Iron in PDB 3kv5: Structure of KIAA1718, Human Jumonji Demethylase, in Complex with N-Oxalylglycine

The structure of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with N-Oxalylglycine, PDB code: 3kv5 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)	34.82 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.700, 125.600, 206.100, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.5

The structure of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with N-Oxalylglycine 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 N-Oxalylglycine (pdb code 3kv5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with N-Oxalylglycine, PDB code: 3kv5:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with N-Oxalylglycine


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 N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe491 b:0.4 occ:1.00 NE2 D:HIS354 2.7 32.1 1.0 NE2 D:HIS282 2.8 41.4 1.0 OD2 D:ASP284 3.1 51.2 1.0 OH D:TYR292 3.3 48.4 1.0 OD1 D:ASP284 3.4 51.1 1.0 CE1 D:HIS282 3.5 40.7 1.0 CE1 D:HIS354 3.6 31.7 1.0 CG D:ASP284 3.6 49.2 1.0 CD2 D:HIS354 3.7 31.6 1.0 CD2 D:HIS282 3.8 39.0 1.0 O D:HOH607 4.1 55.4 1.0 CZ D:TYR292 4.3 44.9 1.0 CE2 D:TYR292 4.3 42.9 1.0 ND1 D:HIS282 4.7 40.4 1.0 ND1 D:HIS354 4.7 31.6 1.0 CG D:HIS354 4.8 31.1 1.0 CG D:HIS282 4.9 38.1 1.0 O D:HOH535 5.0 45.0 1.0

Iron binding site 2 out of 3 in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with N-Oxalylglycine


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 N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe491 b:0.3 occ:1.00 NE2 A:HIS354 2.3 33.0 1.0 O2' A:OGA5798 2.6 0.9 1.0 NE2 A:HIS282 2.7 38.6 1.0 OD1 A:ASP284 2.8 49.8 1.0 OH A:TYR292 2.8 43.6 1.0 CE1 A:HIS354 2.8 32.4 1.0 O2 A:OGA5798 2.9 0.7 1.0 OD2 A:ASP284 3.4 50.6 1.0 CG A:ASP284 3.4 47.6 1.0 C2 A:OGA5798 3.4 0.1 1.0 CE1 A:HIS282 3.4 37.2 1.0 CD2 A:HIS354 3.5 31.7 1.0 C1 A:OGA5798 3.6 0.3 1.0 CD2 A:HIS282 3.7 37.2 1.0 CZ A:TYR292 4.0 41.6 1.0 ND1 A:HIS354 4.1 32.0 1.0 CG A:HIS354 4.4 31.4 1.0 CE2 A:TYR292 4.4 40.4 1.0 ND1 A:HIS282 4.6 37.7 1.0 N1 A:OGA5798 4.7 0.8 1.0 CG A:HIS282 4.7 36.3 1.0 O1 A:OGA5798 4.8 0.4 1.0 CB A:ASP284 4.8 44.0 1.0 CG1 A:VAL290 4.9 28.6 1.0

Iron binding site 3 out of 3 in the Structure of KIAA1718, Human Jumonji Demethylase, in Complex with N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of KIAA1718, Human Jumonji Demethylase, in Complex with N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe492 b:0.9 occ:1.00 NE2 A:HIS81 2.8 23.3 1.0 OD1 A:ASP56 3.0 35.6 1.0 CD1 A:ILE57 3.5 30.6 1.0 CE1 A:HIS81 3.7 23.6 1.0 CD2 A:HIS81 3.7 22.3 1.0 CD1 A:LEU93 3.8 30.6 1.0 CG A:ASP56 3.9 34.5 1.0 CB A:ASP56 4.0 31.4 1.0 CD1 A:LEU79 4.1 21.0 1.0 CB A:LEU79 4.3 21.1 1.0 CG1 A:ILE57 4.4 30.0 1.0 ND1 A:HIS81 4.8 23.6 1.0 CG A:LEU79 4.8 22.7 1.0 CG A:HIS81 4.8 22.5 1.0 C A:ASP56 4.9 29.4 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