Iron in PDB 7qtd: Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate

The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate, PDB code: 7qtd was solved by P.Lukat, M.Daum, A.Bechthold, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.90 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.124, 108.215, 116.408, 90, 94.75, 90
R / Rfree (%)	14.1 / 16.5

The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Iron atom in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate (pdb code 7qtd). 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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate, PDB code: 7qtd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and 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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:18.0 occ:0.73 O5 A:AKG303 2.2 20.5 0.8 NE2 A:HIS237 2.2 19.0 1.0 O2 A:AKG303 2.2 27.9 0.8 OD1 A:ASP103 2.2 19.9 1.0 NE2 A:HIS101 2.3 16.9 1.0 O A:HOH583 2.3 29.4 1.0 C2 A:AKG303 2.9 30.8 0.8 C1 A:AKG303 3.0 27.9 0.8 CE1 A:HIS237 3.0 17.9 1.0 HE1 A:HIS237 3.2 21.5 1.0 CD2 A:HIS101 3.2 18.1 1.0 CG A:ASP103 3.2 19.9 1.0 CD2 A:HIS237 3.2 19.3 1.0 CE1 A:HIS101 3.2 22.4 1.0 HD2 A:HIS101 3.3 21.7 1.0 HE1 A:HIS101 3.4 26.9 1.0 HD2 A:HIS237 3.5 23.1 1.0 OD2 A:ASP103 3.6 20.1 1.0 HZ2 A:TRP230 3.8 22.8 1.0 HD13 A:ILE97 4.0 27.4 0.5 HG21 A:ILE97 4.1 23.7 0.5 O A:HOH634 4.1 32.6 1.0 O1 A:AKG303 4.2 30.0 0.8 ND1 A:HIS237 4.2 17.2 1.0 O A:HOH516 4.3 25.7 1.0 CG A:HIS237 4.3 15.7 1.0 ND1 A:HIS101 4.3 18.1 1.0 C3 A:AKG303 4.3 37.6 0.8 CG A:HIS101 4.4 16.6 1.0 HA A:ASP103 4.5 19.6 1.0 HH11 A:ARG251 4.5 37.7 1.0 HH12 A:ARG251 4.5 37.7 1.0 O A:HOH631 4.5 50.4 1.0 CB A:ASP103 4.6 16.2 1.0 CZ2 A:TRP230 4.6 19.0 1.0 H31 A:AKG303 4.6 45.2 0.8 NH1 A:ARG251 4.8 31.4 1.0 HB3 A:ASP103 4.8 19.4 1.0 H42 A:AKG303 4.9 34.0 0.8 H32 A:AKG303 4.9 45.2 0.8 HG23 A:ILE97 4.9 23.7 0.5 CG2 A:ILE97 4.9 19.7 0.5 CD1 A:ILE97 4.9 22.9 0.5 HD1 A:HIS237 4.9 20.6 1.0 CA A:ASP103 5.0 16.4 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and 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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:18.3 occ:0.71 O2 B:AKG302 2.1 20.5 0.8 O5 B:AKG302 2.2 21.4 0.8 NE2 B:HIS237 2.2 18.3 1.0 OD1 B:ASP103 2.2 19.3 1.0 NE2 B:HIS101 2.3 19.1 1.0 O B:HOH582 2.3 29.7 1.0 C2 B:AKG302 2.8 43.9 0.8 C1 B:AKG302 2.9 28.7 0.8 CE1 B:HIS237 2.9 16.6 1.0 HE1 B:HIS237 3.0 19.9 1.0 CE1 B:HIS101 3.2 20.0 1.0 CD2 B:HIS101 3.2 18.7 1.0 CG B:ASP103 3.2 22.3 1.0 CD2 B:HIS237 3.3 18.1 1.0 HE1 B:HIS101 3.4 23.9 1.0 HD2 B:HIS101 3.4 22.4 1.0 OD2 B:ASP103 3.6 20.8 1.0 HD2 B:HIS237 3.6 21.8 1.0 HZ2 B:TRP230 3.9 24.0 1.0 ND1 B:HIS237 4.1 17.4 1.0 O1 B:AKG302 4.1 24.4 0.8 O B:HOH617 4.3 36.9 1.0 CG B:HIS237 4.3 13.4 1.0 C3 B:AKG302 4.3 43.2 0.8 ND1 B:HIS101 4.3 17.4 1.0 O B:HOH511 4.3 21.8 1.0 CG B:HIS101 4.3 15.9 1.0 HA B:ASP103 4.5 17.9 1.0 CB B:ASP103 4.6 16.9 1.0 HH11 B:ARG251 4.6 44.1 1.0 H32 B:AKG302 4.6 51.8 0.8 HH12 B:ARG251 4.6 44.1 1.0 CZ2 B:TRP230 4.7 20.0 1.0 H42 B:AKG302 4.8 51.1 0.8 HD1 B:HIS237 4.8 20.8 1.0 H31 B:AKG302 4.8 51.8 0.8 HB3 B:ASP103 4.9 20.3 1.0 H41 B:AKG302 4.9 51.1 0.8 NH1 B:ARG251 4.9 36.8 1.0 C4 B:AKG302 5.0 42.6 0.8 CA B:ASP103 5.0 14.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and 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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:19.0 occ:0.72 O1 C:AKG302 2.2 23.7 0.8 O5 C:AKG302 2.2 22.2 0.8 O C:HOH581 2.2 27.2 1.0 NE2 C:HIS237 2.2 18.5 1.0 OD1 C:ASP103 2.2 18.3 1.0 NE2 C:HIS101 2.3 18.8 1.0 C1 C:AKG302 2.8 25.3 0.8 C2 C:AKG302 2.8 33.1 0.8 CE1 C:HIS237 3.0 17.8 1.0 HE1 C:HIS237 3.1 21.4 1.0 CD2 C:HIS101 3.2 18.8 1.0 CG C:ASP103 3.2 16.6 1.0 CE1 C:HIS101 3.3 20.2 1.0 CD2 C:HIS237 3.3 17.6 1.0 HD2 C:HIS101 3.3 22.6 1.0 HE1 C:HIS101 3.5 24.2 1.0 HD2 C:HIS237 3.5 21.1 1.0 OD2 C:ASP103 3.5 19.8 1.0 HZ2 C:TRP230 3.8 23.0 1.0 O2 C:AKG302 4.1 27.3 0.8 O C:HOH614 4.1 35.5 1.0 ND1 C:HIS237 4.2 18.1 1.0 HG21 C:ILE97 4.3 34.4 0.5 C3 C:AKG302 4.3 32.3 0.8 CG C:HIS237 4.3 13.8 1.0 CG C:HIS101 4.3 15.8 1.0 ND1 C:HIS101 4.3 16.0 1.0 O C:HOH504 4.3 22.6 1.0 HH12 C:ARG251 4.5 35.4 1.0 HA C:ASP103 4.5 19.0 1.0 HH11 C:ARG251 4.5 35.4 1.0 CB C:ASP103 4.6 16.4 1.0 CZ2 C:TRP230 4.6 19.2 1.0 H32 C:AKG302 4.6 38.7 0.8 HG12 C:ILE97 4.7 28.2 0.5 NH1 C:ARG251 4.8 29.5 1.0 H31 C:AKG302 4.8 38.7 0.8 HG23 C:ILE97 4.9 34.4 0.5 H42 C:AKG302 4.9 37.9 0.8 HB3 C:ASP103 4.9 19.7 1.0 HD1 C:HIS237 4.9 21.8 1.0 CA C:ASP103 5.0 15.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and 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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:18.7 occ:0.70 NE2 D:HIS237 2.2 21.8 1.0 O1 D:AKG302 2.2 22.8 0.8 O5 D:AKG302 2.2 25.4 0.8 OD1 D:ASP103 2.2 19.7 1.0 NE2 D:HIS101 2.3 18.9 1.0 O D:HOH569 2.3 28.3 1.0 C1 D:AKG302 2.8 30.1 0.8 C2 D:AKG302 2.8 47.6 0.8 CE1 D:HIS237 2.9 18.8 1.0 HE1 D:HIS237 3.0 22.6 1.0 CD2 D:HIS101 3.2 18.4 1.0 CG D:ASP103 3.2 22.1 1.0 CD2 D:HIS237 3.3 19.5 1.0 CE1 D:HIS101 3.3 20.0 1.0 HD2 D:HIS101 3.3 22.0 1.0 HE1 D:HIS101 3.4 24.0 1.0 HD2 D:HIS237 3.5 23.4 1.0 OD2 D:ASP103 3.6 21.4 1.0 HZ2 D:TRP230 3.8 22.4 1.0 O2 D:AKG302 4.1 27.8 0.8 ND1 D:HIS237 4.1 19.8 1.0 O D:HOH612 4.3 34.9 1.0 CG D:HIS237 4.3 16.2 1.0 C3 D:AKG302 4.3 52.2 0.8 O D:HOH561 4.3 45.2 1.0 O D:HOH496 4.3 24.6 1.0 ND1 D:HIS101 4.3 18.5 1.0 CG D:HIS101 4.4 16.1 1.0 HA D:ASP103 4.5 18.7 1.0 CB D:ASP103 4.6 15.5 1.0 H32 D:AKG302 4.6 62.7 0.8 CZ2 D:TRP230 4.6 18.7 1.0 HH11 D:ARG251 4.6 41.6 1.0 HH12 D:ARG251 4.7 41.6 1.0 H31 D:AKG302 4.8 62.7 0.8 HD1 D:HIS237 4.8 23.8 1.0 H42 D:AKG302 4.9 56.4 0.8 H41 D:AKG302 4.9 56.4 0.8 HB3 D:ASP103 4.9 18.6 1.0 CA D:ASP103 5.0 15.6 1.0 C4 D:AKG302 5.0 47.0 0.8 NH1 D:ARG251 5.0 34.7 1.0

P.Lukat, M.Daum, D.Zechel, A.Bechthold, O.Einsle. Structural Investigations on the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygense PLAO1 From Streptomyces Sp. TU6071 To Be Published.