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Iron in PDB 7dyg: Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 2- (1H-Pyrazol-3-Yl)Isonicotinic Acid

Enzymatic activity of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 2- (1H-Pyrazol-3-Yl)Isonicotinic Acid

All present enzymatic activity of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 2- (1H-Pyrazol-3-Yl)Isonicotinic Acid:
1.14.11.66;

Protein crystallography data

The structure of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 2- (1H-Pyrazol-3-Yl)Isonicotinic Acid, PDB code: 7dyg was solved by T.Wang, L.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.98 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 71.72, 71.72, 151.242, 90, 90, 90
R / Rfree (%) 16.1 / 18.6

Iron Binding Sites:

The binding sites of Iron atom in the Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 2- (1H-Pyrazol-3-Yl)Isonicotinic Acid (pdb code 7dyg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 2- (1H-Pyrazol-3-Yl)Isonicotinic Acid, PDB code: 7dyg:

Iron binding site 1 out of 1 in 7dyg

Go back to Iron Binding Sites List in 7dyg
Iron binding site 1 out of 1 in the Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 2- (1H-Pyrazol-3-Yl)Isonicotinic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 2- (1H-Pyrazol-3-Yl)Isonicotinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:27.1
occ:1.00
 OE2 A:GLU194 2.1 17.4 1.0
N A:0WS401 2.2 30.8 1.0
NE2 A:HIS192 2.2 17.0 1.0
NE2 A:HIS280 2.2 18.6 1.0
N1 A:0WS401 2.3 36.1 1.0
C6 A:0WS401 2.9 48.3 1.0
HE1 A:HIS280 2.9 15.3 1.0
CE1 A:HIS280 2.9 12.8 1.0
C3 A:0WS401 2.9 39.9 1.0
CE1 A:HIS192 3.1 19.0 1.0
C4 A:0WS401 3.1 37.3 1.0
CD A:GLU194 3.2 23.4 1.0
H3 A:0WS401 3.2 44.7 1.0
HE1 A:HIS192 3.2 22.7 1.0
CD2 A:HIS192 3.3 20.8 1.0
CD2 A:HIS280 3.4 13.3 1.0
N2 A:0WS401 3.4 53.4 1.0
HD2 A:HIS192 3.5 24.8 1.0
OE1 A:GLU194 3.6 21.3 1.0
H A:0WS401 3.7 64.0 1.0
HD2 A:HIS280 3.7 15.8 1.0
HG A:SER200 3.8 23.3 1.0
ND1 A:HIS280 4.1 15.8 1.0
C8 A:0WS401 4.2 47.5 1.0
ND1 A:HIS192 4.2 19.1 1.0
C2 A:0WS401 4.3 38.6 1.0
CG A:HIS192 4.4 16.7 1.0
HG21 A:THR274 4.4 11.8 1.0
C5 A:0WS401 4.4 36.4 1.0
CG A:HIS280 4.4 14.0 1.0
C7 A:0WS401 4.4 54.2 1.0
HG2 A:GLU194 4.4 19.8 1.0
CG A:GLU194 4.5 16.6 1.0
O A:HOH760 4.5 29.1 1.0
OG A:SER200 4.6 19.5 1.0
HG1 A:THR274 4.6 38.1 1.0
HA A:GLU194 4.7 16.0 1.0
HB3 A:SER200 4.7 18.9 1.0
HZ3 A:TRP212 4.8 20.8 1.0
HD1 A:HIS280 4.9 18.8 1.0
C1 A:0WS401 4.9 36.3 1.0
HD1 A:PHE189 4.9 35.1 1.0
H2 A:0WS401 5.0 46.2 1.0
HG3 A:GLU194 5.0 19.8 1.0

Reference:

T.Wang, L.Yang. Crystal Structure of Histone Lysine Demethylase 4D (KDM4D) in Complex with the Inhibitor 2-(1H-Pyrazol-3-Yl)Isonicotinic Acid To Be Published.
Page generated: Thu Aug 8 04:36:43 2024

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