Iron in PDB 6t0f: Crystal Structure of CYP124 in Complex with Cholest-4-En-3-One

All present enzymatic activity of Crystal Structure of CYP124 in Complex with Cholest-4-En-3-One:
1.14.15.14; 1.14.15.28;

The structure of Crystal Structure of CYP124 in Complex with Cholest-4-En-3-One, PDB code: 6t0f was solved by S.Bukhdruker, E.Marin, T.Varaksa, A.Gilep, N.Strushkevich, V.Borshchevskiy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.75 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.670, 81.270, 155.850, 90.00, 107.29, 90.00
R / Rfree (%)	15.2 / 18.5

The binding sites of Iron atom in the Crystal Structure of CYP124 in Complex with Cholest-4-En-3-One (pdb code 6t0f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of CYP124 in Complex with Cholest-4-En-3-One, PDB code: 6t0f:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Crystal Structure of CYP124 in Complex with Cholest-4-En-3-One


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 CYP124 in Complex with Cholest-4-En-3-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.6 occ:0.50 FE A:HEM501 0.0 19.6 0.5 FE A:HEM501 0.1 19.6 0.5 NC A:HEM501 2.0 21.2 0.5 NB A:HEM501 2.0 19.0 0.5 NB A:HEM501 2.0 19.1 0.5 NA A:HEM501 2.1 18.4 0.5 NC A:HEM501 2.1 21.2 0.5 NA A:HEM501 2.1 18.4 0.5 ND A:HEM501 2.1 19.5 0.5 ND A:HEM501 2.1 19.5 0.5 SG A:CYS379 2.4 21.5 1.0 C1C A:HEM501 3.0 21.1 0.5 C4B A:HEM501 3.0 18.7 0.5 C1B A:HEM501 3.0 18.7 0.5 C4B A:HEM501 3.0 18.8 0.5 C1B A:HEM501 3.1 18.7 0.5 C4A A:HEM501 3.1 18.5 0.5 C1C A:HEM501 3.1 21.1 0.5 C4C A:HEM501 3.1 20.3 0.5 C4A A:HEM501 3.1 18.5 0.5 C1D A:HEM501 3.1 19.6 0.5 C1A A:HEM501 3.1 17.7 0.5 C4D A:HEM501 3.1 18.2 0.5 C1D A:HEM501 3.1 19.5 0.5 C4C A:HEM501 3.1 20.3 0.5 C4D A:HEM501 3.1 18.2 0.5 C1A A:HEM501 3.1 17.8 0.5 CB A:CYS379 3.4 20.4 1.0 CHC A:HEM501 3.4 19.8 0.5 CHC A:HEM501 3.4 19.7 0.5 CHB A:HEM501 3.4 18.3 0.5 CHD A:HEM501 3.4 19.4 0.5 CHB A:HEM501 3.4 18.4 0.5 CHA A:HEM501 3.5 17.2 0.5 CHD A:HEM501 3.5 19.5 0.5 CHA A:HEM501 3.5 17.2 0.5 CA A:CYS379 3.9 19.7 1.0 C26 A:K2B502 4.0 19.8 1.0 C2B A:HEM501 4.2 19.1 0.5 C3B A:HEM501 4.2 19.1 0.5 C2B A:HEM501 4.2 19.1 0.5 C2C A:HEM501 4.3 20.5 0.5 C3B A:HEM501 4.3 19.0 0.5 C3C A:HEM501 4.3 20.1 0.5 C3A A:HEM501 4.3 18.6 0.5 C2C A:HEM501 4.3 20.4 0.5 C2D A:HEM501 4.3 18.7 0.5 C2A A:HEM501 4.3 18.1 0.5 C3A A:HEM501 4.3 18.6 0.5 C2D A:HEM501 4.3 18.8 0.5 C3C A:HEM501 4.3 20.0 0.5 C3D A:HEM501 4.3 18.6 0.5 C3D A:HEM501 4.3 18.5 0.5 C2A A:HEM501 4.3 18.1 0.5 N A:GLY381 4.4 21.2 1.0 N A:LEU380 4.5 23.3 1.0 C A:CYS379 4.5 20.3 1.0 CA A:GLY381 4.9 22.7 1.0 CB A:ALA267 4.9 19.9 1.0

Iron binding site 2 out of 5 in the Crystal Structure of CYP124 in Complex with Cholest-4-En-3-One


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 CYP124 in Complex with Cholest-4-En-3-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.6 occ:0.50 FE A:HEM501 0.0 19.6 0.5 FE A:HEM501 0.1 19.6 0.5 NA A:HEM501 2.0 18.4 0.5 NA A:HEM501 2.0 18.4 0.5 NB A:HEM501 2.0 19.0 0.5 NB A:HEM501 2.1 19.1 0.5 NC A:HEM501 2.1 21.2 0.5 ND A:HEM501 2.1 19.5 0.5 ND A:HEM501 2.1 19.5 0.5 NC A:HEM501 2.1 21.2 0.5 SG A:CYS379 2.4 21.5 1.0 C4A A:HEM501 3.0 18.5 0.5 C4A A:HEM501 3.0 18.5 0.5 C1B A:HEM501 3.0 18.7 0.5 C1A A:HEM501 3.0 17.7 0.5 C1B A:HEM501 3.0 18.7 0.5 C4D A:HEM501 3.1 18.2 0.5 C4B A:HEM501 3.1 18.7 0.5 C1A A:HEM501 3.1 17.8 0.5 C4B A:HEM501 3.1 18.8 0.5 C1D A:HEM501 3.1 19.6 0.5 C1C A:HEM501 3.1 21.1 0.5 C4D A:HEM501 3.1 18.2 0.5 C4C A:HEM501 3.1 20.3 0.5 C1C A:HEM501 3.1 21.1 0.5 C1D A:HEM501 3.1 19.5 0.5 C4C A:HEM501 3.2 20.3 0.5 CB A:CYS379 3.4 20.4 1.0 CHB A:HEM501 3.4 18.3 0.5 CHB A:HEM501 3.4 18.4 0.5 CHA A:HEM501 3.4 17.2 0.5 CHD A:HEM501 3.5 19.4 0.5 CHA A:HEM501 3.5 17.2 0.5 CHC A:HEM501 3.5 19.8 0.5 CHC A:HEM501 3.5 19.7 0.5 CHD A:HEM501 3.5 19.5 0.5 CA A:CYS379 3.9 19.7 1.0 C26 A:K2B502 3.9 19.8 1.0 C3A A:HEM501 4.2 18.6 0.5 C2A A:HEM501 4.2 18.1 0.5 C2B A:HEM501 4.3 19.1 0.5 C3A A:HEM501 4.3 18.6 0.5 C2B A:HEM501 4.3 19.1 0.5 C3B A:HEM501 4.3 19.1 0.5 C2A A:HEM501 4.3 18.1 0.5 C3B A:HEM501 4.3 19.0 0.5 C2D A:HEM501 4.3 18.7 0.5 C3D A:HEM501 4.3 18.6 0.5 C3D A:HEM501 4.3 18.5 0.5 C2D A:HEM501 4.3 18.8 0.5 C2C A:HEM501 4.3 20.5 0.5 C3C A:HEM501 4.3 20.1 0.5 C2C A:HEM501 4.4 20.4 0.5 C3C A:HEM501 4.4 20.0 0.5 N A:GLY381 4.4 21.2 1.0 N A:LEU380 4.5 23.3 1.0 C A:CYS379 4.5 20.3 1.0 CB A:ALA267 4.9 19.9 1.0 CA A:GLY381 4.9 22.7 1.0

Iron binding site 3 out of 5 in the Crystal Structure of CYP124 in Complex with Cholest-4-En-3-One


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 CYP124 in Complex with Cholest-4-En-3-One within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:18.6 occ:1.00 FE B:HEM501 0.0 18.6 1.0 NA B:HEM501 2.0 15.5 1.0 ND B:HEM501 2.1 18.8 1.0 NC B:HEM501 2.1 20.1 1.0 NB B:HEM501 2.1 18.6 1.0 SG B:CYS379 2.4 18.9 1.0 C1C B:HEM501 3.1 18.7 1.0 C4A B:HEM501 3.1 17.9 1.0 C4D B:HEM501 3.1 17.4 1.0 C1A B:HEM501 3.1 18.4 1.0 C1B B:HEM501 3.1 17.6 1.0 C1D B:HEM501 3.1 20.2 1.0 C4B B:HEM501 3.1 17.9 1.0 C4C B:HEM501 3.1 19.2 1.0 CHC B:HEM501 3.4 17.7 1.0 CB B:CYS379 3.4 17.1 1.0 CHB B:HEM501 3.5 17.6 1.0 CHA B:HEM501 3.5 16.9 1.0 CHD B:HEM501 3.5 19.6 1.0 CA B:CYS379 4.0 17.4 1.0 C26 B:K2B502 4.0 19.1 1.0 C3A B:HEM501 4.3 17.1 1.0 C2D B:HEM501 4.3 20.1 1.0 C2C B:HEM501 4.3 20.4 1.0 C3B B:HEM501 4.3 19.4 1.0 C2B B:HEM501 4.3 17.2 1.0 C2A B:HEM501 4.3 20.3 1.0 C3D B:HEM501 4.3 18.5 1.0 C3C B:HEM501 4.3 17.9 1.0 N B:GLY381 4.4 20.5 1.0 N B:LEU380 4.5 18.8 1.0 C B:CYS379 4.5 19.6 1.0 CB B:ALA267 4.8 20.3 1.0 CA B:GLY381 4.9 20.7 1.0

Iron binding site 4 out of 5 in the Crystal Structure of CYP124 in Complex with Cholest-4-En-3-One


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 CYP124 in Complex with Cholest-4-En-3-One within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:17.6 occ:1.00 FE C:HEM501 0.0 17.6 1.0 NA C:HEM501 2.0 15.2 1.0 NC C:HEM501 2.0 18.1 1.0 NB C:HEM501 2.1 16.0 1.0 ND C:HEM501 2.1 19.7 1.0 SG C:CYS379 2.4 17.6 1.0 C1C C:HEM501 3.0 18.7 1.0 C4A C:HEM501 3.0 16.8 1.0 C1A C:HEM501 3.0 17.9 1.0 C1B C:HEM501 3.1 15.7 1.0 C4B C:HEM501 3.1 16.0 1.0 C4D C:HEM501 3.1 19.6 1.0 C4C C:HEM501 3.1 17.8 1.0 C1D C:HEM501 3.2 19.3 1.0 CB C:CYS379 3.4 15.1 1.0 CHC C:HEM501 3.4 19.0 1.0 CHA C:HEM501 3.4 17.9 1.0 CHB C:HEM501 3.4 15.3 1.0 CHD C:HEM501 3.5 20.2 1.0 C26 C:K2B502 3.9 16.8 1.0 CA C:CYS379 4.0 17.7 1.0 C3A C:HEM501 4.3 18.3 1.0 C2C C:HEM501 4.3 17.3 1.0 C2B C:HEM501 4.3 17.1 1.0 C2A C:HEM501 4.3 15.6 1.0 C3B C:HEM501 4.3 14.0 1.0 C3C C:HEM501 4.3 17.9 1.0 C2D C:HEM501 4.4 19.1 1.0 C3D C:HEM501 4.4 19.7 1.0 N C:GLY381 4.5 18.9 1.0 C C:CYS379 4.5 18.1 1.0 N C:LEU380 4.5 19.3 1.0 CB C:ALA267 4.9 16.8 1.0 CA C:GLY381 5.0 19.0 1.0

Iron binding site 5 out of 5 in the Crystal Structure of CYP124 in Complex with Cholest-4-En-3-One


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of CYP124 in Complex with Cholest-4-En-3-One within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:17.3 occ:1.00 FE D:HEM501 0.0 17.3 1.0 NB D:HEM501 2.0 18.2 1.0 NA D:HEM501 2.1 16.6 1.0 ND D:HEM501 2.1 17.7 1.0 NC D:HEM501 2.1 18.8 1.0 SG D:CYS379 2.4 18.9 1.0 C4B D:HEM501 3.0 18.0 1.0 C1B D:HEM501 3.0 16.3 1.0 C4D D:HEM501 3.1 16.4 1.0 C1A D:HEM501 3.1 18.4 1.0 C1D D:HEM501 3.1 17.7 1.0 C4A D:HEM501 3.1 15.2 1.0 C1C D:HEM501 3.1 18.9 1.0 C4C D:HEM501 3.2 17.7 1.0 CB D:CYS379 3.3 16.3 1.0 CHC D:HEM501 3.4 18.4 1.0 CHA D:HEM501 3.4 17.7 1.0 CHB D:HEM501 3.5 16.7 1.0 CHD D:HEM501 3.5 17.0 1.0 CA D:CYS379 3.9 19.1 1.0 C26 D:K2B502 4.0 18.6 1.0 C3B D:HEM501 4.2 19.1 1.0 C2B D:HEM501 4.2 16.7 1.0 C2D D:HEM501 4.3 19.1 1.0 C3A D:HEM501 4.3 14.9 1.0 C3D D:HEM501 4.3 18.8 1.0 C2C D:HEM501 4.3 19.1 1.0 C2A D:HEM501 4.3 16.2 1.0 C3C D:HEM501 4.4 16.8 1.0 N D:GLY381 4.4 19.1 1.0 N D:LEU380 4.5 17.9 1.0 C D:CYS379 4.5 18.2 1.0 CA D:GLY381 4.9 19.3 1.0 CB D:ALA267 4.9 19.2 1.0

T.Varaksa, S.Bukhdruker, I.Grabovec, E.Marin, A.Kavaleuski, A.Gusach, K.Kovalev, I.Maslov, A.Luginina, D.Zabelskiy, R.Astashkin, M.Shevtsov, S.Smolskaya, A.Kavaleuskaya, P.Shabunya, A.Baranovsky, V.Dolgopalets, Y.Charnou, A.Savachka, R.Litvinovskaya, E.Shevchenko, A.Rogachev, A.Mishin, V.Gordeliy, A.Gabrielian, D.E.Hurt, B.Nikonenko, K.Majorov, A.Apt, A.Rosenthal, A.Gilep, V.Borshchevskiy, N.Strushkevich. Metabolic Fate of Human Immunoactive Oxysterols in Mycobacterium Tuberculosis To Be Published.