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Iron in PDB 2xue: Crystal Structure of JMJD3

Protein crystallography data

The structure of Crystal Structure of JMJD3, PDB code: 2xue was solved by C.Chung, P.Rowland, J.Mosley, P.J.Thomas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.13 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.215, 65.154, 77.462, 86.09, 67.19, 68.26
R / Rfree (%) 17.932 / 21.574

Other elements in 2xue:

The structure of Crystal Structure of JMJD3 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of JMJD3 (pdb code 2xue). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of JMJD3, PDB code: 2xue:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 2xue

Go back to Iron Binding Sites List in 2xue
Iron binding site 1 out of 2 in the Crystal Structure of JMJD3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of JMJD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe3000

b:49.1
occ:1.00
OE1 A:GLU1392 1.9 36.4 1.0
O1 A:AKG4000 2.0 47.6 1.0
NE2 A:HIS1470 2.1 36.2 1.0
NE2 A:HIS1390 2.1 36.4 1.0
O5 A:AKG4000 2.1 47.4 1.0
O A:HOH2144 2.2 36.8 1.0
C1 A:AKG4000 2.7 47.9 1.0
C2 A:AKG4000 2.8 47.2 1.0
CE1 A:HIS1470 2.9 34.9 1.0
CE1 A:HIS1390 3.0 36.2 1.0
CD A:GLU1392 3.1 35.7 1.0
CD2 A:HIS1390 3.2 33.9 1.0
CD2 A:HIS1470 3.2 33.4 1.0
OE2 A:GLU1392 3.7 37.9 1.0
O2 A:AKG4000 4.0 45.5 1.0
ND1 A:HIS1470 4.1 31.4 1.0
ND1 A:HIS1390 4.1 33.0 1.0
C3 A:AKG4000 4.3 47.7 1.0
CG A:HIS1390 4.3 32.8 1.0
CG A:HIS1470 4.3 31.6 1.0
CG A:GLU1392 4.3 32.2 1.0
O A:HOH2134 4.4 53.3 1.0
OG A:SER1398 4.5 38.6 1.0
O A:HOH2135 4.5 60.0 1.0
CB A:SER1398 4.9 34.4 1.0
O A:HOH2148 4.9 42.0 1.0
O A:HOH2045 5.0 69.1 1.0

Iron binding site 2 out of 2 in 2xue

Go back to Iron Binding Sites List in 2xue
Iron binding site 2 out of 2 in the Crystal Structure of JMJD3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of JMJD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe3000

b:49.6
occ:1.00
OE1 B:GLU1392 1.9 34.7 1.0
O1 B:AKG4000 2.0 47.2 1.0
O5 B:AKG4000 2.1 46.0 1.0
NE2 B:HIS1390 2.1 33.3 1.0
NE2 B:HIS1470 2.1 32.2 1.0
O B:HOH2100 2.3 32.6 1.0
C1 B:AKG4000 2.7 47.3 1.0
C2 B:AKG4000 2.8 46.8 1.0
CE1 B:HIS1390 2.9 32.9 1.0
CE1 B:HIS1470 3.0 29.6 1.0
CD B:GLU1392 3.1 34.6 1.0
CD2 B:HIS1470 3.2 29.6 1.0
CD2 B:HIS1390 3.2 30.4 1.0
OE2 B:GLU1392 3.7 36.6 1.0
O2 B:AKG4000 4.0 46.3 1.0
O B:HOH2093 4.1 57.9 1.0
ND1 B:HIS1390 4.1 32.5 1.0
ND1 B:HIS1470 4.2 30.0 1.0
CG B:GLU1392 4.3 33.4 1.0
C3 B:AKG4000 4.3 47.4 1.0
CG B:HIS1390 4.3 29.3 1.0
CG B:HIS1470 4.3 29.2 1.0
OG B:SER1398 4.5 38.7 1.0
O B:HOH2105 4.8 63.5 1.0
CB B:SER1398 4.9 33.8 1.0

Reference:

L.Kruidenier, C.Chung, Z.Cheng, J.Liddle, K.Che, G.Joberty, M.Bantscheff, C.Bountra, A.Bridges, H.Diallo, D.Eberhard, S.Hutchinson, E.Jones, R.Katso, M.Leveridge, P.K.Mander, J.Mosley, C.Ramirez-Molina, P.Rowland, C.J.Schofield, R.J.Sheppard, J.E.Smith, C.Swales, R.Tanner, P.Thomas, A.Tumber, G.Drewes, U.Oppermann, D.J.Patel, K.Lee, D.M.Wilson. A Selective Jumonji H3K27 Demethylase Inhibitor Modulates the Proinflammatory Macrophage Response Nature V. 488 404 2012.
ISSN: ISSN 0028-0836
PubMed: 22842901
DOI: 10.1038/NATURE11262
Page generated: Sun Dec 13 14:57:03 2020

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