Iron in PDB 6euo: Crystal Structure of Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5

The structure of Crystal Structure of Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5, PDB code: 6euo 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)	62.20 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.280, 98.930, 166.050, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.5

The binding sites of Iron atom in the Crystal Structure of Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 (pdb code 6euo). 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 Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5, PDB code: 6euo:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5


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 Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:50.2 occ:1.00 O2 A:MLT402 1.7 82.8 1.0 OE2 A:GLU178 2.0 51.6 1.0 NE2 A:HIS312 2.1 44.2 1.0 NE2 A:HIS176 2.1 45.7 1.0 C1 A:MLT402 2.5 79.1 1.0 CE1 A:HIS176 2.9 46.4 1.0 O1 A:MLT402 2.9 73.5 1.0 CE1 A:HIS312 3.0 43.2 1.0 CD A:GLU178 3.1 59.2 1.0 CD2 A:HIS312 3.1 44.7 1.0 CD2 A:HIS176 3.3 45.5 1.0 OE1 A:GLU178 3.4 67.7 1.0 C2 A:MLT402 3.6 82.6 1.0 O3 A:MLT402 3.7 88.6 1.0 ND1 A:HIS176 4.1 47.7 1.0 ND1 A:HIS312 4.2 43.8 1.0 CG A:HIS312 4.2 43.5 1.0 CG A:HIS176 4.3 44.9 1.0 CG A:GLU178 4.4 47.3 1.0 CB A:GLU178 4.7 39.9 1.0 O A:HOH575 4.8 66.5 1.0 CA A:GLU178 4.8 39.9 1.0 CZ A:PHE191 4.8 49.7 1.0 C3 A:MLT402 4.9 80.3 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5


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 Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:60.9 occ:1.00 NE2 B:HIS312 2.1 57.6 1.0 OE2 B:GLU178 2.1 59.7 1.0 NE2 B:HIS176 2.2 71.9 1.0 O B:HOH522 2.5 76.2 1.0 CE1 B:HIS176 2.9 72.1 1.0 CE1 B:HIS312 3.1 56.2 1.0 CD2 B:HIS312 3.1 58.9 1.0 CD B:GLU178 3.1 73.6 1.0 O5 B:MLT402 3.2 0.2 1.0 CD2 B:HIS176 3.3 72.2 1.0 OE1 B:GLU178 3.5 74.2 1.0 C4 B:MLT402 4.1 0.2 1.0 ND1 B:HIS176 4.2 72.8 1.0 O4 B:MLT402 4.2 0.2 1.0 ND1 B:HIS312 4.2 57.5 1.0 CG B:HIS312 4.2 57.8 1.0 CG B:HIS176 4.3 70.0 1.0 CG B:GLU178 4.5 56.0 1.0 O B:HOH570 4.6 66.2 1.0 CB B:GLU178 4.8 51.7 1.0 CA B:GLU178 4.8 51.8 1.0 CZ B:PHE191 4.9 60.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5


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 Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:68.7 occ:1.00 O1 C:MLT402 1.7 1.0 1.0 OE1 C:GLU178 1.9 68.7 1.0 NE2 C:HIS312 2.1 63.4 1.0 NE2 C:HIS176 2.2 77.4 1.0 C1 C:MLT402 2.9 0.6 1.0 CE1 C:HIS176 2.9 78.6 1.0 CE1 C:HIS312 3.0 62.6 1.0 CD C:GLU178 3.0 81.7 1.0 CD2 C:HIS312 3.2 64.2 1.0 O C:HOH568 3.2 77.4 1.0 CD2 C:HIS176 3.3 77.9 1.0 OE2 C:GLU178 3.4 88.5 1.0 O2 C:MLT402 3.5 0.5 1.0 C2 C:MLT402 4.0 0.7 1.0 ND1 C:HIS176 4.1 80.7 1.0 ND1 C:HIS312 4.2 63.6 1.0 CG C:HIS312 4.2 62.9 1.0 CG C:HIS176 4.3 77.6 1.0 O3 C:MLT402 4.3 0.2 1.0 C3 C:MLT402 4.3 0.8 1.0 CG C:GLU178 4.3 62.1 1.0 CB C:GLU178 4.7 56.8 1.0 CA C:GLU178 4.7 58.0 1.0 CZ C:PHE191 4.9 64.9 1.0 NH1 C:ARG338 5.0 84.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5


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 Apo Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:65.1 occ:1.00 OE2 D:GLU178 2.0 58.9 1.0 NE2 D:HIS176 2.1 63.5 1.0 NE2 D:HIS312 2.2 57.6 1.0 O2 D:MLT402 2.6 91.0 1.0 CE1 D:HIS176 2.8 63.9 1.0 CD D:GLU178 3.0 75.7 1.0 CE1 D:HIS312 3.0 54.9 1.0 CD2 D:HIS312 3.2 57.9 1.0 O3 D:MLT402 3.2 99.0 1.0 CD2 D:HIS176 3.2 62.6 1.0 C1 D:MLT402 3.2 95.9 1.0 OE1 D:GLU178 3.4 89.1 1.0 C2 D:MLT402 3.7 96.0 1.0 O1 D:MLT402 4.0 0.3 1.0 ND1 D:HIS176 4.0 63.5 1.0 ND1 D:HIS312 4.2 54.2 1.0 CG D:HIS176 4.2 60.4 1.0 CG D:HIS312 4.3 54.4 1.0 CG D:GLU178 4.4 59.3 1.0 O D:HOH567 4.4 66.2 1.0 O D:HOH626 4.5 81.7 1.0 CA D:GLU178 4.7 56.3 1.0 CB D:GLU178 4.7 56.8 1.0 CD2 D:LEU173 4.9 88.1 1.0 CZ D:PHE191 5.0 66.3 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