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:
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
|