Iron in PDB 6eur: Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Alpha-Ketoglutarate

The structure of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Alpha-Ketoglutarate, PDB code: 6eur was solved by T.Isabet, E.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)	33.67 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.420, 99.460, 166.200, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.3

The binding sites of Iron atom in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Alpha-Ketoglutarate (pdb code 6eur). 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 KDO5 with Fe(II)/Alpha-Ketoglutarate, PDB code: 6eur:
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 KDO5 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 KDO5 with Fe(II)/Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:50.3 occ:1.00 O1 A:AKG402 2.1 63.3 1.0 NE2 A:HIS312 2.1 40.6 1.0 OE2 A:GLU178 2.2 45.9 1.0 NE2 A:HIS176 2.3 38.7 1.0 O5 A:AKG402 2.3 74.2 1.0 C2 A:AKG402 2.9 71.4 1.0 C1 A:AKG402 2.9 66.6 1.0 CE1 A:HIS176 3.0 39.1 1.0 CE1 A:HIS312 3.1 39.1 1.0 CD2 A:HIS312 3.1 40.9 1.0 CD A:GLU178 3.1 53.6 1.0 OE1 A:GLU178 3.4 52.8 1.0 CD2 A:HIS176 3.4 38.3 1.0 O2 A:AKG402 4.1 64.8 1.0 ND1 A:HIS176 4.2 40.6 1.0 ND1 A:HIS312 4.2 39.7 1.0 CG A:HIS312 4.2 38.8 1.0 C3 A:AKG402 4.4 70.0 1.0 CG A:HIS176 4.4 38.0 1.0 NH1 A:ARG338 4.5 43.9 1.0 CG A:GLU178 4.5 38.4 1.0 CZ A:PHE191 4.8 45.0 1.0 C4 A:AKG402 4.9 66.2 1.0 CB A:GLU178 4.9 32.8 1.0 O A:HOH605 5.0 59.4 1.0 CE1 A:PHE191 5.0 44.3 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 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 KDO5 with Fe(II)/Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:51.2 occ:1.00 NE2 B:HIS176 2.2 54.5 1.0 NE2 B:HIS312 2.2 42.7 1.0 OE2 B:GLU178 2.3 49.0 1.0 O2 B:AKG402 2.4 93.7 1.0 O5 B:AKG402 2.4 95.0 1.0 CE1 B:HIS176 2.7 54.0 1.0 O B:HOH620 3.1 68.2 1.0 C2 B:AKG402 3.1 95.8 1.0 C1 B:AKG402 3.1 95.3 1.0 CE1 B:HIS312 3.2 41.2 1.0 CD B:GLU178 3.2 65.8 1.0 CD2 B:HIS312 3.3 44.1 1.0 OE1 B:GLU178 3.4 82.0 1.0 CD2 B:HIS176 3.4 54.8 1.0 ND1 B:HIS176 3.9 54.6 1.0 CG B:HIS176 4.2 52.0 1.0 O1 B:AKG402 4.2 96.3 1.0 ND1 B:HIS312 4.3 42.2 1.0 CG B:HIS312 4.4 43.1 1.0 C3 B:AKG402 4.5 97.4 1.0 CG B:GLU178 4.6 44.8 1.0 O B:HOH604 4.7 46.8 1.0 O B:HOH590 4.8 60.8 1.0 NH1 B:ARG338 4.8 55.5 1.0 CB B:GLU178 4.9 35.6 1.0 CA B:GLU178 4.9 35.9 1.0 C4 B:AKG402 4.9 98.7 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 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 KDO5 with Fe(II)/Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:58.8 occ:1.00 NE2 C:HIS312 2.1 51.3 1.0 NE2 C:HIS176 2.1 57.2 1.0 O5 C:AKG402 2.4 84.3 1.0 OE1 C:GLU178 2.6 72.8 1.0 O1 C:AKG402 2.7 82.3 1.0 CE1 C:HIS176 2.9 58.3 1.0 OE2 C:GLU178 2.9 57.9 1.0 CE1 C:HIS312 2.9 50.3 1.0 O C:HOH595 3.0 68.5 1.0 CD C:GLU178 3.1 63.6 1.0 C2 C:AKG402 3.1 84.9 1.0 CD2 C:HIS312 3.2 51.7 1.0 CD2 C:HIS176 3.3 58.0 1.0 C1 C:AKG402 3.3 83.8 1.0 ND1 C:HIS176 4.1 60.7 1.0 ND1 C:HIS312 4.1 50.9 1.0 CG C:HIS312 4.2 50.1 1.0 CG C:HIS176 4.3 57.9 1.0 O2 C:AKG402 4.4 83.3 1.0 CG C:GLU178 4.5 52.1 1.0 C3 C:AKG402 4.5 83.3 1.0 NH1 C:ARG338 4.7 60.1 1.0 CB C:GLU178 4.9 45.4 1.0 C4 C:AKG402 4.9 82.0 1.0 CZ C:PHE191 4.9 52.2 1.0 CA C:GLU178 5.0 45.8 1.0 O C:HOH566 5.0 51.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 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 KDO5 with Fe(II)/Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:62.0 occ:1.00 OE2 D:GLU178 2.1 64.7 1.0 NE2 D:HIS176 2.2 51.5 1.0 NE2 D:HIS312 2.2 52.3 1.0 O5 D:AKG402 2.3 86.2 1.0 O2 D:AKG402 2.3 80.8 1.0 CE1 D:HIS176 2.9 52.1 1.0 C2 D:AKG402 3.0 86.7 1.0 CD D:GLU178 3.1 78.3 1.0 C1 D:AKG402 3.1 84.3 1.0 CD2 D:HIS312 3.2 53.0 1.0 CE1 D:HIS312 3.2 50.0 1.0 CD2 D:HIS176 3.3 50.3 1.0 OE1 D:GLU178 3.3 84.1 1.0 ND1 D:HIS176 4.1 51.7 1.0 CG D:HIS312 4.3 50.3 1.0 CG D:HIS176 4.3 48.7 1.0 O1 D:AKG402 4.3 86.1 1.0 ND1 D:HIS312 4.3 50.0 1.0 C3 D:AKG402 4.4 89.3 1.0 O D:HOH640 4.4 62.8 1.0 CG D:GLU178 4.5 56.9 1.0 NH1 D:ARG338 4.8 65.1 1.0 C4 D:AKG402 4.8 89.1 1.0 O D:HOH599 4.8 53.4 1.0 CB D:GLU178 4.9 43.2 1.0 CZ D:PHE191 4.9 58.2 1.0 CA D:GLU178 4.9 42.0 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