Iron in PDB 3kv6: Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate

The structure of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate, PDB code: 3kv6 was solved by J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.54 / 2.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.400, 125.200, 206.000, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.3

The structure of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Iron atom in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate (pdb code 3kv6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate, PDB code: 3kv6:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe491 b:65.3 occ:1.00 O2 A:AKG702 2.3 99.2 1.0 NE2 A:HIS354 2.3 31.0 1.0 NE2 A:HIS282 2.6 38.8 1.0 OD2 A:ASP284 2.6 45.0 1.0 CE1 A:HIS354 2.9 28.7 1.0 OH A:TYR292 3.1 43.3 1.0 OD1 A:ASP284 3.1 44.8 1.0 CG A:ASP284 3.1 43.0 1.0 CE1 A:HIS282 3.3 38.5 1.0 CD2 A:HIS354 3.5 29.3 1.0 C1 A:AKG702 3.5 99.0 1.0 CD2 A:HIS282 3.5 37.7 1.0 O5 A:AKG702 3.6 98.0 1.0 C2 A:AKG702 4.0 98.5 1.0 ND1 A:HIS354 4.1 28.8 1.0 CZ A:TYR292 4.3 42.8 1.0 ND1 A:HIS282 4.3 38.2 1.0 CG A:HIS354 4.4 27.9 1.0 CB A:ASP284 4.5 39.7 1.0 O1 A:AKG702 4.5 99.5 1.0 CG A:HIS282 4.5 37.0 1.0 O A:HOH550 4.5 32.2 1.0 N A:ASP284 4.8 36.1 1.0 CE2 A:TYR292 4.8 41.9 1.0 CA A:ASP284 4.8 37.9 1.0

Iron binding site 2 out of 2 in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe491 b:69.4 occ:1.00 O2 D:AKG701 2.2 0.4 1.0 NE2 D:HIS354 2.2 28.9 1.0 NE2 D:HIS282 2.3 34.8 1.0 O5 D:AKG701 2.7 0.5 1.0 OD1 D:ASP284 2.7 45.9 1.0 CE1 D:HIS354 2.8 28.0 1.0 OH D:TYR292 3.0 34.2 0.5 C1 D:AKG701 3.0 0.7 1.0 CE1 D:HIS282 3.2 34.2 1.0 CD2 D:HIS282 3.2 33.5 1.0 C2 D:AKG701 3.2 0.6 1.0 CG D:ASP284 3.3 44.4 1.0 CD2 D:HIS354 3.4 28.0 1.0 OD2 D:ASP284 3.4 45.9 1.0 ND1 D:HIS354 4.0 27.7 1.0 O1 D:AKG701 4.2 0.6 1.0 ND1 D:HIS282 4.3 34.2 1.0 CZ D:TYR292 4.3 35.1 0.5 CG D:HIS354 4.3 27.5 1.0 CG D:HIS282 4.3 32.6 1.0 CB D:ASP284 4.6 40.6 1.0 C3 D:AKG701 4.8 0.5 1.0 CA D:ASP284 4.8 37.5 1.0 N D:ASP284 4.8 34.5 1.0 CE2 D:TYR292 4.9 34.9 0.5

J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, X.Cheng. Enzymatic and Structural Insights For Substrate Specificity of A Family of Jumonji Histone Lysine Demethylases. Nat.Struct.Mol.Biol. V. 17 38 2010.
ISSN: ISSN 1545-9993
PubMed: 20023638
DOI: 10.1038/NSMB.1753