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

The structure of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Lysine, PDB code: 6exf 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)	28.55 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.721, 99.618, 165.819, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 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)/Lysine (pdb code 6exf). 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)/Lysine, PDB code: 6exf:
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)/Lysine


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)/Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:55.3 occ:1.00 NE2 A:HIS312 2.2 41.7 1.0 NE2 A:HIS176 2.2 45.9 1.0 OE2 A:GLU178 2.4 47.3 1.0 O A:HOH672 2.6 62.1 1.0 CE1 A:HIS176 2.8 47.1 1.0 CE1 A:HIS312 3.0 40.4 1.0 O A:HOH684 3.1 58.5 1.0 CD2 A:HIS312 3.2 42.1 1.0 CE A:LYS403 3.3 0.6 1.0 CD2 A:HIS176 3.4 45.4 1.0 CD A:GLU178 3.5 56.9 1.0 OE1 A:GLU178 3.8 79.1 1.0 ND1 A:HIS176 4.0 48.4 1.0 CD A:LYS403 4.2 97.5 1.0 NZ A:LYS403 4.2 0.3 1.0 ND1 A:HIS312 4.2 41.5 1.0 CG A:HIS176 4.3 44.7 1.0 CG A:HIS312 4.3 41.5 1.0 O A:HOH635 4.4 58.1 1.0 CG A:GLU178 4.8 37.4 1.0 N A:LYS402 4.8 95.6 1.0 NH1 A:ARG338 4.9 59.4 1.0 CZ A:PHE191 5.0 49.4 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)/Lysine


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)/Lysine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:53.0 occ:1.00 NE2 B:HIS312 2.2 43.0 1.0 NE2 B:HIS176 2.2 57.0 1.0 OE2 B:GLU178 2.4 57.7 1.0 O B:HOH634 2.6 53.2 1.0 O B:HOH640 2.8 70.6 1.0 CE1 B:HIS176 2.9 57.3 1.0 CD2 B:HIS312 3.1 44.6 1.0 CE1 B:HIS312 3.2 41.9 1.0 CD2 B:HIS176 3.3 57.2 1.0 CB B:LYS402 3.4 81.8 1.0 CD B:GLU178 3.5 68.1 1.0 OE1 B:GLU178 3.9 83.5 1.0 ND1 B:HIS176 4.1 57.9 1.0 N B:LYS402 4.1 76.3 1.0 CG B:HIS312 4.3 43.4 1.0 CG B:HIS176 4.3 54.8 1.0 CA B:LYS402 4.3 79.3 1.0 ND1 B:HIS312 4.3 43.3 1.0 O B:HOH600 4.3 46.0 1.0 O B:LYS402 4.4 0.8 1.0 CG B:LYS402 4.6 99.1 1.0 CD B:LYS402 4.7 0.3 1.0 CG B:GLU178 4.8 41.5 1.0 O B:GLY313 4.8 66.8 1.0 C B:LYS402 4.9 1.0 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)/Lysine


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)/Lysine within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:70.7 occ:1.00 NE2 C:HIS312 2.2 52.8 1.0 OE1 C:GLU178 2.4 54.0 1.0 NE2 C:HIS176 2.4 61.7 1.0 O C:HOH662 2.5 72.3 1.0 CE1 C:HIS176 2.7 62.3 1.0 CE1 C:HIS312 3.1 52.1 1.0 CD2 C:HIS312 3.3 53.2 1.0 CD C:GLU178 3.4 70.2 1.0 CD2 C:HIS176 3.7 62.3 1.0 OE2 C:GLU178 3.7 67.5 1.0 CD C:LYS402 3.9 0.8 1.0 ND1 C:HIS176 4.0 64.0 1.0 NZ C:LYS402 4.1 0.1 1.0 ND1 C:HIS312 4.3 53.0 1.0 CG C:HIS312 4.4 51.6 1.0 O C:HOH613 4.4 65.0 1.0 CE C:LYS402 4.4 0.8 1.0 CG C:HIS176 4.4 61.1 1.0 NH1 C:ARG338 4.7 72.4 1.0 CG C:GLU178 4.7 54.2 1.0 CD2 C:LEU173 4.8 82.3 1.0 CB C:LYS402 4.9 0.8 1.0 CG C:LYS402 5.0 0.4 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)/Lysine


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)/Lysine within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:70.6 occ:1.00 NE2 D:HIS176 2.1 56.9 1.0 OE2 D:GLU178 2.2 52.0 1.0 NE2 D:HIS312 2.3 55.7 1.0 O D:HOH673 2.8 75.3 1.0 CE1 D:HIS176 2.9 57.7 1.0 CE1 D:HIS312 3.1 53.6 1.0 N D:LYS402 3.2 81.9 1.0 CD2 D:HIS176 3.3 55.6 1.0 CD D:GLU178 3.3 67.9 1.0 CD2 D:HIS312 3.4 55.9 1.0 OE1 D:GLU178 3.7 79.0 1.0 CB D:LYS402 3.8 86.3 1.0 ND1 D:HIS176 4.1 57.8 1.0 CA D:LYS402 4.1 84.5 1.0 O D:HOH616 4.2 51.6 1.0 CG D:HIS176 4.3 54.1 1.0 ND1 D:HIS312 4.3 53.1 1.0 CG D:HIS312 4.4 52.8 1.0 CG D:GLU178 4.6 56.8 1.0 CD D:LYS402 4.7 86.4 1.0 CG D:LYS402 4.8 89.1 1.0 CA D:GLU178 4.9 45.4 1.0 OXT D:LYS402 4.9 0.0 1.0 NH1 D:ARG338 4.9 67.8 1.0 CB D:GLU178 4.9 46.3 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