Iron in PDB 5yvz: Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Fe(III)

The structure of Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Fe(III), PDB code: 5yvz was solved by H.S.Chung, C.W.Pemble, S.H.Joo, C.R.Raetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.55 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.710, 59.204, 116.264, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 18.2

The binding sites of Iron atom in the Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Fe(III) (pdb code 5yvz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Fe(III), PDB code: 5yvz:

Iron binding site 1 out of 1 in the Crystal Structure of the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Fe(III)


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 the Kdo Hydroxylase Kdoo, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate and Fe(III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:16.9 occ:0.74 OD1 A:ASP148 2.1 20.2 1.0 O1 A:AKG402 2.1 23.9 1.0 O5 A:AKG402 2.2 24.8 1.0 O A:HOH582 2.2 29.8 1.0 NE2 A:HIS260 2.2 17.9 1.0 NE2 A:HIS146 2.3 18.9 1.0 C1 A:AKG402 2.8 35.2 1.0 C2 A:AKG402 2.9 34.8 1.0 CG A:ASP148 3.1 20.6 1.0 CE1 A:HIS260 3.1 17.2 1.0 CE1 A:HIS146 3.2 17.1 1.0 CD2 A:HIS260 3.2 17.3 1.0 CD2 A:HIS146 3.3 17.4 1.0 OD2 A:ASP148 3.4 23.4 1.0 O2 A:AKG402 4.1 34.2 1.0 OD2 A:ASP142 4.2 47.1 0.9 ND1 A:HIS260 4.3 16.2 1.0 ND1 A:HIS146 4.3 18.1 1.0 CG A:HIS260 4.3 16.5 1.0 C3 A:AKG402 4.3 33.3 1.0 CG A:HIS146 4.4 16.2 1.0 O A:HOH636 4.4 32.6 1.0 CB A:ASP148 4.4 17.8 1.0 O A:HOH624 4.7 50.2 1.0 NH1 A:ARG162 4.7 31.2 1.0 CA A:ASP148 4.7 15.4 1.0 CG A:ASP142 4.7 45.4 0.5 N A:ASP148 4.9 15.8 1.0 O A:HOH511 4.9 49.7 1.0 CB A:THR255 5.0 18.2 1.0

S.H.Joo, C.W.Pemble, E.G.Yang, C.R.H.Raetz, H.S.Chung. Biochemical and Structural Insights Into An Fe(II)/ Alpha-Ketoglutarate/O2-Dependent Dioxygenase, Kdo 3-Hydroxylase (Kdoo). J. Mol. Biol. V. 430 4036 2018.
ISSN: ESSN 1089-8638
PubMed: 30092253
DOI: 10.1016/J.JMB.2018.07.029