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Iron in PDB 3zby: Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis

Protein crystallography data

The structure of Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis, PDB code: 3zby 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) 266.44 / 1.93
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.051, 162.847, 266.443, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23

Iron Binding Sites:

The binding sites of Iron atom in the Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis (pdb code 3zby). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis, PDB code: 3zby:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3zby

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Iron binding site 1 out of 6 in the Ligand-Free 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 Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1402

b:14.6
occ:1.00
FE A:HEM1402 0.0 14.6 1.0
O1 A:EDO1406 1.8 23.3 1.0
NC A:HEM1402 2.1 15.1 1.0
NB A:HEM1402 2.1 13.7 1.0
NA A:HEM1402 2.1 13.6 1.0
ND A:HEM1402 2.1 15.1 1.0
SG A:CYS343 2.2 15.8 1.0
C4C A:HEM1402 3.0 13.8 1.0
C4B A:HEM1402 3.1 15.0 1.0
C4A A:HEM1402 3.1 12.1 1.0
C1B A:HEM1402 3.1 15.0 1.0
C1A A:HEM1402 3.1 15.0 1.0
C1C A:HEM1402 3.1 15.0 1.0
C1D A:HEM1402 3.1 17.1 1.0
C4D A:HEM1402 3.2 16.6 1.0
C1 A:EDO1406 3.2 19.7 1.0
CB A:CYS343 3.3 14.2 1.0
CHD A:HEM1402 3.4 14.4 1.0
CHB A:HEM1402 3.4 15.3 1.0
CHC A:HEM1402 3.5 11.9 1.0
CHA A:HEM1402 3.5 13.1 1.0
C2 A:EDO1406 4.0 22.4 1.0
CA A:CYS343 4.0 14.6 1.0
O A:GLY233 4.1 16.7 1.0
C3C A:HEM1402 4.3 14.7 1.0
C3B A:HEM1402 4.3 15.1 1.0
C3A A:HEM1402 4.3 14.0 1.0
C2B A:HEM1402 4.3 12.4 1.0
C2A A:HEM1402 4.3 14.6 1.0
C2C A:HEM1402 4.3 16.3 1.0
C3D A:HEM1402 4.4 17.7 1.0
C2D A:HEM1402 4.4 15.1 1.0
N A:GLY345 4.6 14.6 1.0
C A:CYS343 4.7 15.1 1.0
N A:LEU344 4.8 16.3 1.0
C A:GLY233 4.8 17.1 1.0

Iron binding site 2 out of 6 in 3zby

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Iron binding site 2 out of 6 in the Ligand-Free 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 Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1402

b:13.6
occ:1.00
FE B:HEM1402 0.0 13.6 1.0
O2 B:EDO1409 1.9 20.4 1.0
NB B:HEM1402 2.0 13.7 1.0
NC B:HEM1402 2.1 13.6 1.0
NA B:HEM1402 2.1 12.5 1.0
ND B:HEM1402 2.1 14.7 1.0
SG B:CYS343 2.2 14.6 1.0
C4C B:HEM1402 3.0 14.1 1.0
C4B B:HEM1402 3.0 12.1 1.0
C1D B:HEM1402 3.1 14.9 1.0
C4A B:HEM1402 3.1 11.7 1.0
C1C B:HEM1402 3.1 13.4 1.0
C1B B:HEM1402 3.1 15.8 1.0
C1A B:HEM1402 3.1 12.3 1.0
C4D B:HEM1402 3.1 14.9 1.0
C2 B:EDO1409 3.2 19.9 1.0
CB B:CYS343 3.3 13.3 1.0
CHD B:HEM1402 3.4 14.8 1.0
CHC B:HEM1402 3.4 12.8 1.0
CHB B:HEM1402 3.5 13.1 1.0
CHA B:HEM1402 3.5 13.0 1.0
C1 B:EDO1409 3.9 22.4 1.0
CA B:CYS343 4.1 13.1 1.0
O B:GLY233 4.2 16.7 1.0
C3B B:HEM1402 4.3 12.4 1.0
C3C B:HEM1402 4.3 15.8 1.0
C3A B:HEM1402 4.3 10.4 1.0
C2A B:HEM1402 4.3 13.6 1.0
C2B B:HEM1402 4.3 11.1 1.0
C2C B:HEM1402 4.3 15.2 1.0
C2D B:HEM1402 4.3 13.5 1.0
C3D B:HEM1402 4.3 14.1 1.0
N B:GLY345 4.7 13.7 1.0
C B:CYS343 4.7 14.2 1.0
N B:LEU344 4.8 13.8 1.0
C B:GLY233 4.9 17.4 1.0

Iron binding site 3 out of 6 in 3zby

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Iron binding site 3 out of 6 in the Ligand-Free 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 Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1402

b:14.2
occ:1.00
FE C:HEM1402 0.0 14.2 1.0
O2 C:EDO1407 1.8 26.4 1.0
NC C:HEM1402 2.1 15.2 1.0
NA C:HEM1402 2.1 14.3 1.0
NB C:HEM1402 2.1 12.5 1.0
ND C:HEM1402 2.2 17.1 1.0
SG C:CYS343 2.2 15.6 1.0
C4C C:HEM1402 3.0 15.0 1.0
C4A C:HEM1402 3.1 12.8 1.0
C4B C:HEM1402 3.1 15.0 1.0
C1A C:HEM1402 3.1 16.3 1.0
C1C C:HEM1402 3.1 15.5 1.0
C1B C:HEM1402 3.1 14.8 1.0
C1D C:HEM1402 3.1 16.5 1.0
C4D C:HEM1402 3.2 15.5 1.0
C2 C:EDO1407 3.2 21.6 1.0
CB C:CYS343 3.3 14.9 1.0
CHD C:HEM1402 3.4 15.5 1.0
CHB C:HEM1402 3.5 11.6 1.0
CHC C:HEM1402 3.5 11.3 1.0
CHA C:HEM1402 3.5 12.1 1.0
C1 C:EDO1407 4.0 23.4 1.0
CA C:CYS343 4.1 13.9 1.0
O C:GLY233 4.1 17.9 1.0
C3C C:HEM1402 4.2 15.4 1.0
C3B C:HEM1402 4.3 15.1 1.0
C2C C:HEM1402 4.3 16.6 1.0
C3A C:HEM1402 4.3 11.4 1.0
C2A C:HEM1402 4.3 13.9 1.0
C2B C:HEM1402 4.3 12.7 1.0
C3D C:HEM1402 4.4 17.7 1.0
C2D C:HEM1402 4.4 16.3 1.0
C C:CYS343 4.7 14.9 1.0
N C:GLY345 4.7 14.5 1.0
N C:LEU344 4.8 15.2 1.0
O1 C:EDO1407 4.8 30.8 1.0
C C:GLY233 4.8 17.6 1.0

Iron binding site 4 out of 6 in 3zby

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Iron binding site 4 out of 6 in the Ligand-Free 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 Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1402

b:14.6
occ:1.00
FE D:HEM1402 0.0 14.6 1.0
O2 D:EDO1407 2.0 20.8 1.0
NB D:HEM1402 2.0 14.2 1.0
ND D:HEM1402 2.0 16.7 1.0
NC D:HEM1402 2.0 13.6 1.0
NA D:HEM1402 2.1 14.6 1.0
SG D:CYS343 2.2 15.2 1.0
C4C D:HEM1402 3.0 14.2 1.0
C4B D:HEM1402 3.0 14.1 1.0
C1D D:HEM1402 3.0 15.8 1.0
C1B D:HEM1402 3.1 15.3 1.0
C4A D:HEM1402 3.1 14.5 1.0
C1A D:HEM1402 3.1 16.3 1.0
C4D D:HEM1402 3.1 15.7 1.0
C1C D:HEM1402 3.1 15.4 1.0
CB D:CYS343 3.3 14.5 1.0
C2 D:EDO1407 3.3 19.5 1.0
CHD D:HEM1402 3.4 12.7 1.0
CHB D:HEM1402 3.4 12.8 1.0
CHA D:HEM1402 3.4 13.4 1.0
CHC D:HEM1402 3.5 16.0 1.0
C1 D:EDO1407 4.0 21.6 1.0
CA D:CYS343 4.1 14.7 1.0
O D:GLY233 4.2 15.8 1.0
C3B D:HEM1402 4.3 15.1 1.0
C3C D:HEM1402 4.3 15.9 1.0
C2B D:HEM1402 4.3 12.9 1.0
C3A D:HEM1402 4.3 13.2 1.0
C2A D:HEM1402 4.3 13.4 1.0
C2C D:HEM1402 4.3 16.4 1.0
C2D D:HEM1402 4.3 16.2 1.0
C3D D:HEM1402 4.3 14.6 1.0
N D:GLY345 4.6 13.9 1.0
C D:CYS343 4.7 15.9 1.0
N D:LEU344 4.7 13.8 1.0
C D:GLY233 4.9 16.7 1.0

Iron binding site 5 out of 6 in 3zby

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Iron binding site 5 out of 6 in the Ligand-Free 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 5 of Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1402

b:14.4
occ:1.00
FE E:HEM1402 0.0 14.4 1.0
O1 E:EDO1407 2.0 22.1 1.0
NB E:HEM1402 2.0 14.7 1.0
NC E:HEM1402 2.0 14.7 1.0
NA E:HEM1402 2.1 15.1 1.0
ND E:HEM1402 2.1 17.1 1.0
SG E:CYS343 2.3 15.4 1.0
C4B E:HEM1402 3.0 14.7 1.0
C4A E:HEM1402 3.0 13.2 1.0
C4C E:HEM1402 3.0 18.0 1.0
C1B E:HEM1402 3.1 15.9 1.0
C1C E:HEM1402 3.1 14.1 1.0
C1A E:HEM1402 3.1 17.5 1.0
C1D E:HEM1402 3.1 17.0 1.0
C4D E:HEM1402 3.2 17.4 1.0
C1 E:EDO1407 3.3 23.1 1.0
CB E:CYS343 3.4 14.9 1.0
CHC E:HEM1402 3.4 12.3 1.0
CHB E:HEM1402 3.4 13.2 1.0
CHD E:HEM1402 3.4 15.6 1.0
CHA E:HEM1402 3.5 13.4 1.0
C2 E:EDO1407 4.0 23.7 1.0
CA E:CYS343 4.1 13.8 1.0
O E:GLY233 4.2 17.7 1.0
C3B E:HEM1402 4.2 15.8 1.0
C2B E:HEM1402 4.3 12.6 1.0
C3A E:HEM1402 4.3 12.3 1.0
C3C E:HEM1402 4.3 15.6 1.0
C2C E:HEM1402 4.3 16.7 1.0
C2A E:HEM1402 4.3 15.9 1.0
C2D E:HEM1402 4.4 15.6 1.0
C3D E:HEM1402 4.4 17.3 1.0
N E:GLY345 4.7 15.9 1.0
C E:CYS343 4.7 15.0 1.0
N E:LEU344 4.8 14.6 1.0
C E:GLY233 4.8 17.0 1.0

Iron binding site 6 out of 6 in 3zby

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Iron binding site 6 out of 6 in the Ligand-Free 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 6 of Ligand-Free Structure of CYP142 From Mycobacterium Smegmatis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe1402

b:14.3
occ:1.00
FE F:HEM1402 0.0 14.3 1.0
O2 F:EDO1407 1.9 22.7 1.0
NC F:HEM1402 2.0 15.9 1.0
NB F:HEM1402 2.1 13.8 1.0
NA F:HEM1402 2.1 14.0 1.0
ND F:HEM1402 2.1 17.0 1.0
SG F:CYS343 2.2 15.8 1.0
C4B F:HEM1402 3.0 14.7 1.0
C1C F:HEM1402 3.0 12.5 1.0
C4C F:HEM1402 3.0 16.1 1.0
C1D F:HEM1402 3.1 19.4 1.0
C4A F:HEM1402 3.1 12.2 1.0
C1A F:HEM1402 3.1 14.6 1.0
C1B F:HEM1402 3.1 15.9 1.0
C4D F:HEM1402 3.1 16.2 1.0
C2 F:EDO1407 3.3 18.4 1.0
CB F:CYS343 3.3 13.3 1.0
CHC F:HEM1402 3.4 15.5 1.0
CHD F:HEM1402 3.4 15.3 1.0
CHB F:HEM1402 3.5 12.6 1.0
CHA F:HEM1402 3.5 14.7 1.0
C1 F:EDO1407 4.0 21.5 1.0
CA F:CYS343 4.0 13.7 1.0
O F:GLY233 4.2 17.0 1.0
C3C F:HEM1402 4.2 16.8 1.0
C3B F:HEM1402 4.3 13.8 1.0
C3A F:HEM1402 4.3 12.4 1.0
C2C F:HEM1402 4.3 15.4 1.0
C2A F:HEM1402 4.3 16.5 1.0
C2B F:HEM1402 4.3 12.8 1.0
C2D F:HEM1402 4.3 15.7 1.0
C3D F:HEM1402 4.3 17.0 1.0
N F:GLY345 4.6 14.0 1.0
C F:CYS343 4.7 13.4 1.0
N F:LEU344 4.7 12.9 1.0
C F:GLY233 4.9 16.8 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 22:59:57 2024

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