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Iron in PDB 3na1: Crystal Structure of Human CYP11A1 in Complex with 20- Hydroxycholesterol

Enzymatic activity of Crystal Structure of Human CYP11A1 in Complex with 20- Hydroxycholesterol

All present enzymatic activity of Crystal Structure of Human CYP11A1 in Complex with 20- Hydroxycholesterol:
1.14.15.6;

Protein crystallography data

The structure of Crystal Structure of Human CYP11A1 in Complex with 20- Hydroxycholesterol, PDB code: 3na1 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) 50.00 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.810, 115.149, 85.727, 90.00, 101.45, 90.00
R / Rfree (%) 19.3 / 23.2

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Human CYP11A1 in Complex with 20- Hydroxycholesterol (pdb code 3na1). 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 20- Hydroxycholesterol, PDB code: 3na1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3na1

Go back to Iron Binding Sites List in 3na1
Iron binding site 1 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with 20- Hydroxycholesterol


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 20- Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:15.0
occ:1.00
 FE A:HEM601 0.0 15.0 1.0
NA A:HEM601 2.0 13.6 1.0
NB A:HEM601 2.1 14.4 1.0
ND A:HEM601 2.1 14.9 1.0
NC A:HEM601 2.1 14.9 1.0
O A:HOH759 2.2 30.8 1.0
SG A:CYS423 2.4 14.1 1.0
C4A A:HEM601 3.0 14.4 1.0
C1A A:HEM601 3.1 14.7 1.0
C1B A:HEM601 3.1 15.0 1.0
C1D A:HEM601 3.1 15.6 1.0
C4B A:HEM601 3.1 15.2 1.0
C4C A:HEM601 3.1 15.4 1.0
C4D A:HEM601 3.1 14.8 1.0
C1C A:HEM601 3.1 14.8 1.0
CHB A:HEM601 3.4 14.7 1.0
CHD A:HEM601 3.4 15.4 1.0
CHA A:HEM601 3.5 14.2 1.0
CHC A:HEM601 3.5 14.9 1.0
CB A:CYS423 3.5 14.5 1.0
O2 A:HCD602 3.8 14.3 1.0
CA A:CYS423 4.1 14.9 1.0
C3A A:HEM601 4.2 14.7 1.0
C2A A:HEM601 4.3 14.3 1.0
C2B A:HEM601 4.3 14.9 1.0
C3B A:HEM601 4.3 14.8 1.0
C3C A:HEM601 4.3 15.0 1.0
C2D A:HEM601 4.3 15.7 1.0
C2C A:HEM601 4.3 15.3 1.0
C3D A:HEM601 4.4 15.3 1.0
N A:GLY425 4.6 15.1 1.0
N A:LEU424 4.7 15.2 1.0
C A:CYS423 4.8 15.0 1.0
C22 A:HCD602 4.8 14.8 1.0
O A:GLY287 4.9 18.1 1.0
C20 A:HCD602 4.9 14.1 1.0

Iron binding site 2 out of 6 in 3na1

Go back to Iron Binding Sites List in 3na1
Iron binding site 2 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with 20- Hydroxycholesterol


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 20- Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:15.1
occ:1.00
 FE B:HEM601 0.0 15.1 1.0
NB B:HEM601 2.0 13.0 1.0
NA B:HEM601 2.1 13.4 1.0
NC B:HEM601 2.1 14.4 1.0
ND B:HEM601 2.1 14.3 1.0
O B:HOH755 2.3 28.7 1.0
SG B:CYS423 2.4 13.6 1.0
C1B B:HEM601 3.0 13.6 1.0
C4A B:HEM601 3.1 13.6 1.0
C4B B:HEM601 3.1 14.3 1.0
C1D B:HEM601 3.1 14.6 1.0
C4C B:HEM601 3.1 15.1 1.0
C1A B:HEM601 3.1 13.5 1.0
C1C B:HEM601 3.1 14.6 1.0
C4D B:HEM601 3.1 14.0 1.0
CHD B:HEM601 3.4 15.0 1.0
CHB B:HEM601 3.4 13.4 1.0
CHA B:HEM601 3.5 13.6 1.0
CHC B:HEM601 3.5 14.5 1.0
CB B:CYS423 3.5 14.6 1.0
O2 B:HCD602 3.7 13.6 1.0
CA B:CYS423 4.1 15.1 1.0
C2B B:HEM601 4.3 13.7 1.0
C3B B:HEM601 4.3 13.8 1.0
C3A B:HEM601 4.3 13.0 1.0
C3C B:HEM601 4.3 14.9 1.0
C2C B:HEM601 4.3 15.4 1.0
C2A B:HEM601 4.3 12.9 1.0
C2D B:HEM601 4.3 14.8 1.0
C3D B:HEM601 4.3 14.8 1.0
N B:GLY425 4.6 14.5 1.0
N B:LEU424 4.7 15.0 1.0
C B:CYS423 4.8 15.2 1.0
C22 B:HCD602 4.9 13.9 1.0
O B:GLY287 4.9 18.8 1.0
C20 B:HCD602 5.0 13.0 1.0

Iron binding site 3 out of 6 in 3na1

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Iron binding site 3 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with 20- Hydroxycholesterol


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 20- Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:99.7
occ:1.00
 FE1 C:FES150 0.0 99.7 1.0
SG C:CYS46 2.1 77.5 1.0
S2 C:FES150 2.2 99.7 1.0
S1 C:FES150 2.2 99.6 1.0
SG C:CYS52 2.6 81.2 1.0
FE2 C:FES150 3.1 0.2 1.0
CB C:CYS46 3.4 78.2 1.0
N C:CYS46 3.7 78.1 1.0
CB C:CYS52 3.8 81.5 1.0
N C:CYS52 3.9 81.2 1.0
CA C:CYS46 4.0 78.2 1.0
CA C:CYS52 4.2 81.5 1.0
C C:CYS52 4.2 81.8 1.0
N C:ALA51 4.2 80.3 1.0
O C:CYS52 4.3 81.8 1.0
N C:GLU47 4.4 78.6 1.0
C C:CYS46 4.5 78.3 1.0
N C:GLY48 4.6 78.9 1.0
C C:ALA51 4.6 80.9 1.0
N C:ALA45 4.6 78.0 1.0
N C:LEU50 4.6 79.5 1.0
SG C:CYS55 4.7 84.2 1.0
N C:SER53 4.7 82.2 1.0
OG1 C:THR54 4.8 83.2 1.0
C C:ALA45 4.8 78.0 1.0
N C:THR49 4.9 79.1 1.0
CA C:LEU50 4.9 79.8 1.0
CA C:ALA51 5.0 80.7 1.0

Iron binding site 4 out of 6 in 3na1

Go back to Iron Binding Sites List in 3na1
Iron binding site 4 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with 20- Hydroxycholesterol


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 20- Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:0.2
occ:1.00
 FE2 C:FES150 0.0 0.2 1.0
S1 C:FES150 2.2 99.6 1.0
S2 C:FES150 2.2 99.7 1.0
SG C:CYS55 2.5 84.2 1.0
SG C:CYS92 2.6 98.3 1.0
FE1 C:FES150 3.1 99.7 1.0
CB C:CYS92 3.4 98.6 1.0
CB C:CYS55 3.8 83.6 1.0
N C:CYS92 4.0 98.6 1.0
CD2 C:LEU90 4.2 98.2 1.0
CA C:CYS92 4.3 98.6 1.0
SG C:CYS46 4.5 77.5 1.0
CA C:GLY48 4.6 79.0 1.0
N C:GLY48 4.7 78.9 1.0
N C:LEU50 4.8 79.5 1.0
N C:GLY91 4.9 98.6 1.0
CG C:LEU90 5.0 98.4 1.0

Iron binding site 5 out of 6 in 3na1

Go back to Iron Binding Sites List in 3na1
Iron binding site 5 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with 20- Hydroxycholesterol


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 20- Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe151

b:0.4
occ:1.00
 FE1 D:FES151 0.0 0.4 1.0
SG D:CYS46 2.2 79.1 1.0
S1 D:FES151 2.2 0.6 1.0
S2 D:FES151 2.2 0.4 1.0
SG D:CYS52 2.7 81.2 1.0
FE2 D:FES151 3.0 0.5 1.0
CB D:CYS46 3.6 79.4 1.0
N D:CYS52 3.8 81.0 1.0
CB D:CYS52 3.9 81.2 1.0
N D:CYS46 4.0 79.3 1.0
N D:ALA51 4.2 80.4 1.0
CA D:CYS52 4.2 81.3 1.0
C D:CYS52 4.2 81.5 1.0
O D:CYS52 4.2 81.5 1.0
CA D:CYS46 4.2 79.4 1.0
N D:LEU50 4.3 80.0 1.0
N D:GLU47 4.4 79.7 1.0
N D:GLY48 4.5 80.0 1.0
SG D:CYS55 4.5 82.4 1.0
N D:THR49 4.5 79.9 1.0
C D:CYS46 4.6 79.6 1.0
C D:ALA51 4.6 80.8 1.0
CA D:LEU50 4.7 80.1 1.0
N D:ALA45 4.8 79.2 1.0
N D:SER53 4.8 81.7 1.0
SG D:CYS92 4.9 97.4 1.0
CA D:ALA51 4.9 80.6 1.0
C D:LEU50 5.0 80.2 1.0
OG1 D:THR54 5.0 82.2 1.0

Iron binding site 6 out of 6 in 3na1

Go back to Iron Binding Sites List in 3na1
Iron binding site 6 out of 6 in the Crystal Structure of Human CYP11A1 in Complex with 20- Hydroxycholesterol


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 20- Hydroxycholesterol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe151

b:0.5
occ:1.00
 FE2 D:FES151 0.0 0.5 1.0
SG D:CYS55 2.2 82.4 1.0
S2 D:FES151 2.2 0.4 1.0
S1 D:FES151 2.2 0.6 1.0
SG D:CYS92 2.9 97.4 1.0
FE1 D:FES151 3.0 0.4 1.0
CB D:CYS92 3.3 97.6 1.0
CB D:CYS55 3.8 82.3 1.0
N D:CYS92 4.0 97.6 1.0
CD2 D:LEU90 4.2 97.5 1.0
CA D:CYS92 4.3 97.6 1.0
CB D:LEU90 4.5 97.5 1.0
N D:GLY91 4.5 97.5 1.0
CG D:LEU90 4.7 97.5 1.0
CD1 D:LEU90 4.7 97.4 1.0
C D:GLY91 4.8 97.6 1.0
CA D:CYS55 4.9 82.3 1.0
SG D:CYS52 4.9 81.2 1.0
SG D:CYS46 5.0 79.1 1.0
N D:CYS55 5.0 82.2 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: Sun Aug 4 16:24:57 2024

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