Iron in PDB 6f2b: Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate

The structure of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate, PDB code: 6f2b was solved by T.Isabet, E.A.Stura, P.Legrand, A.Zaparucha, K.Bastard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.820, 67.970, 110.430, 107.78, 102.79, 93.45
R / Rfree (%)	17.1 / 20.1

The binding sites of Iron atom in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate (pdb code 6f2b). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate, PDB code: 6f2b:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate


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 Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:46.0 occ:0.80 O A:HOH536 2.1 35.9 1.0 O1 A:AKG402 2.2 68.6 1.0 O5 A:AKG402 2.2 65.8 1.0 NE2 A:HIS314 2.2 38.0 1.0 NE2 A:HIS178 2.2 37.1 1.0 OE1 A:GLU180 2.4 39.7 1.0 C2 A:AKG402 2.9 65.1 1.0 C1 A:AKG402 2.9 68.1 1.0 CE1 A:HIS178 3.1 36.9 1.0 CD2 A:HIS314 3.1 38.3 1.0 CE1 A:HIS314 3.3 37.3 1.0 CD2 A:HIS178 3.3 37.0 1.0 CD A:GLU180 3.6 52.4 1.0 O A:HOH774 4.0 67.3 1.0 O2 A:AKG402 4.1 71.8 1.0 NH1 A:ARG332 4.1 45.4 1.0 OE2 A:GLU180 4.1 57.5 1.0 CG A:HIS314 4.3 35.4 1.0 ND1 A:HIS178 4.3 37.4 1.0 ND1 A:HIS314 4.4 37.6 1.0 CG A:HIS178 4.4 34.8 1.0 C3 A:AKG402 4.4 61.5 1.0 CG A:GLU180 4.8 35.9 1.0 CD2 A:LEU175 5.0 38.0 1.0 CB A:GLU180 5.0 27.3 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate


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 the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:69.8 occ:1.00 O1 B:AKG402 2.2 73.7 1.0 NE2 B:HIS178 2.3 55.9 1.0 OE1 B:GLU180 2.3 54.9 1.0 NE2 B:HIS314 2.5 51.2 1.0 O5 B:AKG402 2.8 73.8 1.0 O B:HOH654 2.9 91.3 1.0 CE1 B:HIS178 3.0 56.7 1.0 C1 B:AKG402 3.2 73.5 1.0 CD B:GLU180 3.3 58.8 1.0 C2 B:AKG402 3.4 72.0 1.0 CD2 B:HIS178 3.4 55.8 1.0 CD2 B:HIS314 3.4 51.8 1.0 CE1 B:HIS314 3.4 49.6 1.0 OE2 B:GLU180 3.6 54.1 1.0 NH1 B:ARG332 4.0 57.3 1.0 O2 B:AKG402 4.2 76.4 1.0 ND1 B:HIS178 4.3 57.6 1.0 CG B:HIS178 4.4 54.7 1.0 CG B:HIS314 4.5 48.2 1.0 ND1 B:HIS314 4.5 49.5 1.0 CG B:GLU180 4.7 41.9 1.0 C3 B:AKG402 4.8 68.5 1.0 CD2 B:LEU175 4.9 80.7 1.0 CB B:GLU180 5.0 35.5 1.0 CA B:GLU180 5.0 35.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:47.8 occ:0.80 O C:HOH600 2.1 38.0 1.0 NE2 C:HIS178 2.2 39.7 1.0 O2 C:AKG402 2.2 63.8 1.0 OE1 C:GLU180 2.3 41.5 1.0 NE2 C:HIS314 2.3 35.2 1.0 O5 C:AKG402 2.3 68.0 1.0 C1 C:AKG402 3.1 67.1 1.0 C2 C:AKG402 3.1 66.3 1.0 CE1 C:HIS178 3.1 39.6 1.0 CD2 C:HIS314 3.2 35.2 1.0 CD2 C:HIS178 3.3 39.7 1.0 CE1 C:HIS314 3.4 34.5 1.0 CD C:GLU180 3.5 54.6 1.0 NH1 C:ARG332 4.0 57.7 1.0 OE2 C:GLU180 4.0 59.0 1.0 O1 C:AKG402 4.2 71.4 1.0 ND1 C:HIS178 4.3 40.2 1.0 CG C:HIS178 4.4 37.2 1.0 CG C:HIS314 4.4 32.9 1.0 O C:HOH571 4.4 84.2 1.0 ND1 C:HIS314 4.5 35.0 1.0 C3 C:AKG402 4.5 63.5 1.0 CG C:GLU180 4.7 33.4 1.0 CB C:GLU180 4.8 24.8 1.0 O C:HOH654 4.9 55.5 1.0 CA C:GLU180 5.0 23.9 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:67.3 occ:1.00 NE2 D:HIS314 2.3 51.6 1.0 NE2 D:HIS178 2.3 54.6 1.0 OE1 D:GLU180 2.3 50.0 1.0 O2 D:AKG402 2.4 80.4 1.0 O D:HOH693 2.4 68.5 1.0 O5 D:AKG402 2.4 82.4 1.0 CE1 D:HIS178 2.9 55.5 1.0 C2 D:AKG402 3.2 79.8 1.0 C1 D:AKG402 3.2 80.8 1.0 CE1 D:HIS314 3.2 50.0 1.0 CD2 D:HIS314 3.3 52.0 1.0 CD D:GLU180 3.4 62.3 1.0 CD2 D:HIS178 3.5 54.3 1.0 OE2 D:GLU180 3.9 68.0 1.0 NH1 D:ARG332 4.1 52.1 1.0 ND1 D:HIS178 4.2 56.2 1.0 O1 D:AKG402 4.3 82.9 1.0 ND1 D:HIS314 4.4 49.8 1.0 CG D:HIS314 4.4 48.2 1.0 CG D:HIS178 4.4 53.0 1.0 C3 D:AKG402 4.7 74.9 1.0 CG D:GLU180 4.7 43.2 1.0 CB D:GLU180 4.8 34.7 1.0 CA D:GLU180 4.9 34.2 1.0 CD2 D:LEU175 4.9 78.4 1.0

K.Bastard, T.Isabet, E.A.Stura, P.Legrand, A.Zaparucha. Structural Studies Based on Two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity Within the Clavaminate Synthase-Like Family. Sci Rep V. 8 16587 2018.
ISSN: ESSN 2045-2322
PubMed: 30410048
DOI: 10.1038/S41598-018-34795-9