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Iron in PDB 7sh5: Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One

Protein crystallography data

The structure of Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One, PDB code: 7sh5 was solved by D.Z.Doherty, S.G.Bell, J.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.81 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 112.685, 59.2, 114.937, 90, 91.3, 90
R / Rfree (%) 17 / 20

Other elements in 7sh5:

The structure of Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One also contains other interesting chemical elements:

Sodium (Na) 13 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One (pdb code 7sh5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One, PDB code: 7sh5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7sh5

Go back to Iron Binding Sites List in 7sh5
Iron binding site 1 out of 4 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


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 CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:14.4
occ:1.00
FE A:HEM501 0.0 14.4 1.0
NB A:HEM501 2.0 12.5 1.0
NC A:HEM501 2.1 14.5 1.0
ND A:HEM501 2.1 13.0 1.0
NA A:HEM501 2.1 12.6 1.0
SG A:CYS344 2.3 15.5 1.0
C1C A:HEM501 3.0 12.6 1.0
C4B A:HEM501 3.0 13.1 1.0
C4D A:HEM501 3.1 9.7 1.0
C1B A:HEM501 3.1 12.3 1.0
C1A A:HEM501 3.1 13.1 1.0
C4A A:HEM501 3.1 12.1 1.0
C1D A:HEM501 3.1 13.7 1.0
C4C A:HEM501 3.1 15.0 1.0
CB A:CYS344 3.3 14.1 1.0
CHC A:HEM501 3.4 13.4 1.0
CHA A:HEM501 3.4 11.4 1.0
CHB A:HEM501 3.5 13.5 1.0
CHD A:HEM501 3.5 14.5 1.0
CA A:CYS344 4.0 15.2 1.0
C26 A:K2B502 4.2 14.8 1.0
C2C A:HEM501 4.3 13.6 1.0
C3B A:HEM501 4.3 13.1 1.0
C2B A:HEM501 4.3 13.1 1.0
C3C A:HEM501 4.3 14.6 1.0
C3D A:HEM501 4.3 11.8 1.0
C3A A:HEM501 4.3 10.7 1.0
C2D A:HEM501 4.3 13.6 1.0
C2A A:HEM501 4.3 13.4 1.0
N A:GLY346 4.7 13.4 1.0
C A:CYS344 4.7 16.3 1.0
O A:GLY234 4.7 18.2 1.0
N A:MET345 4.8 13.6 1.0
CD1 A:PHE337 5.0 13.1 1.0

Iron binding site 2 out of 4 in 7sh5

Go back to Iron Binding Sites List in 7sh5
Iron binding site 2 out of 4 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


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 CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:14.0
occ:1.00
FE B:HEM501 0.0 14.0 1.0
ND B:HEM501 2.1 13.5 1.0
NC B:HEM501 2.1 15.7 1.0
NB B:HEM501 2.1 13.9 1.0
NA B:HEM501 2.1 12.9 1.0
SG B:CYS344 2.3 15.0 1.0
C1D B:HEM501 3.1 13.2 1.0
C1C B:HEM501 3.1 13.7 1.0
C1B B:HEM501 3.1 13.7 1.0
C4A B:HEM501 3.1 12.8 1.0
C4C B:HEM501 3.1 15.3 1.0
C4B B:HEM501 3.1 12.6 1.0
C4D B:HEM501 3.1 11.2 1.0
C1A B:HEM501 3.1 11.9 1.0
CB B:CYS344 3.3 15.0 1.0
CHD B:HEM501 3.4 14.2 1.0
CHB B:HEM501 3.4 12.9 1.0
CHC B:HEM501 3.4 13.2 1.0
CHA B:HEM501 3.5 15.7 1.0
CA B:CYS344 3.9 14.4 1.0
C26 B:K2B502 4.2 14.8 1.0
C2C B:HEM501 4.3 14.7 1.0
C2D B:HEM501 4.3 15.1 1.0
C3C B:HEM501 4.3 14.6 1.0
C2B B:HEM501 4.3 12.1 1.0
C3A B:HEM501 4.3 13.7 1.0
C3B B:HEM501 4.3 11.7 1.0
C3D B:HEM501 4.3 12.7 1.0
C2A B:HEM501 4.3 12.2 1.0
C B:CYS344 4.6 14.3 1.0
N B:GLY346 4.6 15.2 1.0
N B:MET345 4.7 13.8 1.0
O B:GLY234 4.8 17.2 1.0

Iron binding site 3 out of 4 in 7sh5

Go back to Iron Binding Sites List in 7sh5
Iron binding site 3 out of 4 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


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 CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:12.2
occ:1.00
FE C:HEM501 0.0 12.2 1.0
NC C:HEM501 2.0 11.0 1.0
ND C:HEM501 2.0 10.8 1.0
NB C:HEM501 2.1 12.5 1.0
NA C:HEM501 2.1 11.2 1.0
SG C:CYS344 2.3 13.7 1.0
C1C C:HEM501 3.0 13.2 1.0
C4B C:HEM501 3.1 13.0 1.0
C1D C:HEM501 3.1 14.4 1.0
C4C C:HEM501 3.1 10.9 1.0
C4D C:HEM501 3.1 11.4 1.0
C1B C:HEM501 3.1 12.4 1.0
C1A C:HEM501 3.1 10.8 1.0
C4A C:HEM501 3.1 10.5 1.0
CB C:CYS344 3.3 13.9 1.0
CHC C:HEM501 3.4 11.8 1.0
CHD C:HEM501 3.4 12.5 1.0
CHA C:HEM501 3.4 12.2 1.0
CHB C:HEM501 3.5 10.8 1.0
CA C:CYS344 4.0 13.9 1.0
C27 C:K2B502 4.1 13.5 1.0
C2C C:HEM501 4.2 14.1 1.0
C3C C:HEM501 4.3 12.0 1.0
C2D C:HEM501 4.3 12.3 1.0
C3B C:HEM501 4.3 10.8 1.0
C3D C:HEM501 4.3 12.4 1.0
C2B C:HEM501 4.3 9.9 1.0
C3A C:HEM501 4.3 12.8 1.0
C2A C:HEM501 4.3 13.3 1.0
N C:GLY346 4.6 13.7 1.0
C C:CYS344 4.7 11.6 1.0
O C:GLY234 4.7 13.4 1.0
N C:MET345 4.7 14.2 1.0
CA C:GLY234 5.0 12.8 1.0
CD1 C:PHE337 5.0 10.4 1.0

Iron binding site 4 out of 4 in 7sh5

Go back to Iron Binding Sites List in 7sh5
Iron binding site 4 out of 4 in the Crystal Structure of CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One


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 CYP142A3 From Mycobacterium Ulcerans Bound to Cholest-4-En-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:16.1
occ:1.00
FE D:HEM501 0.0 16.1 1.0
ND D:HEM501 2.0 15.7 1.0
NC D:HEM501 2.1 18.0 1.0
NB D:HEM501 2.1 15.6 1.0
NA D:HEM501 2.1 13.6 1.0
SG D:CYS344 2.3 18.1 1.0
C1D D:HEM501 3.0 15.2 1.0
C1C D:HEM501 3.1 14.3 1.0
C4C D:HEM501 3.1 16.9 1.0
C1B D:HEM501 3.1 14.9 1.0
C4B D:HEM501 3.1 15.3 1.0
C4A D:HEM501 3.1 15.8 1.0
C4D D:HEM501 3.1 14.2 1.0
C1A D:HEM501 3.1 13.2 1.0
CB D:CYS344 3.3 15.9 1.0
CHD D:HEM501 3.4 20.5 1.0
CHC D:HEM501 3.4 16.8 1.0
CHB D:HEM501 3.4 15.2 1.0
CHA D:HEM501 3.5 15.3 1.0
C26 D:K2B502 4.1 18.5 1.0
CA D:CYS344 4.1 16.4 1.0
C2C D:HEM501 4.3 16.7 1.0
C3C D:HEM501 4.3 18.0 1.0
C2D D:HEM501 4.3 14.1 1.0
C2B D:HEM501 4.3 16.0 1.0
C3B D:HEM501 4.3 14.5 1.0
C3D D:HEM501 4.3 15.2 1.0
C3A D:HEM501 4.3 14.0 1.0
C2A D:HEM501 4.3 15.0 1.0
N D:GLY346 4.6 16.4 1.0
C D:CYS344 4.7 19.3 1.0
N D:MET345 4.8 18.1 1.0
O D:GLY234 4.8 19.5 1.0
CD1 D:PHE337 4.9 13.7 1.0

Reference:

A.Ghith, D.Z.Doherty, J.B.Bruning, R.A.Russell, J.J.De Voss, S.G.Bell. The Structures of the Steroid Binding CYP142 Cytochrome P450 Enzymes From Mycobacterium Ulcerans and Mycobacterium Marinum. Acs Infect Dis. V. 8 1606 2022.
ISSN: ESSN 2373-8227
PubMed: 35881654
DOI: 10.1021/ACSINFECDIS.2C00215
Page generated: Fri Aug 9 00:51:32 2024

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