Iron in PDB 8qrd: Olep in Complex with Testosterone in High Salt Crystallization Conditions

The structure of Olep in Complex with Testosterone in High Salt Crystallization Conditions, PDB code: 8qrd was solved by F.Fata, A.Costanzo, I.Freda, E.Gugole, G.Bulfaro, L.Barbizzi, M.Di Renzo, C.Savino, B.Vallone, L.C.Montemiglio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.75 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	248.195, 109.738, 160.13, 90, 129.41, 90
R / Rfree (%)	16.5 / 21.2

The structure of Olep in Complex with Testosterone in High Salt Crystallization Conditions also contains other interesting chemical elements:

Sodium

(Na)

6 atoms

The binding sites of Iron atom in the Olep in Complex with Testosterone in High Salt Crystallization Conditions (pdb code 8qrd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Olep in Complex with Testosterone in High Salt Crystallization Conditions, PDB code: 8qrd:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Olep in Complex with Testosterone in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Olep in Complex with Testosterone in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:36.8 occ:1.00 FE A:HEM501 0.0 36.8 1.0 ND A:HEM501 1.9 36.5 1.0 NA A:HEM501 2.0 36.6 1.0 NC A:HEM501 2.1 36.6 1.0 NB A:HEM501 2.1 35.3 1.0 SG A:CYS356 2.3 37.2 1.0 C4D A:HEM501 2.9 33.9 1.0 C1D A:HEM501 2.9 35.9 1.0 C1A A:HEM501 3.0 33.7 1.0 C4C A:HEM501 3.0 38.5 1.0 C4A A:HEM501 3.0 36.7 1.0 C1B A:HEM501 3.1 35.7 1.0 C4B A:HEM501 3.1 35.9 1.0 C1C A:HEM501 3.1 38.3 1.0 CHA A:HEM501 3.3 33.0 1.0 CHD A:HEM501 3.4 36.2 1.0 CB A:CYS356 3.4 33.8 1.0 CHB A:HEM501 3.5 37.2 1.0 CHC A:HEM501 3.5 38.0 1.0 CA A:CYS356 4.1 33.8 1.0 C3D A:HEM501 4.1 32.6 1.0 C2D A:HEM501 4.1 34.3 1.0 C2A A:HEM501 4.2 34.2 1.0 C3A A:HEM501 4.2 34.3 1.0 C3C A:HEM501 4.2 39.8 1.0 C2C A:HEM501 4.3 40.0 1.0 C2B A:HEM501 4.3 35.8 1.0 C3B A:HEM501 4.3 36.2 1.0 C6 A:TES502 4.4 52.5 1.0 C7 A:TES502 4.5 54.2 1.0 CB A:ALA244 4.7 43.9 1.0 C A:CYS356 4.8 35.8 1.0 N A:GLY358 4.8 37.1 1.0 N A:ILE357 4.9 37.4 1.0 CG2 A:THR248 4.9 46.7 1.0

Iron binding site 2 out of 6 in the Olep in Complex with Testosterone in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Olep in Complex with Testosterone in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:34.1 occ:1.00 FE B:HEM501 0.0 34.1 1.0 ND B:HEM501 1.9 33.8 1.0 NA B:HEM501 2.0 31.7 1.0 NC B:HEM501 2.1 31.1 1.0 NB B:HEM501 2.1 33.9 1.0 SG B:CYS356 2.4 34.7 1.0 C4D B:HEM501 2.9 32.2 1.0 C1D B:HEM501 2.9 34.0 1.0 C1A B:HEM501 3.0 30.5 1.0 C4C B:HEM501 3.0 35.9 1.0 C4A B:HEM501 3.0 31.7 1.0 C1B B:HEM501 3.1 35.0 1.0 C4B B:HEM501 3.1 32.3 1.0 C1C B:HEM501 3.1 30.7 1.0 CHA B:HEM501 3.3 31.0 1.0 CHD B:HEM501 3.4 37.8 1.0 CB B:CYS356 3.4 34.7 1.0 CHB B:HEM501 3.5 32.5 1.0 CHC B:HEM501 3.5 31.1 1.0 C3D B:HEM501 4.1 32.8 1.0 C2D B:HEM501 4.1 29.6 1.0 CA B:CYS356 4.1 35.5 1.0 C2A B:HEM501 4.2 30.4 1.0 C3A B:HEM501 4.2 33.1 1.0 C3C B:HEM501 4.2 34.2 1.0 C2C B:HEM501 4.3 33.5 1.0 C2B B:HEM501 4.3 32.2 1.0 C3B B:HEM501 4.3 34.7 1.0 C6 B:TES502 4.4 40.9 1.0 C7 B:TES502 4.6 42.5 1.0 CB B:ALA244 4.7 41.7 1.0 CG2 B:THR248 4.8 44.4 1.0 C B:CYS356 4.9 36.7 1.0 N B:GLY358 4.9 37.1 1.0 N B:ILE357 4.9 37.2 1.0

Iron binding site 3 out of 6 in the Olep in Complex with Testosterone in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Olep in Complex with Testosterone in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:33.5 occ:1.00 FE C:HEM501 0.0 33.5 1.0 ND C:HEM501 1.9 33.3 1.0 NA C:HEM501 2.0 30.7 1.0 NC C:HEM501 2.1 31.1 1.0 NB C:HEM501 2.1 31.1 1.0 SG C:CYS356 2.4 38.5 1.0 C4D C:HEM501 2.9 31.9 1.0 C1D C:HEM501 2.9 34.9 1.0 C1A C:HEM501 3.0 31.1 1.0 C4C C:HEM501 3.0 33.7 1.0 C4A C:HEM501 3.0 33.2 1.0 C1B C:HEM501 3.1 33.3 1.0 C4B C:HEM501 3.1 31.8 1.0 C1C C:HEM501 3.1 30.9 1.0 CHA C:HEM501 3.3 31.6 1.0 CHD C:HEM501 3.3 31.4 1.0 CB C:CYS356 3.5 34.3 1.0 CHB C:HEM501 3.5 31.4 1.0 CHC C:HEM501 3.5 30.6 1.0 C2D C:HEM501 4.1 33.9 1.0 C3D C:HEM501 4.1 32.0 1.0 CA C:CYS356 4.1 35.0 1.0 C2A C:HEM501 4.2 32.1 1.0 C3C C:HEM501 4.2 28.7 1.0 C3A C:HEM501 4.2 35.6 1.0 C2C C:HEM501 4.2 31.1 1.0 C2B C:HEM501 4.3 32.8 1.0 C3B C:HEM501 4.3 33.4 1.0 C6 C:TES502 4.7 43.7 1.0 C7 C:TES502 4.7 47.1 1.0 CB C:ALA244 4.7 38.5 1.0 CG2 C:THR248 4.9 40.5 1.0 C C:CYS356 4.9 34.5 1.0 N C:GLY358 4.9 32.5 1.0

Iron binding site 4 out of 6 in the Olep in Complex with Testosterone in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Olep in Complex with Testosterone in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:41.0 occ:1.00 FE D:HEM501 0.0 41.0 1.0 ND D:HEM501 1.9 38.0 1.0 NA D:HEM501 2.0 36.7 1.0 NC D:HEM501 2.1 37.6 1.0 NB D:HEM501 2.1 38.4 1.0 SG D:CYS356 2.4 41.6 1.0 C4D D:HEM501 2.8 38.2 1.0 C1D D:HEM501 2.9 37.6 1.0 C1A D:HEM501 3.0 37.9 1.0 C4C D:HEM501 3.0 39.8 1.0 C4A D:HEM501 3.0 40.0 1.0 C1B D:HEM501 3.1 39.0 1.0 C4B D:HEM501 3.1 40.5 1.0 C1C D:HEM501 3.1 37.9 1.0 CHA D:HEM501 3.3 38.4 1.0 CHD D:HEM501 3.4 39.9 1.0 CHB D:HEM501 3.5 41.4 1.0 CHC D:HEM501 3.5 38.7 1.0 CB D:CYS356 3.5 43.9 1.0 C3D D:HEM501 4.1 39.1 1.0 C2D D:HEM501 4.1 38.2 1.0 C2A D:HEM501 4.2 40.3 1.0 CA D:CYS356 4.2 43.8 1.0 C3A D:HEM501 4.2 39.0 1.0 C3C D:HEM501 4.2 41.0 1.0 C2C D:HEM501 4.3 40.9 1.0 C2B D:HEM501 4.3 38.9 1.0 C3B D:HEM501 4.3 40.7 1.0 C6 D:TES502 4.5 52.4 1.0 C7 D:TES502 4.6 52.4 1.0 CB D:ALA244 4.8 49.9 1.0 CG2 D:THR248 4.8 56.7 1.0 C D:CYS356 4.9 41.5 1.0 N D:ILE357 4.9 40.7 1.0 N D:GLY358 5.0 39.4 1.0

Iron binding site 5 out of 6 in the Olep in Complex with Testosterone in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Olep in Complex with Testosterone in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe501 b:44.3 occ:1.00 FE E:HEM501 0.0 44.3 1.0 ND E:HEM501 1.9 45.9 1.0 NA E:HEM501 2.0 46.4 1.0 NC E:HEM501 2.1 45.0 1.0 NB E:HEM501 2.1 49.6 1.0 SG E:CYS356 2.4 50.8 1.0 C4D E:HEM501 2.9 44.8 1.0 C1D E:HEM501 2.9 44.5 1.0 C1A E:HEM501 3.0 48.5 1.0 C4C E:HEM501 3.0 46.2 1.0 C4A E:HEM501 3.0 50.4 1.0 C1B E:HEM501 3.1 51.0 1.0 C4B E:HEM501 3.1 49.2 1.0 C1C E:HEM501 3.1 45.7 1.0 CHA E:HEM501 3.3 45.2 1.0 CB E:CYS356 3.3 49.6 1.0 CHD E:HEM501 3.3 46.7 1.0 CHB E:HEM501 3.5 52.8 1.0 CHC E:HEM501 3.5 46.0 1.0 CA E:CYS356 4.1 50.4 1.0 C3D E:HEM501 4.1 46.5 1.0 C2D E:HEM501 4.1 47.1 1.0 C2A E:HEM501 4.2 49.3 1.0 C3A E:HEM501 4.2 48.3 1.0 C3C E:HEM501 4.2 45.4 1.0 C2C E:HEM501 4.3 45.3 1.0 C2B E:HEM501 4.3 51.5 1.0 C3B E:HEM501 4.3 51.8 1.0 C6 E:TES502 4.5 51.1 1.0 C7 E:TES502 4.6 51.7 1.0 CB E:ALA244 4.8 49.4 1.0 CG2 E:THR248 4.9 59.2 1.0 C E:CYS356 4.9 49.6 1.0 N E:GLY358 5.0 49.1 1.0 N E:ILE357 5.0 48.3 1.0

Iron binding site 6 out of 6 in the Olep in Complex with Testosterone in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Olep in Complex with Testosterone in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:55.8 occ:1.00 FE F:HEM501 0.0 55.8 1.0 ND F:HEM501 1.9 57.4 1.0 NA F:HEM501 2.0 57.8 1.0 NC F:HEM501 2.1 56.0 1.0 NB F:HEM501 2.1 59.8 1.0 SG F:CYS356 2.5 56.5 1.0 C4D F:HEM501 2.9 53.4 1.0 C1D F:HEM501 2.9 52.0 1.0 C1A F:HEM501 3.0 53.9 1.0 C4C F:HEM501 3.0 55.5 1.0 C4A F:HEM501 3.0 57.6 1.0 C1B F:HEM501 3.1 60.3 1.0 C4B F:HEM501 3.1 61.6 1.0 C1C F:HEM501 3.1 60.2 1.0 CHA F:HEM501 3.3 51.1 1.0 CHD F:HEM501 3.3 54.0 1.0 CB F:CYS356 3.4 54.6 1.0 CHB F:HEM501 3.5 61.4 1.0 CHC F:HEM501 3.5 61.5 1.0 CA F:CYS356 4.1 53.3 1.0 C3D F:HEM501 4.1 52.2 1.0 C2D F:HEM501 4.1 51.2 1.0 C2A F:HEM501 4.2 55.7 1.0 C3C F:HEM501 4.2 56.9 1.0 C3A F:HEM501 4.2 57.0 1.0 C2C F:HEM501 4.2 60.3 1.0 C2B F:HEM501 4.3 62.0 1.0 C3B F:HEM501 4.3 64.8 1.0 C7 F:TES502 4.6 61.3 1.0 C6 F:TES502 4.6 64.3 1.0 CB F:ALA244 4.7 58.9 1.0 C F:CYS356 4.8 53.0 1.0 N F:ILE357 4.9 53.0 1.0

F.Fata, A.Costanzo, I.Freda, E.Gugole, G.Bulfaro, L.Barbizzi, M.Di Renzo, C.Savino, B.Vallone, L.C.Montemiglio. Olep in Complex with Testosterone in High Salt Crystallization Conditions To Be Published.