Iron in PDB 8afj: Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock

The structure of Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock, PDB code: 8afj was solved by P.Van Der Linden, S.Engilberge, M.Atta, P.Carpentier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.62 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.276, 51.845, 78.183, 90, 90.63, 90
R / Rfree (%)	20 / 22.8

The structure of Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock also contains other interesting chemical elements:

Calcium	(Ca)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Iron atom in the Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock (pdb code 8afj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock, PDB code: 8afj:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:19.4 occ:1.00 OE1 B:GLU69 2.0 16.8 1.0 O B:HOH470 2.1 16.1 1.0 OE2 B:GLU38 2.2 14.6 1.0 ND1 B:HIS72 2.2 19.4 1.0 O B:HOH432 2.2 18.6 1.0 O3 B:TRS303 2.4 18.8 1.0 O B:HOH401 2.9 19.8 1.0 CE1 B:HIS72 3.0 18.9 1.0 CD B:GLU69 3.1 18.8 1.0 CD B:GLU38 3.1 17.6 1.0 FE B:FE302 3.2 23.0 1.0 CG B:HIS72 3.3 15.8 1.0 OE1 B:GLU38 3.4 22.8 1.0 C3 B:TRS303 3.5 16.0 1.0 OE2 B:GLU69 3.6 15.9 1.0 CB B:HIS72 3.7 14.5 1.0 OE2 B:GLU151 4.2 29.7 1.0 NE2 B:HIS72 4.2 21.6 1.0 OE1 B:GLU151 4.2 22.6 1.0 CD2 B:HIS72 4.4 19.5 1.0 CG B:GLU69 4.4 10.9 1.0 CD B:GLU151 4.4 18.7 1.0 CA B:GLU69 4.5 15.6 1.0 CG B:GLU38 4.5 11.5 1.0 OG B:SER150 4.5 24.1 1.0 C B:TRS303 4.6 26.4 1.0 CE1 B:HIS154 4.6 17.5 1.0 CB B:GLU69 4.6 13.4 1.0 C1 B:TRS303 4.7 34.0 1.0 ND1 B:HIS154 4.8 19.0 1.0 CB B:GLU38 4.9 15.0 1.0 CD2 B:LEU147 4.9 16.7 1.0 N B:TRS303 4.9 27.1 1.0

Iron binding site 2 out of 4 in the Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:23.0 occ:1.00 OE1 B:GLU122 2.1 25.3 1.0 O B:HOH470 2.2 16.1 1.0 O3 B:TRS303 2.3 18.8 1.0 OE2 B:GLU69 2.3 15.9 1.0 OE1 B:GLU151 2.4 22.6 1.0 ND1 B:HIS154 2.5 19.0 1.0 CD B:GLU122 3.1 27.3 1.0 CD B:GLU69 3.1 18.8 1.0 OE1 B:GLU69 3.2 16.8 1.0 FE B:FE301 3.2 19.4 1.0 CE1 B:HIS154 3.3 17.5 1.0 C3 B:TRS303 3.3 16.0 1.0 CD B:GLU151 3.4 18.7 1.0 OE2 B:GLU122 3.4 38.2 1.0 CG B:HIS154 3.6 17.3 1.0 O B:HOH428 3.9 22.2 1.0 OE2 B:GLU151 3.9 29.7 1.0 N B:TRS303 4.0 27.1 1.0 CB B:HIS154 4.0 20.3 1.0 O B:HOH401 4.1 19.8 1.0 O B:HOH432 4.3 18.6 1.0 C B:TRS303 4.3 26.4 1.0 CG B:GLU122 4.4 21.3 1.0 NE2 B:HIS154 4.5 21.8 1.0 CA B:GLU151 4.5 17.2 1.0 CG B:GLU69 4.6 10.9 1.0 CG B:GLU151 4.6 18.7 1.0 CD2 B:HIS154 4.7 18.2 1.0 OG B:SER150 4.8 24.1 1.0 ND1 B:HIS72 4.9 19.4 1.0 OE2 B:GLU38 4.9 14.6 1.0 N B:GLU151 4.9 19.4 1.0 CB B:GLU151 4.9 16.5 1.0 CB B:GLU122 5.0 20.5 1.0 O B:SER150 5.0 17.8 1.0 CE1 B:HIS72 5.0 18.9 1.0

Iron binding site 3 out of 4 in the Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:21.2 occ:1.00 OE1 A:GLU69 2.0 15.7 1.0 O A:HOH426 2.1 19.1 1.0 OE1 A:GLU38 2.2 19.4 1.0 ND1 A:HIS72 2.2 17.6 1.0 O3 A:TRS304 2.3 20.5 0.5 O3 A:TRS304 2.3 20.5 0.5 O A:HOH411 2.3 21.6 1.0 CD A:GLU69 3.0 17.4 1.0 CE1 A:HIS72 3.1 21.0 1.0 CD A:GLU38 3.1 18.2 1.0 FE A:FE303 3.3 21.1 1.0 CG A:HIS72 3.3 16.7 1.0 C3 A:TRS304 3.4 21.2 0.5 OE2 A:GLU38 3.4 22.7 1.0 C3 A:TRS304 3.4 21.2 0.5 OE2 A:GLU69 3.4 19.9 1.0 CB A:HIS72 3.7 15.3 1.0 OE2 A:GLU151 4.0 28.3 1.0 OE1 A:GLU151 4.2 27.6 1.0 NE2 A:HIS72 4.2 22.0 1.0 CD A:GLU151 4.3 21.9 1.0 CG A:GLU69 4.4 15.2 1.0 CD2 A:HIS72 4.4 14.7 1.0 OG A:SER150 4.4 33.9 1.0 O1 A:TRS304 4.4 24.3 0.5 CE1 A:HIS154 4.5 25.5 1.0 CA A:GLU69 4.5 16.5 1.0 C A:TRS304 4.5 24.7 0.5 CG A:GLU38 4.5 16.0 1.0 C1 A:TRS304 4.6 23.6 0.5 C A:TRS304 4.6 24.6 0.5 ND1 A:HIS154 4.6 19.8 1.0 CB A:GLU69 4.7 18.1 1.0 CB A:GLU38 4.9 18.0 1.0 C1 A:TRS304 4.9 23.9 0.5 N A:TRS304 5.0 21.0 0.5

Iron binding site 4 out of 4 in the Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:21.1 occ:1.00 O A:HOH426 1.9 19.1 1.0 OE1 A:GLU122 2.1 23.1 1.0 OE2 A:GLU69 2.2 19.9 1.0 ND1 A:HIS154 2.3 19.8 1.0 O3 A:TRS304 2.4 20.5 0.5 OE1 A:GLU151 2.4 27.6 1.0 O3 A:TRS304 2.4 20.5 0.5 CE1 A:HIS154 3.1 25.5 1.0 CD A:GLU69 3.1 17.4 1.0 CD A:GLU122 3.1 26.8 1.0 FE A:FE302 3.3 21.2 1.0 C3 A:TRS304 3.3 21.2 0.5 OE1 A:GLU69 3.3 15.7 1.0 C3 A:TRS304 3.4 21.2 0.5 CD A:GLU151 3.4 21.9 1.0 CG A:HIS154 3.4 18.7 1.0 OE2 A:GLU122 3.6 28.1 1.0 O A:HOH417 3.7 22.5 1.0 CB A:HIS154 3.9 18.2 1.0 N A:TRS304 3.9 21.2 0.5 OE2 A:GLU151 3.9 28.3 1.0 N A:TRS304 4.0 21.0 0.5 C A:TRS304 4.3 24.6 0.5 NE2 A:HIS154 4.3 24.2 1.0 C A:TRS304 4.3 24.7 0.5 O A:HOH411 4.4 21.6 1.0 CG A:GLU122 4.4 15.3 1.0 CD2 A:HIS154 4.5 20.5 1.0 CG A:GLU69 4.5 15.2 1.0 CG A:GLU151 4.5 21.9 1.0 OG A:SER150 4.5 33.9 1.0 CA A:GLU151 4.5 22.0 1.0 ND1 A:HIS72 4.9 17.6 1.0 CB A:GLU151 4.9 19.3 1.0 OE1 A:GLU38 4.9 19.4 1.0 O A:SER150 5.0 22.4 1.0 CB A:GLU122 5.0 16.6 1.0 N A:GLU151 5.0 20.0 1.0

P.Van Der Linden, S.Engilberge, M.Atta, P.Carpentier. Trna Modifying Enzyme Miae Soaked in Na-Dithionite in A Glovebox and Flash-Cooled Using A Miniature-Airlock To Be Published.