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Iron in PDB 3n9y: Crystal Structure of Human CYP11A1 in Complex with Cholesterol

Enzymatic activity of Crystal Structure of Human CYP11A1 in Complex with Cholesterol

All present enzymatic activity of Crystal Structure of Human CYP11A1 in Complex with Cholesterol:
1.14.15.6;

Protein crystallography data

The structure of Crystal Structure of Human CYP11A1 in Complex with Cholesterol, PDB code: 3n9y was solved by N.V.Strushkevich, F.Mackenzie, W.Tempel, A.Botchkarev, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.U.Weigelt, H.Park, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.999, 114.686, 86.019, 90.00, 101.96, 90.00
R / Rfree (%) 20.5 / 24.2

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human CYP11A1 in Complex with Cholesterol (pdb code 3n9y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Human CYP11A1 in Complex with Cholesterol, PDB code: 3n9y:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3n9y

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Iron binding site 1 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with Cholesterol


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 Human CYP11A1 in Complex with Cholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:21.2
occ:1.00
 FE A:HEM601 0.0 21.2 1.0
NA A:HEM601 2.0 19.8 1.0
NC A:HEM601 2.0 21.0 1.0
NB A:HEM601 2.1 21.6 1.0
ND A:HEM601 2.1 20.3 1.0
SG A:CYS423 2.5 21.0 1.0
C1A A:HEM601 3.0 20.7 1.0
C4A A:HEM601 3.0 19.6 1.0
C1C A:HEM601 3.0 21.8 1.0
C4C A:HEM601 3.1 20.3 1.0
C4B A:HEM601 3.1 22.0 1.0
C1B A:HEM601 3.1 21.6 1.0
C4D A:HEM601 3.1 21.3 1.0
C1D A:HEM601 3.1 21.3 1.0
CHC A:HEM601 3.4 20.9 1.0
CHA A:HEM601 3.4 19.8 1.0
CHD A:HEM601 3.5 20.5 1.0
CHB A:HEM601 3.5 20.7 1.0
CB A:CYS423 3.5 20.8 1.0
CA A:CYS423 4.1 21.1 1.0
C3A A:HEM601 4.2 18.7 1.0
C2A A:HEM601 4.2 19.4 1.0
C3C A:HEM601 4.2 21.2 1.0
C2C A:HEM601 4.3 21.6 1.0
C3B A:HEM601 4.3 21.9 1.0
C22 A:CLR602 4.3 19.0 1.0
C2B A:HEM601 4.3 21.4 1.0
C3D A:HEM601 4.4 19.8 1.0
C2D A:HEM601 4.4 21.4 1.0
C20 A:CLR602 4.5 19.1 1.0
N A:GLY425 4.6 21.8 1.0
N A:LEU424 4.7 22.3 1.0
C A:CYS423 4.7 21.8 1.0

Iron binding site 2 out of 6 in 3n9y

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Iron binding site 2 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with Cholesterol


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 Human CYP11A1 in Complex with Cholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:19.4
occ:1.00
 FE B:HEM601 0.0 19.4 1.0
NB B:HEM601 2.0 17.9 1.0
NA B:HEM601 2.0 18.1 1.0
NC B:HEM601 2.1 18.9 1.0
ND B:HEM601 2.1 19.0 1.0
SG B:CYS423 2.5 20.5 1.0
C4B B:HEM601 3.0 19.0 1.0
C1A B:HEM601 3.0 19.3 1.0
C4A B:HEM601 3.1 17.7 1.0
C1B B:HEM601 3.1 19.0 1.0
C4D B:HEM601 3.1 20.9 1.0
C1C B:HEM601 3.1 20.1 1.0
C4C B:HEM601 3.1 21.0 1.0
C1D B:HEM601 3.1 21.3 1.0
CB B:CYS423 3.4 20.9 1.0
CHC B:HEM601 3.4 18.1 1.0
CHA B:HEM601 3.4 18.7 1.0
CHB B:HEM601 3.5 17.4 1.0
CHD B:HEM601 3.5 20.4 1.0
CA B:CYS423 4.1 21.3 1.0
C3B B:HEM601 4.3 17.9 1.0
C2A B:HEM601 4.3 18.6 1.0
C3A B:HEM601 4.3 17.6 1.0
C2B B:HEM601 4.3 18.0 1.0
C3C B:HEM601 4.3 20.8 1.0
C2C B:HEM601 4.3 20.7 1.0
C3D B:HEM601 4.3 20.4 1.0
C22 B:CLR602 4.3 18.8 1.0
C2D B:HEM601 4.4 21.0 1.0
C20 B:CLR602 4.5 20.1 1.0
N B:GLY425 4.6 22.0 1.0
C B:CYS423 4.7 21.9 1.0
N B:LEU424 4.7 21.8 1.0

Iron binding site 3 out of 6 in 3n9y

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Iron binding site 3 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with Cholesterol


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 Human CYP11A1 in Complex with Cholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:47.1
occ:1.00
 FE1 C:FES150 0.0 47.1 1.0
SG C:CYS46 2.1 55.6 1.0
S1 C:FES150 2.2 48.9 1.0
S2 C:FES150 2.2 50.8 1.0
SG C:CYS52 2.4 54.8 1.0
FE2 C:FES150 3.0 50.4 1.0
CB C:CYS46 3.3 56.8 1.0
N C:CYS52 3.4 55.4 1.0
CB C:CYS52 3.5 56.0 1.0
N C:CYS46 3.8 57.8 1.0
CA C:CYS52 3.8 56.2 1.0
N C:ALA51 4.0 53.5 1.0
CA C:CYS46 4.0 56.8 1.0
C C:CYS52 4.0 57.0 1.0
O C:CYS52 4.2 57.7 1.0
C C:ALA51 4.2 54.7 1.0
N C:GLU47 4.3 56.1 1.0
N C:GLY48 4.4 54.5 1.0
C C:CYS46 4.4 56.5 1.0
N C:LEU50 4.5 52.5 1.0
SG C:CYS92 4.5 60.1 1.0
N C:SER53 4.5 57.8 1.0
SG C:CYS55 4.6 62.6 1.0
N C:THR49 4.6 53.2 1.0
CA C:ALA51 4.7 54.1 1.0
CA C:LEU50 4.7 52.7 1.0
OG1 C:THR54 4.8 60.5 1.0
N C:ALA45 4.8 60.8 1.0
C C:LEU50 4.8 53.0 1.0
CA C:GLY48 4.9 54.1 1.0
C C:GLY44 4.9 62.1 1.0
CA C:GLY44 5.0 63.3 1.0
N C:THR54 5.0 59.8 1.0

Iron binding site 4 out of 6 in 3n9y

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Iron binding site 4 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with Cholesterol


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 Human CYP11A1 in Complex with Cholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:50.4
occ:1.00
 FE2 C:FES150 0.0 50.4 1.0
SG C:CYS55 2.2 62.6 1.0
S2 C:FES150 2.2 50.8 1.0
S1 C:FES150 2.2 48.9 1.0
SG C:CYS92 2.2 60.1 1.0
FE1 C:FES150 3.0 47.1 1.0
CB C:CYS92 3.1 62.2 1.0
CB C:CYS55 3.2 63.4 1.0
N C:CYS92 4.0 62.9 1.0
CA C:CYS92 4.2 62.0 1.0
CA C:CYS55 4.4 63.4 1.0
N C:CYS55 4.5 62.5 1.0
CA C:GLY48 4.6 54.1 1.0
SG C:CYS46 4.6 55.6 1.0
SG C:CYS52 4.7 54.8 1.0
CB C:LEU90 4.7 66.0 1.0
N C:GLY48 4.7 54.5 1.0
N C:LEU50 4.9 52.5 1.0
CD2 C:LEU90 4.9 65.8 1.0
CA C:LEU50 5.0 52.7 1.0

Iron binding site 5 out of 6 in 3n9y

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Iron binding site 5 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with Cholesterol


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 Human CYP11A1 in Complex with Cholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe151

b:47.5
occ:1.00
 FE1 D:FES151 0.0 47.5 1.0
SG D:CYS46 2.0 59.3 1.0
S1 D:FES151 2.2 48.3 1.0
S2 D:FES151 2.2 50.0 1.0
SG D:CYS52 2.5 58.3 1.0
FE2 D:FES151 3.1 51.5 1.0
CB D:CYS46 3.2 59.9 1.0
N D:CYS52 3.4 58.9 1.0
CB D:CYS52 3.6 59.5 1.0
N D:CYS46 3.8 60.8 1.0
N D:ALA51 3.9 56.7 1.0
CA D:CYS52 3.9 59.5 1.0
CA D:CYS46 4.0 59.9 1.0
C D:CYS52 4.1 60.3 1.0
N D:GLY48 4.2 56.6 1.0
N D:LEU50 4.3 55.3 1.0
O D:CYS52 4.3 60.7 1.0
C D:ALA51 4.3 58.0 1.0
C D:CYS46 4.4 59.3 1.0
N D:THR49 4.4 55.6 1.0
SG D:CYS92 4.5 65.7 1.0
CA D:GLY48 4.6 56.2 1.0
CA D:LEU50 4.6 55.8 1.0
N D:GLU47 4.6 58.6 1.0
CA D:ALA51 4.6 57.4 1.0
N D:SER53 4.7 61.0 1.0
C D:LEU50 4.7 56.2 1.0
OG1 D:THR54 4.8 63.5 1.0
SG D:CYS55 4.8 66.2 1.0
N D:ALA45 4.8 63.8 1.0
C D:GLY44 4.8 65.1 1.0
C D:GLY48 4.9 56.0 1.0
CA D:GLY44 4.9 66.2 1.0
O D:CYS46 5.0 59.2 1.0

Iron binding site 6 out of 6 in 3n9y

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Iron binding site 6 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with Cholesterol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Human CYP11A1 in Complex with Cholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe151

b:51.5
occ:1.00
 FE2 D:FES151 0.0 51.5 1.0
SG D:CYS55 2.1 66.2 1.0
S2 D:FES151 2.2 50.0 1.0
S1 D:FES151 2.2 48.3 1.0
SG D:CYS92 2.4 65.7 1.0
FE1 D:FES151 3.1 47.5 1.0
CB D:CYS55 3.1 66.9 1.0
CB D:CYS92 3.3 67.1 1.0
N D:CYS92 4.1 67.5 1.0
CA D:CYS92 4.3 66.9 1.0
CA D:CYS55 4.3 67.0 1.0
N D:CYS55 4.3 65.8 1.0
SG D:CYS52 4.6 58.3 1.0
CA D:GLY48 4.6 56.2 1.0
CB D:LEU90 4.7 70.2 1.0
CD1 D:LEU90 4.7 69.7 1.0
SG D:CYS46 4.7 59.3 1.0
CD2 D:LEU90 4.8 69.5 1.0
N D:LEU50 4.8 55.3 1.0
CA D:LEU50 4.9 55.8 1.0
CD1 D:LEU30 4.9 90.2 1.0
CG D:LEU90 5.0 70.0 1.0

Reference:

N.Strushkevich, F.Mackenzie, T.Cherkesova, I.Grabovec, S.Usanov, H.W.Park. Structural Basis For Pregnenolone Biosynthesis By the Mitochondrial Monooxygenase System. Proc.Natl.Acad.Sci.Usa V. 108 10139 2011.
ISSN: ISSN 0027-8424
PubMed: 21636783
DOI: 10.1073/PNAS.1019441108
Page generated: Tue Aug 5 04:42:11 2025

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