CD2 A:HIS188 3.2 25.8 1.0
CD2 A:HIS276 3.3 29.1 1.0
OE1 A:GLU190 3.5 35.1 1.0
ND1 A:HIS188 4.2 26.9 1.0
CG A:HIS188 4.3 24.1 1.0
ND1 A:HIS276 4.4 28.9 1.0
O A:HOH2069 4.4 52.9 1.0
CG A:HIS276 4.5 26.9 1.0
C07 A:DZA605 4.5 59.4 1.0
CG A:GLU190 4.5 34.7 1.0
OG A:SER196 4.6 36.8 1.0

Nickel binding site 2 out of 2 in 4ai9

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


Mono view


Stereo pair view

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

b:37.3
occ:1.00
NE2 B:HIS276 2.1 26.6 1.0
OE2 B:GLU190 2.1 31.2 1.0
O01 B:DZA603 2.2 65.0 1.0
N04 B:DZA603 2.2 68.2 1.0
NE2 B:HIS188 2.3 27.2 1.0
O B:HOH2182 2.5 33.8 1.0
C06 B:DZA603 2.6 66.1 1.0
C02 B:DZA603 2.8 68.9 1.0
N03 B:DZA603 2.9 68.8 1.0
CE1 B:HIS188 3.0 28.6 1.0
CE1 B:HIS276 3.0 22.5 1.0
CD2 B:HIS276 3.1 23.7 1.0
C05 B:DZA603 3.2 67.6 1.0
CD B:GLU190 3.3 29.1 1.0
CD2 B:HIS188 3.4 27.8 1.0
OE1 B:GLU190 3.7 26.3 1.0
ND1 B:HIS276 4.2 25.7 1.0
ND1 B:HIS188 4.2 30.6 1.0
CG B:HIS276 4.2 25.2 1.0
C07 B:DZA603 4.4 68.9 1.0
CG B:HIS188 4.4 26.8 1.0
OG B:SER196 4.5 34.1 1.0
CG B:GLU190 4.5 27.5 1.0
CG2 B:THR270 4.9 29.8 1.0
C08 B:DZA603 5.0 69.3 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: Wed Dec 16 01:29:07 2020

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