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Iron in PDB 2yoo: Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis

Protein crystallography data

The structure of Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis, PDB code: 2yoo was solved by E.Garcia-Fernandez, D.J.Frank, B.Galan, P.M.Kells, L.M.Podust, J.L.Garcia, P.R.Ortiz De Montellano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 126.53 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.683, 106.213, 126.536, 90.00, 90.67, 90.00
R / Rfree (%) 16.5 / 21.9

Other elements in 2yoo:

The structure of Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis (pdb code 2yoo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis, PDB code: 2yoo:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2yoo

Go back to Iron Binding Sites List in 2yoo
Iron binding site 1 out of 4 in the Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1402

b:9.0
occ:1.00
FE A:HEM1402 0.0 9.0 1.0
NB A:HEM1402 2.1 8.4 1.0
NC A:HEM1402 2.1 6.1 1.0
NA A:HEM1402 2.1 8.7 1.0
ND A:HEM1402 2.1 9.6 1.0
SG A:CYS343 2.4 8.1 1.0
C4B A:HEM1402 3.1 8.6 1.0
C4A A:HEM1402 3.1 7.8 1.0
C4C A:HEM1402 3.1 4.2 1.0
C1B A:HEM1402 3.1 8.2 1.0
C1C A:HEM1402 3.1 8.5 1.0
C1A A:HEM1402 3.1 9.4 1.0
C4D A:HEM1402 3.1 9.3 1.0
C1D A:HEM1402 3.2 8.1 1.0
CHC A:HEM1402 3.4 7.4 1.0
CB A:CYS343 3.4 8.5 1.0
CHB A:HEM1402 3.5 4.4 1.0
CHA A:HEM1402 3.5 7.6 1.0
CHD A:HEM1402 3.5 7.9 1.0
CA A:CYS343 4.0 7.7 1.0
C26 A:K2B1404 4.1 12.6 1.0
C3B A:HEM1402 4.3 12.7 1.0
C3C A:HEM1402 4.3 7.4 1.0
C2C A:HEM1402 4.3 7.5 1.0
C2B A:HEM1402 4.3 8.2 1.0
C2A A:HEM1402 4.3 6.4 1.0
C3A A:HEM1402 4.3 5.9 1.0
C2D A:HEM1402 4.4 11.1 1.0
C3D A:HEM1402 4.4 6.2 1.0
N A:GLY345 4.6 9.8 1.0
N A:LEU344 4.6 7.5 1.0
C A:CYS343 4.7 7.8 1.0
CA A:GLY233 4.9 9.3 1.0

Iron binding site 2 out of 4 in 2yoo

Go back to Iron Binding Sites List in 2yoo
Iron binding site 2 out of 4 in the Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1402

b:8.2
occ:1.00
FE B:HEM1402 0.0 8.2 1.0
NB B:HEM1402 2.0 6.3 1.0
NA B:HEM1402 2.1 6.9 1.0
ND B:HEM1402 2.1 6.6 1.0
NC B:HEM1402 2.1 5.0 1.0
SG B:CYS343 2.4 8.4 1.0
C4B B:HEM1402 3.1 7.2 1.0
C4A B:HEM1402 3.1 6.1 1.0
C4D B:HEM1402 3.1 4.0 1.0
C1B B:HEM1402 3.1 8.8 1.0
C1A B:HEM1402 3.1 5.6 1.0
C1C B:HEM1402 3.1 9.1 1.0
C4C B:HEM1402 3.1 6.4 1.0
C1D B:HEM1402 3.2 10.4 1.0
CB B:CYS343 3.4 6.5 1.0
CHC B:HEM1402 3.4 7.4 1.0
CHA B:HEM1402 3.4 4.8 1.0
CHB B:HEM1402 3.4 5.7 1.0
CHD B:HEM1402 3.5 5.3 1.0
C26 B:K2B1404 3.9 11.1 1.0
CA B:CYS343 4.0 7.6 1.0
C3B B:HEM1402 4.3 5.1 1.0
C2B B:HEM1402 4.3 7.4 1.0
C3A B:HEM1402 4.3 9.0 1.0
C2A B:HEM1402 4.3 8.6 1.0
C3D B:HEM1402 4.3 7.6 1.0
C3C B:HEM1402 4.4 5.3 1.0
C2C B:HEM1402 4.4 8.3 1.0
C2D B:HEM1402 4.4 9.7 1.0
N B:GLY345 4.5 7.2 1.0
C B:CYS343 4.6 7.8 1.0
N B:LEU344 4.7 6.6 1.0
CD1 B:PHE336 5.0 4.0 1.0

Iron binding site 3 out of 4 in 2yoo

Go back to Iron Binding Sites List in 2yoo
Iron binding site 3 out of 4 in the Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1402

b:8.4
occ:1.00
FE C:HEM1402 0.0 8.4 1.0
NB C:HEM1402 2.0 8.0 1.0
NA C:HEM1402 2.1 8.3 1.0
ND C:HEM1402 2.1 9.5 1.0
NC C:HEM1402 2.2 7.5 1.0
SG C:CYS343 2.4 7.8 1.0
C1A C:HEM1402 3.0 7.1 1.0
C4D C:HEM1402 3.1 6.7 1.0
C4B C:HEM1402 3.1 9.6 1.0
C4A C:HEM1402 3.1 5.3 1.0
C1C C:HEM1402 3.1 9.1 1.0
C1B C:HEM1402 3.1 8.0 1.0
C1D C:HEM1402 3.1 8.6 1.0
C4C C:HEM1402 3.2 5.6 1.0
CHA C:HEM1402 3.4 7.7 1.0
CHC C:HEM1402 3.4 11.6 1.0
CB C:CYS343 3.4 5.4 1.0
CHD C:HEM1402 3.5 7.7 1.0
CHB C:HEM1402 3.5 8.9 1.0
C26 C:K2B1404 4.0 11.8 1.0
CA C:CYS343 4.0 5.4 1.0
C2A C:HEM1402 4.3 7.9 1.0
C3A C:HEM1402 4.3 7.2 1.0
C3B C:HEM1402 4.3 8.5 1.0
C2B C:HEM1402 4.3 9.2 1.0
C3D C:HEM1402 4.3 10.7 1.0
C2D C:HEM1402 4.3 10.1 1.0
C2C C:HEM1402 4.3 8.9 1.0
C3C C:HEM1402 4.4 10.3 1.0
N C:GLY345 4.6 7.7 1.0
C C:CYS343 4.6 5.9 1.0
N C:LEU344 4.6 7.9 1.0

Iron binding site 4 out of 4 in 2yoo

Go back to Iron Binding Sites List in 2yoo
Iron binding site 4 out of 4 in the Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cholest-4-En-3-One Bound Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1402

b:8.1
occ:1.00
FE D:HEM1402 0.0 8.1 1.0
NC D:HEM1402 2.1 6.3 1.0
ND D:HEM1402 2.1 9.8 1.0
NB D:HEM1402 2.1 9.1 1.0
NA D:HEM1402 2.1 5.5 1.0
SG D:CYS343 2.4 9.0 1.0
C4C D:HEM1402 3.0 7.5 1.0
C1C D:HEM1402 3.1 8.7 1.0
C4A D:HEM1402 3.1 2.7 1.0
C1D D:HEM1402 3.1 7.4 1.0
C4D D:HEM1402 3.1 9.6 1.0
C1A D:HEM1402 3.1 4.6 1.0
C4B D:HEM1402 3.1 7.4 1.0
C1B D:HEM1402 3.1 6.3 1.0
CHD D:HEM1402 3.4 8.7 1.0
CB D:CYS343 3.4 7.3 1.0
CHB D:HEM1402 3.5 3.1 1.0
CHA D:HEM1402 3.5 6.7 1.0
CHC D:HEM1402 3.5 8.6 1.0
CA D:CYS343 4.0 8.1 1.0
C26 D:K2B1404 4.0 11.4 1.0
C3C D:HEM1402 4.3 9.2 1.0
C2C D:HEM1402 4.3 6.9 1.0
C3A D:HEM1402 4.3 6.1 1.0
C3D D:HEM1402 4.3 8.1 1.0
C2D D:HEM1402 4.3 8.0 1.0
C2A D:HEM1402 4.3 5.3 1.0
C2B D:HEM1402 4.3 8.5 1.0
C3B D:HEM1402 4.4 8.0 1.0
N D:GLY345 4.5 7.8 1.0
N D:LEU344 4.6 7.7 1.0
C D:CYS343 4.6 7.4 1.0
O D:GLY233 5.0 9.6 1.0

Reference:

E.Garcia-Fernandez, D.J.Frank, B.Galan, P.M.Kells, L.M.Podust, J.L.Garcia, P.R.Ortiz De Montellano. A Highly Conserved Mycobacterial Cholesterol Catabolic Pathway. Environ.Microbiol. V. 15 2342 2013.
ISSN: ISSN 1462-2912
PubMed: 23489718
DOI: 10.1111/1462-2920.12108
Page generated: Sun Aug 4 05:40:59 2024

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