Iron in PDB 6gdy: Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG

The structure of Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG, PDB code: 6gdy was solved by M.S.Islam, C.J.Schofield, M.A.Mcdonough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.23 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.150, 96.990, 93.760, 90.00, 95.84, 90.00
R / Rfree (%)	18 / 21.6

The structure of Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iron atom in the Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG (pdb code 6gdy). 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 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG, PDB code: 6gdy:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG


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 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:25.9 occ:1.00 O5 A:AKG402 2.2 26.3 1.0 O A:HOH682 2.3 29.8 1.0 O2 A:AKG402 2.3 32.9 1.0 NE2 A:HIS187 2.3 27.6 1.0 NE2 A:HIS273 2.3 26.2 1.0 OD1 A:ASP189 2.3 25.8 1.0 C2 A:AKG402 2.8 30.7 1.0 C1 A:AKG402 2.9 36.7 1.0 CE1 A:HIS187 3.0 29.2 1.0 CD2 A:HIS273 3.2 26.8 1.0 CG A:ASP189 3.3 26.7 1.0 CE1 A:HIS273 3.3 26.1 1.0 CD2 A:HIS187 3.5 30.3 1.0 OD2 A:ASP189 3.5 29.6 1.0 O A:HOH670 3.9 30.5 1.0 O A:HOH542 4.0 30.5 1.0 O A:HOH558 4.0 43.5 1.0 O1 A:AKG402 4.1 40.1 1.0 ND1 A:HIS187 4.3 26.6 1.0 C3 A:AKG402 4.3 33.8 1.0 CG A:HIS273 4.4 28.1 1.0 ND1 A:HIS273 4.4 25.6 1.0 CG A:HIS187 4.5 30.4 1.0 CB A:ASP189 4.7 25.4 1.0 C4 A:AKG402 4.9 31.6 1.0

Iron binding site 2 out of 2 in the Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG


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 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:24.8 occ:1.00 OD1 B:ASP189 2.2 24.4 1.0 O1 B:AKG402 2.2 34.3 1.0 NE2 B:HIS273 2.3 27.8 1.0 NE2 B:HIS187 2.3 28.6 1.0 O5 B:AKG402 2.3 26.1 1.0 O B:HOH542 2.5 26.2 1.0 C1 B:AKG402 2.8 37.4 1.0 C2 B:AKG402 2.9 30.5 1.0 CE1 B:HIS273 3.1 28.5 1.0 CD2 B:HIS187 3.1 27.9 1.0 CG B:ASP189 3.2 24.3 1.0 CE1 B:HIS187 3.4 27.2 1.0 CD2 B:HIS273 3.4 29.8 1.0 OD2 B:ASP189 3.5 23.7 1.0 O B:HOH507 3.8 43.0 1.0 O2 B:AKG402 4.0 36.9 1.0 O B:HOH613 4.0 35.9 1.0 O B:HOH579 4.1 29.9 1.0 ND1 B:HIS273 4.2 27.2 1.0 CG B:HIS187 4.3 28.2 1.0 O B:HOH668 4.4 48.0 1.0 C3 B:AKG402 4.4 37.0 1.0 ND1 B:HIS187 4.4 26.2 1.0 CG B:HIS273 4.4 26.6 1.0 CB B:ASP189 4.5 26.4 1.0 CA B:ASP189 4.8 23.4 1.0 O B:HOH688 4.9 45.0 1.0 C4 B:AKG402 5.0 26.0 1.0

M.S.Islam, M.A.Mcdonough, R.Chowdhury, J.Gault, A.Khan, E.Pires, C.J.Schofield. Biochemical and Structural Investigations Clarify the Substrate Selectivity of the 2-Oxoglutarate Oxygenase JMJD6. J.Biol.Chem. V. 294 11637 2019.
ISSN: ESSN 1083-351X
PubMed: 31147442
DOI: 10.1074/JBC.RA119.008693