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

Enzymatic activity of 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;

Protein crystallography data

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

Iron Binding Sites:

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 6t0f

Go back to Iron Binding Sites List in 6t0f
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 6t0f

Go back to Iron Binding Sites List in 6t0f
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 6t0f

Go back to Iron Binding Sites List in 6t0f
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 6t0f

Go back to Iron Binding Sites List in 6t0f
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 6t0f

Go back to Iron Binding Sites List in 6t0f
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

Reference:

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.
Page generated: Sun Dec 13 17:06:27 2020

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