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Iron in PDB 7zb9: Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo)

Enzymatic activity of Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo)

All present enzymatic activity of Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo):
1.14.15.14; 1.14.15.28;

Protein crystallography data

The structure of Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo), PDB code: 7zb9 was solved by S.Bukhdruker, T.Varaksa, E.Marin, 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) 29.50 / 1.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.54, 75.08, 56.56, 90, 106.96, 90
R / Rfree (%) 13 / 15.7

Other elements in 7zb9:

The structure of Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Magnesium (Mg) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo) (pdb code 7zb9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo), PDB code: 7zb9:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 7zb9

Go back to Iron Binding Sites List in 7zb9
Iron binding site 1 out of 2 in the Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo)


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 Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:6.2
occ:0.55
 FE A:HEM501 0.0 6.2 0.6
FE A:HEM501 0.1 8.0 0.5
N1 A:M65502 1.9 11.6 0.2
ND A:HEM501 2.0 7.2 0.6
ND A:HEM501 2.0 8.3 0.5
NC A:HEM501 2.0 7.5 0.5
NA A:HEM501 2.0 6.5 0.6
NB A:HEM501 2.0 6.3 0.6
NC A:HEM501 2.0 6.5 0.6
NA A:HEM501 2.0 7.6 0.5
NB A:HEM501 2.0 7.6 0.5
N1 A:M65502 2.1 7.3 0.4
N1 A:M65502 2.2 6.1 0.4
SG A:CYS379 2.3 7.0 1.0
C2 A:M65502 2.4 13.2 0.2
C1D A:HEM501 3.0 7.0 0.6
C4C A:HEM501 3.0 7.3 0.5
C1D A:HEM501 3.0 7.8 0.5
C1C A:HEM501 3.0 7.4 0.5
C4D A:HEM501 3.0 7.7 0.6
C1 A:M65502 3.0 7.0 0.4
C4C A:HEM501 3.0 6.9 0.6
C1B A:HEM501 3.0 5.8 0.6
C4A A:HEM501 3.0 5.8 0.6
C4D A:HEM501 3.0 8.3 0.5
C1A A:HEM501 3.0 7.2 0.5
C1A A:HEM501 3.0 6.7 0.6
C1C A:HEM501 3.1 6.5 0.6
C4B A:HEM501 3.1 7.2 0.5
C4B A:HEM501 3.1 6.6 0.6
C1B A:HEM501 3.1 6.9 0.5
C1 A:M65502 3.1 13.1 0.2
C4A A:HEM501 3.1 6.7 0.5
C2 A:M65502 3.1 8.7 0.4
C1 A:M65502 3.1 6.7 0.4
C2 A:M65502 3.2 5.3 0.4
CHD A:HEM501 3.4 7.2 0.6
CHD A:HEM501 3.4 7.2 0.5
CHA A:HEM501 3.4 7.2 0.6
CHA A:HEM501 3.4 7.6 0.5
CHB A:HEM501 3.4 5.9 0.6
CB A:CYS379 3.4 7.6 1.0
CHC A:HEM501 3.4 7.2 0.5
CHC A:HEM501 3.4 6.3 0.6
CHB A:HEM501 3.5 6.7 0.5
C3 A:M65502 3.6 14.2 0.2
N2 A:M65502 4.0 14.3 0.2
CA A:CYS379 4.1 7.2 1.0
N2 A:M65502 4.2 7.4 0.4
C2D A:HEM501 4.2 7.6 0.6
C3 A:M65502 4.2 8.1 0.4
C3C A:HEM501 4.2 7.3 0.5
C3D A:HEM501 4.2 7.5 0.6
C2C A:HEM501 4.2 7.5 0.5
C3C A:HEM501 4.3 7.2 0.6
C2D A:HEM501 4.3 8.5 0.5
C3A A:HEM501 4.3 6.5 0.6
C2A A:HEM501 4.3 7.0 0.6
C2C A:HEM501 4.3 6.6 0.6
C3D A:HEM501 4.3 8.3 0.5
C2B A:HEM501 4.3 6.3 0.6
C2A A:HEM501 4.3 6.9 0.5
C3B A:HEM501 4.3 6.7 0.6
N2 A:M65502 4.3 7.5 0.4
C3B A:HEM501 4.3 7.1 0.5
C2B A:HEM501 4.3 7.1 0.5
C3A A:HEM501 4.3 6.8 0.5
C3 A:M65502 4.3 6.0 0.4
N A:GLY381 4.6 7.1 1.0
C A:CYS379 4.7 6.9 1.0
N A:LEU380 4.7 7.0 1.0
CB A:ALA267 4.8 10.0 1.0

Iron binding site 2 out of 2 in 7zb9

Go back to Iron Binding Sites List in 7zb9
Iron binding site 2 out of 2 in the Crystal Structure of CYP124 in Complex with Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo)


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 Inhibitor Carbethoxyhexyl Imidazole in the Absence of Glycerol (Nocryo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:8.0
occ:0.45
 FE A:HEM501 0.0 8.0 0.5
FE A:HEM501 0.1 6.2 0.6
N1 A:M65502 1.9 11.6 0.2
NA A:HEM501 2.0 6.5 0.6
ND A:HEM501 2.0 7.2 0.6
NB A:HEM501 2.0 6.3 0.6
NA A:HEM501 2.0 7.6 0.5
NB A:HEM501 2.0 7.6 0.5
ND A:HEM501 2.0 8.3 0.5
N1 A:M65502 2.0 7.3 0.4
NC A:HEM501 2.0 7.5 0.5
NC A:HEM501 2.1 6.5 0.6
N1 A:M65502 2.1 6.1 0.4
SG A:CYS379 2.3 7.0 1.0
C2 A:M65502 2.4 13.2 0.2
C4A A:HEM501 3.0 5.8 0.6
C1B A:HEM501 3.0 5.8 0.6
C1 A:M65502 3.0 7.0 0.4
C1D A:HEM501 3.0 7.0 0.6
C1A A:HEM501 3.0 7.2 0.5
C1B A:HEM501 3.0 6.9 0.5
C1A A:HEM501 3.0 6.7 0.6
C1 A:M65502 3.0 13.1 0.2
C4A A:HEM501 3.0 6.7 0.5
C4D A:HEM501 3.0 7.7 0.6
C2 A:M65502 3.0 8.7 0.4
C1C A:HEM501 3.0 7.4 0.5
C4B A:HEM501 3.0 7.2 0.5
C4B A:HEM501 3.1 6.6 0.6
C4C A:HEM501 3.1 7.3 0.5
C4D A:HEM501 3.1 8.3 0.5
C1D A:HEM501 3.1 7.8 0.5
C1C A:HEM501 3.1 6.5 0.6
C4C A:HEM501 3.1 6.9 0.6
C1 A:M65502 3.1 6.7 0.4
C2 A:M65502 3.2 5.3 0.4
CHB A:HEM501 3.4 5.9 0.6
CHA A:HEM501 3.4 7.2 0.6
CHA A:HEM501 3.4 7.6 0.5
CHD A:HEM501 3.4 7.2 0.6
CHB A:HEM501 3.4 6.7 0.5
CHC A:HEM501 3.4 7.2 0.5
CHD A:HEM501 3.4 7.2 0.5
CB A:CYS379 3.4 7.6 1.0
CHC A:HEM501 3.4 6.3 0.6
C3 A:M65502 3.6 14.2 0.2
N2 A:M65502 3.9 14.3 0.2
CA A:CYS379 4.1 7.2 1.0
N2 A:M65502 4.2 7.4 0.4
C3 A:M65502 4.2 8.1 0.4
C3A A:HEM501 4.2 6.5 0.6
C2B A:HEM501 4.2 6.3 0.6
C2A A:HEM501 4.2 7.0 0.6
N2 A:M65502 4.2 7.5 0.4
C2A A:HEM501 4.2 6.9 0.5
C3B A:HEM501 4.2 6.7 0.6
C2D A:HEM501 4.2 7.6 0.6
C2B A:HEM501 4.3 7.1 0.5
C3A A:HEM501 4.3 6.8 0.5
C3B A:HEM501 4.3 7.1 0.5
C3D A:HEM501 4.3 7.5 0.6
C2C A:HEM501 4.3 7.5 0.5
C3C A:HEM501 4.3 7.3 0.5
C3 A:M65502 4.3 6.0 0.4
C2D A:HEM501 4.3 8.5 0.5
C3C A:HEM501 4.3 7.2 0.6
C2C A:HEM501 4.3 6.6 0.6
C3D A:HEM501 4.3 8.3 0.5
N A:GLY381 4.7 7.1 1.0
C A:CYS379 4.7 6.9 1.0
N A:LEU380 4.8 7.0 1.0
CB A:ALA267 4.8 10.0 1.0

Reference:

S.Bukhdruker, T.Varaksa, P.Orekhov, I.Grabovec, E.Marin, I.Kapranov, K.Kovalev, R.Astashkin, L.Kaluzhskiy, A.Ivanov, A.Mishin, A.Rogachev, V.Gordeliy, A.Gilep, N.Strushkevich, V.Borshchevskiy. Structural Insights Into the Effects of Glycerol on Ligand Binding to Cytochrome P450 Acta Crystallogr.,Sect.D V. 79 66 2023.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798322011019
Page generated: Fri Aug 9 13:53:53 2024

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