Iron in PDB 5opa: The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B
Enzymatic activity of The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B
All present enzymatic activity of The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B:
1.14.21.9;
Protein crystallography data
The structure of The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B, PDB code: 5opa
was solved by
C.W.Levy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
53.50 /
1.35
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.887,
77.887,
263.547,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
13 /
15.7
|
Other elements in 5opa:
The structure of The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B
(pdb code 5opa). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the
The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B, PDB code: 5opa:
Jump to Iron binding site number:
1;
2;
Iron binding site 1 out
of 2 in 5opa
Go back to
Iron Binding Sites List in 5opa
Iron binding site 1 out
of 2 in the The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe404
b:11.3
occ:0.52
|
FE
|
A:HEM404
|
0.0
|
11.3
|
0.5
|
FE
|
A:HEM404
|
0.0
|
12.2
|
0.5
|
ND
|
A:HEM404
|
2.0
|
11.6
|
0.5
|
ND
|
A:HEM404
|
2.0
|
10.5
|
0.5
|
NC
|
A:HEM404
|
2.0
|
12.3
|
0.5
|
NB
|
A:HEM404
|
2.0
|
11.9
|
0.5
|
NB
|
A:HEM404
|
2.0
|
9.2
|
0.5
|
NA
|
A:HEM404
|
2.0
|
10.9
|
0.5
|
NA
|
A:HEM404
|
2.1
|
10.1
|
0.5
|
NC
|
A:HEM404
|
2.1
|
8.8
|
0.5
|
O
|
A:HOH546
|
2.2
|
17.6
|
1.0
|
SG
|
A:CYS345
|
2.3
|
13.3
|
1.0
|
C4D
|
A:HEM404
|
3.0
|
9.3
|
0.5
|
C4C
|
A:HEM404
|
3.0
|
12.1
|
0.5
|
C4B
|
A:HEM404
|
3.0
|
12.3
|
0.5
|
C1D
|
A:HEM404
|
3.0
|
11.1
|
0.5
|
C4D
|
A:HEM404
|
3.0
|
10.0
|
0.5
|
C1C
|
A:HEM404
|
3.0
|
12.4
|
0.5
|
C1D
|
A:HEM404
|
3.0
|
11.2
|
0.5
|
C4B
|
A:HEM404
|
3.0
|
7.9
|
0.5
|
C1B
|
A:HEM404
|
3.1
|
12.3
|
0.5
|
C1B
|
A:HEM404
|
3.1
|
8.6
|
0.5
|
C1A
|
A:HEM404
|
3.1
|
13.5
|
0.5
|
C1C
|
A:HEM404
|
3.1
|
9.6
|
0.5
|
C4A
|
A:HEM404
|
3.1
|
11.3
|
0.5
|
C4A
|
A:HEM404
|
3.1
|
8.3
|
0.5
|
C1A
|
A:HEM404
|
3.1
|
10.2
|
0.5
|
C4C
|
A:HEM404
|
3.1
|
9.0
|
0.5
|
CHD
|
A:HEM404
|
3.4
|
12.2
|
0.5
|
CHC
|
A:HEM404
|
3.4
|
12.6
|
0.5
|
CHA
|
A:HEM404
|
3.4
|
12.7
|
0.5
|
CB
|
A:CYS345
|
3.4
|
12.4
|
1.0
|
CHC
|
A:HEM404
|
3.4
|
8.2
|
0.5
|
CHA
|
A:HEM404
|
3.4
|
8.8
|
0.5
|
CHD
|
A:HEM404
|
3.4
|
9.0
|
0.5
|
CHB
|
A:HEM404
|
3.4
|
12.0
|
0.5
|
CHB
|
A:HEM404
|
3.4
|
7.8
|
0.5
|
CA
|
A:CYS345
|
4.2
|
11.7
|
1.0
|
C3D
|
A:HEM404
|
4.2
|
9.5
|
0.5
|
C3B
|
A:HEM404
|
4.2
|
11.8
|
0.5
|
C2D
|
A:HEM404
|
4.2
|
11.6
|
0.5
|
C3D
|
A:HEM404
|
4.2
|
9.7
|
0.5
|
C2B
|
A:HEM404
|
4.2
|
12.6
|
0.5
|
C2D
|
A:HEM404
|
4.2
|
10.8
|
0.5
|
C3C
|
A:HEM404
|
4.2
|
11.4
|
0.5
|
C2C
|
A:HEM404
|
4.3
|
12.7
|
0.5
|
C3B
|
A:HEM404
|
4.3
|
8.7
|
0.5
|
C2B
|
A:HEM404
|
4.3
|
8.9
|
0.5
|
C2C
|
A:HEM404
|
4.3
|
10.9
|
0.5
|
C3A
|
A:HEM404
|
4.3
|
11.2
|
0.5
|
C3A
|
A:HEM404
|
4.3
|
9.6
|
0.5
|
C3C
|
A:HEM404
|
4.3
|
11.2
|
0.5
|
C2A
|
A:HEM404
|
4.3
|
13.1
|
0.5
|
C2A
|
A:HEM404
|
4.3
|
10.9
|
0.5
|
OG
|
A:SER237
|
4.5
|
11.2
|
1.0
|
O4
|
A:SO4407
|
4.6
|
29.6
|
0.9
|
CD
|
A:PRO346
|
4.8
|
13.2
|
1.0
|
CB
|
A:SER237
|
4.9
|
10.7
|
1.0
|
C
|
A:CYS345
|
4.9
|
13.7
|
1.0
|
N
|
A:GLY347
|
5.0
|
13.4
|
1.0
|
|
Iron binding site 2 out
of 2 in 5opa
Go back to
Iron Binding Sites List in 5opa
Iron binding site 2 out
of 2 in the The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Crystal Structure of P450 CYP121 in Complex with Lead Compound 7B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe404
b:12.2
occ:0.48
|
FE
|
A:HEM404
|
0.0
|
12.2
|
0.5
|
FE
|
A:HEM404
|
0.0
|
11.3
|
0.5
|
ND
|
A:HEM404
|
2.0
|
11.6
|
0.5
|
NC
|
A:HEM404
|
2.0
|
12.3
|
0.5
|
NB
|
A:HEM404
|
2.0
|
11.9
|
0.5
|
ND
|
A:HEM404
|
2.0
|
10.5
|
0.5
|
NB
|
A:HEM404
|
2.0
|
9.2
|
0.5
|
NA
|
A:HEM404
|
2.0
|
10.9
|
0.5
|
NC
|
A:HEM404
|
2.0
|
8.8
|
0.5
|
NA
|
A:HEM404
|
2.1
|
10.1
|
0.5
|
O
|
A:HOH546
|
2.2
|
17.6
|
1.0
|
SG
|
A:CYS345
|
2.3
|
13.3
|
1.0
|
C4B
|
A:HEM404
|
3.0
|
12.3
|
0.5
|
C1C
|
A:HEM404
|
3.0
|
12.4
|
0.5
|
C4C
|
A:HEM404
|
3.0
|
12.1
|
0.5
|
C4B
|
A:HEM404
|
3.0
|
7.9
|
0.5
|
C1D
|
A:HEM404
|
3.0
|
11.2
|
0.5
|
C4D
|
A:HEM404
|
3.0
|
9.3
|
0.5
|
C1B
|
A:HEM404
|
3.0
|
12.3
|
0.5
|
C1D
|
A:HEM404
|
3.0
|
11.1
|
0.5
|
C4D
|
A:HEM404
|
3.0
|
10.0
|
0.5
|
C1C
|
A:HEM404
|
3.1
|
9.6
|
0.5
|
C1B
|
A:HEM404
|
3.1
|
8.6
|
0.5
|
C1A
|
A:HEM404
|
3.1
|
13.5
|
0.5
|
C4C
|
A:HEM404
|
3.1
|
9.0
|
0.5
|
C4A
|
A:HEM404
|
3.1
|
11.3
|
0.5
|
C4A
|
A:HEM404
|
3.1
|
8.3
|
0.5
|
C1A
|
A:HEM404
|
3.1
|
10.2
|
0.5
|
CHC
|
A:HEM404
|
3.4
|
12.6
|
0.5
|
CHD
|
A:HEM404
|
3.4
|
12.2
|
0.5
|
CHC
|
A:HEM404
|
3.4
|
8.2
|
0.5
|
CHA
|
A:HEM404
|
3.4
|
12.7
|
0.5
|
CB
|
A:CYS345
|
3.4
|
12.4
|
1.0
|
CHD
|
A:HEM404
|
3.4
|
9.0
|
0.5
|
CHB
|
A:HEM404
|
3.4
|
12.0
|
0.5
|
CHA
|
A:HEM404
|
3.4
|
8.8
|
0.5
|
CHB
|
A:HEM404
|
3.5
|
7.8
|
0.5
|
CA
|
A:CYS345
|
4.2
|
11.7
|
1.0
|
C3B
|
A:HEM404
|
4.2
|
11.8
|
0.5
|
C2B
|
A:HEM404
|
4.2
|
12.6
|
0.5
|
C2D
|
A:HEM404
|
4.2
|
11.6
|
0.5
|
C3D
|
A:HEM404
|
4.2
|
9.5
|
0.5
|
C3D
|
A:HEM404
|
4.2
|
9.7
|
0.5
|
C3C
|
A:HEM404
|
4.2
|
11.4
|
0.5
|
C2C
|
A:HEM404
|
4.3
|
12.7
|
0.5
|
C2D
|
A:HEM404
|
4.3
|
10.8
|
0.5
|
C3B
|
A:HEM404
|
4.3
|
8.7
|
0.5
|
C2B
|
A:HEM404
|
4.3
|
8.9
|
0.5
|
C2C
|
A:HEM404
|
4.3
|
10.9
|
0.5
|
C3C
|
A:HEM404
|
4.3
|
11.2
|
0.5
|
C3A
|
A:HEM404
|
4.3
|
11.2
|
0.5
|
C2A
|
A:HEM404
|
4.3
|
13.1
|
0.5
|
C3A
|
A:HEM404
|
4.3
|
9.6
|
0.5
|
C2A
|
A:HEM404
|
4.3
|
10.9
|
0.5
|
OG
|
A:SER237
|
4.5
|
11.2
|
1.0
|
O4
|
A:SO4407
|
4.6
|
29.6
|
0.9
|
CD
|
A:PRO346
|
4.8
|
13.2
|
1.0
|
CB
|
A:SER237
|
4.9
|
10.7
|
1.0
|
C
|
A:CYS345
|
4.9
|
13.7
|
1.0
|
N
|
A:GLY347
|
5.0
|
13.4
|
1.0
|
|
Reference:
I.M.Taban,
H.E.A.E.Elshihawy,
B.Torun,
B.Zucchini,
C.J.Williamson,
D.Altuwairigi,
A.S.T.Ngu,
K.J.Mclean,
C.W.Levy,
S.Sood,
L.B.Marino,
A.W.Munro,
L.P.S.De Carvalho,
C.Simons.
Novel Aryl Substituted Pyrazoles As Small Molecule Inhibitors of Cytochrome P450 CYP121A1: Synthesis and Antimycobacterial Evaluation. J. Med. Chem. V. 60 10257 2017.
ISSN: ISSN 1520-4804
PubMed: 29185746
DOI: 10.1021/ACS.JMEDCHEM.7B01562
Page generated: Tue Aug 6 08:29:36 2024
|