Iron in PDB 3kva: Structure of KIAA1718 Jumonji Domain in Complex with Alpha- Ketoglutarate

The structure of Structure of KIAA1718 Jumonji Domain in Complex with Alpha- Ketoglutarate, PDB code: 3kva 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)	34.40 / 2.79
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.100, 78.100, 290.800, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 26.9

The binding sites of Iron atom in the Structure of KIAA1718 Jumonji Domain in Complex with Alpha- Ketoglutarate (pdb code 3kva). 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 Jumonji Domain in Complex with Alpha- Ketoglutarate, PDB code: 3kva:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structure of KIAA1718 Jumonji Domain 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 Jumonji Domain in Complex with Alpha- Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe489 b:63.5 occ:1.00 NE2 A:HIS282 2.2 33.5 1.0 O5 A:AKG701 2.3 69.6 1.0 O2 A:AKG701 2.4 71.8 1.0 NE2 A:HIS354 2.5 40.2 1.0 OD1 A:ASP284 2.6 42.4 1.0 CE1 A:HIS282 2.9 33.4 1.0 CE1 A:HIS354 3.0 38.8 1.0 OD2 A:ASP284 3.0 44.1 1.0 CG A:ASP284 3.0 41.3 1.0 C2 A:AKG701 3.1 70.5 1.0 C1 A:AKG701 3.1 71.7 1.0 CD2 A:HIS282 3.3 32.8 1.0 CD2 A:HIS354 3.6 39.0 1.0 ND1 A:HIS282 4.0 33.8 1.0 ND1 A:HIS354 4.1 38.6 1.0 CG A:HIS282 4.3 32.7 1.0 O1 A:AKG701 4.3 72.0 1.0 CB A:ASP284 4.3 37.0 1.0 CG A:HIS354 4.5 37.7 1.0 CA A:ASP284 4.5 35.1 1.0 N A:ASP284 4.6 34.2 1.0 C3 A:AKG701 4.6 68.7 1.0

Iron binding site 2 out of 2 in the Structure of KIAA1718 Jumonji Domain 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 Jumonji Domain in Complex with Alpha- Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe490 b:53.6 occ:1.00 OG A:SER249 3.2 41.4 1.0 N A:TRP250 3.2 37.7 1.0 N A:LEU370 3.2 34.9 1.0 N A:VAL251 3.2 37.5 1.0 CG2 A:VAL251 3.7 36.2 1.0 CA A:PHE369 3.8 35.5 1.0 CB A:VAL251 3.8 37.9 1.0 CA A:SER249 3.8 40.1 1.0 C A:SER249 3.8 39.0 1.0 CB A:SER249 3.9 40.6 1.0 O A:LEU370 3.9 35.2 1.0 CA A:TRP250 3.9 36.3 1.0 CB A:TRP250 3.9 34.0 1.0 C A:PHE369 4.0 35.7 1.0 C A:TRP250 4.1 36.8 1.0 CB A:LEU370 4.1 34.2 1.0 CA A:LEU370 4.1 34.7 1.0 CA A:VAL251 4.1 38.8 1.0 CB A:PHE369 4.1 35.9 1.0 CG A:LEU370 4.5 34.3 1.0 C A:LEU370 4.5 35.0 1.0 CZ A:PHE396 4.5 49.2 1.0 O A:ASN368 4.8 35.4 1.0 CE1 A:PHE396 4.8 50.1 1.0 O A:SER249 4.8 39.0 1.0 CD1 A:LEU370 4.9 32.5 1.0 N A:PHE369 5.0 35.6 1.0

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