Iron in PDB 4egm: The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid
Protein crystallography data
The structure of The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid, PDB code: 4egm
was solved by
W.Zhou,
S.G.Bell,
W.Yang,
R.M.Zhou,
A.B.H.Tan,
L.-L.Wong,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.57 /
2.91
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.864,
143.279,
172.513,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.2 /
24.9
|
Other elements in 4egm:
The structure of The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid
(pdb code 4egm). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid, PDB code: 4egm:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4egm
Go back to
Iron Binding Sites List in 4egm
Iron binding site 1 out
of 4 in the The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:29.8
occ:1.00
|
FE
|
A:HEM501
|
0.0
|
29.8
|
1.0
|
NB
|
A:HEM501
|
2.0
|
29.5
|
1.0
|
NA
|
A:HEM501
|
2.0
|
28.2
|
1.0
|
NC
|
A:HEM501
|
2.1
|
30.4
|
1.0
|
ND
|
A:HEM501
|
2.1
|
27.6
|
1.0
|
SG
|
A:CYS358
|
2.2
|
23.6
|
1.0
|
C1B
|
A:HEM501
|
3.0
|
30.0
|
1.0
|
C4B
|
A:HEM501
|
3.0
|
27.7
|
1.0
|
C4A
|
A:HEM501
|
3.0
|
27.7
|
1.0
|
C1D
|
A:HEM501
|
3.0
|
27.3
|
1.0
|
C4D
|
A:HEM501
|
3.1
|
26.8
|
1.0
|
C1A
|
A:HEM501
|
3.1
|
27.2
|
1.0
|
C4C
|
A:HEM501
|
3.1
|
30.6
|
1.0
|
C1C
|
A:HEM501
|
3.1
|
30.0
|
1.0
|
CHB
|
A:HEM501
|
3.3
|
28.4
|
1.0
|
CHD
|
A:HEM501
|
3.4
|
28.7
|
1.0
|
CHA
|
A:HEM501
|
3.4
|
27.5
|
1.0
|
CHC
|
A:HEM501
|
3.4
|
28.2
|
1.0
|
CB
|
A:CYS358
|
3.4
|
27.1
|
1.0
|
C9
|
A:EGM502
|
3.5
|
26.7
|
1.0
|
CA
|
A:CYS358
|
4.2
|
27.1
|
1.0
|
C3B
|
A:HEM501
|
4.2
|
27.8
|
1.0
|
C2B
|
A:HEM501
|
4.2
|
28.9
|
1.0
|
C3A
|
A:HEM501
|
4.3
|
25.9
|
1.0
|
C2D
|
A:HEM501
|
4.3
|
27.6
|
1.0
|
C3D
|
A:HEM501
|
4.3
|
26.7
|
1.0
|
C2A
|
A:HEM501
|
4.3
|
25.7
|
1.0
|
C3C
|
A:HEM501
|
4.3
|
31.4
|
1.0
|
C2C
|
A:HEM501
|
4.3
|
31.8
|
1.0
|
CB
|
A:ALA248
|
4.8
|
25.6
|
1.0
|
N
|
A:GLY360
|
4.8
|
32.1
|
1.0
|
C8
|
A:EGM502
|
4.8
|
25.0
|
1.0
|
O
|
A:ALA248
|
4.9
|
25.8
|
1.0
|
C
|
A:CYS358
|
5.0
|
28.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 4egm
Go back to
Iron Binding Sites List in 4egm
Iron binding site 2 out
of 4 in the The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:27.1
occ:1.00
|
FE
|
B:HEM501
|
0.0
|
27.1
|
1.0
|
NB
|
B:HEM501
|
2.0
|
22.5
|
1.0
|
ND
|
B:HEM501
|
2.0
|
23.2
|
1.0
|
NA
|
B:HEM501
|
2.1
|
24.2
|
1.0
|
NC
|
B:HEM501
|
2.1
|
25.2
|
1.0
|
SG
|
B:CYS358
|
2.3
|
26.1
|
1.0
|
C1B
|
B:HEM501
|
3.0
|
22.9
|
1.0
|
C1D
|
B:HEM501
|
3.0
|
23.6
|
1.0
|
C4C
|
B:HEM501
|
3.0
|
25.2
|
1.0
|
C4B
|
B:HEM501
|
3.0
|
21.4
|
1.0
|
C4D
|
B:HEM501
|
3.1
|
22.4
|
1.0
|
C4A
|
B:HEM501
|
3.1
|
23.1
|
1.0
|
C1A
|
B:HEM501
|
3.1
|
23.1
|
1.0
|
C1C
|
B:HEM501
|
3.1
|
22.8
|
1.0
|
CHD
|
B:HEM501
|
3.3
|
25.4
|
1.0
|
CB
|
B:CYS358
|
3.3
|
27.3
|
1.0
|
CHB
|
B:HEM501
|
3.4
|
22.2
|
1.0
|
CHA
|
B:HEM501
|
3.4
|
24.4
|
1.0
|
CHC
|
B:HEM501
|
3.5
|
20.5
|
1.0
|
C9
|
B:EGM502
|
3.6
|
19.0
|
1.0
|
CA
|
B:CYS358
|
4.0
|
27.3
|
1.0
|
C2B
|
B:HEM501
|
4.2
|
22.5
|
1.0
|
C3B
|
B:HEM501
|
4.2
|
21.3
|
1.0
|
C2D
|
B:HEM501
|
4.2
|
20.4
|
1.0
|
C3C
|
B:HEM501
|
4.3
|
24.4
|
1.0
|
C3D
|
B:HEM501
|
4.3
|
20.8
|
1.0
|
C3A
|
B:HEM501
|
4.3
|
22.1
|
1.0
|
C2A
|
B:HEM501
|
4.3
|
22.7
|
1.0
|
C2C
|
B:HEM501
|
4.3
|
23.6
|
1.0
|
CB
|
B:ALA248
|
4.8
|
27.1
|
1.0
|
C
|
B:CYS358
|
4.8
|
27.6
|
1.0
|
N
|
B:GLY360
|
4.8
|
29.1
|
1.0
|
O
|
B:ALA248
|
5.0
|
28.7
|
1.0
|
N
|
B:VAL359
|
5.0
|
27.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 4egm
Go back to
Iron Binding Sites List in 4egm
Iron binding site 3 out
of 4 in the The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:30.2
occ:1.00
|
FE
|
C:HEM501
|
0.0
|
30.2
|
1.0
|
ND
|
C:HEM501
|
2.0
|
26.6
|
1.0
|
NB
|
C:HEM501
|
2.0
|
26.8
|
1.0
|
NA
|
C:HEM501
|
2.1
|
24.9
|
1.0
|
NC
|
C:HEM501
|
2.1
|
25.3
|
1.0
|
SG
|
C:CYS358
|
2.3
|
35.5
|
1.0
|
C4B
|
C:HEM501
|
3.0
|
26.2
|
1.0
|
C4D
|
C:HEM501
|
3.0
|
27.7
|
1.0
|
C1A
|
C:HEM501
|
3.0
|
24.1
|
1.0
|
C1D
|
C:HEM501
|
3.0
|
26.5
|
1.0
|
C1C
|
C:HEM501
|
3.1
|
25.5
|
1.0
|
C1B
|
C:HEM501
|
3.1
|
27.7
|
1.0
|
C4C
|
C:HEM501
|
3.1
|
24.8
|
1.0
|
C4A
|
C:HEM501
|
3.1
|
25.1
|
1.0
|
CB
|
C:CYS358
|
3.2
|
33.6
|
1.0
|
CHC
|
C:HEM501
|
3.3
|
25.5
|
1.0
|
CHA
|
C:HEM501
|
3.3
|
26.0
|
1.0
|
CHD
|
C:HEM501
|
3.4
|
25.4
|
1.0
|
CHB
|
C:HEM501
|
3.5
|
25.9
|
1.0
|
C9
|
C:EGM502
|
3.6
|
23.2
|
1.0
|
CA
|
C:CYS358
|
4.0
|
33.7
|
1.0
|
C3B
|
C:HEM501
|
4.2
|
26.4
|
1.0
|
C2B
|
C:HEM501
|
4.2
|
26.2
|
1.0
|
C3D
|
C:HEM501
|
4.3
|
29.3
|
1.0
|
C2D
|
C:HEM501
|
4.3
|
26.7
|
1.0
|
C3C
|
C:HEM501
|
4.3
|
25.6
|
1.0
|
C2A
|
C:HEM501
|
4.3
|
22.9
|
1.0
|
C2C
|
C:HEM501
|
4.3
|
25.2
|
1.0
|
C3A
|
C:HEM501
|
4.3
|
23.7
|
1.0
|
C
|
C:CYS358
|
4.7
|
34.0
|
1.0
|
CB
|
C:ALA248
|
4.8
|
30.6
|
1.0
|
N
|
C:GLY360
|
4.8
|
33.2
|
1.0
|
N
|
C:VAL359
|
4.9
|
33.6
|
1.0
|
O
|
C:ALA248
|
4.9
|
31.7
|
1.0
|
|
Iron binding site 4 out
of 4 in 4egm
Go back to
Iron Binding Sites List in 4egm
Iron binding site 4 out
of 4 in the The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The X-Ray Crystal Structure of CYP199A4 in Complex with 4-Ethylbenzoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:33.2
occ:1.00
|
FE
|
D:HEM501
|
0.0
|
33.2
|
1.0
|
ND
|
D:HEM501
|
2.0
|
30.5
|
1.0
|
NA
|
D:HEM501
|
2.0
|
30.4
|
1.0
|
NB
|
D:HEM501
|
2.0
|
32.0
|
1.0
|
NC
|
D:HEM501
|
2.1
|
32.9
|
1.0
|
SG
|
D:CYS358
|
2.2
|
31.3
|
1.0
|
C1D
|
D:HEM501
|
3.0
|
30.6
|
1.0
|
C4D
|
D:HEM501
|
3.0
|
29.6
|
1.0
|
C4A
|
D:HEM501
|
3.0
|
30.8
|
1.0
|
C1A
|
D:HEM501
|
3.0
|
28.8
|
1.0
|
C1B
|
D:HEM501
|
3.0
|
30.1
|
1.0
|
C4B
|
D:HEM501
|
3.1
|
31.2
|
1.0
|
C4C
|
D:HEM501
|
3.1
|
33.2
|
1.0
|
C1C
|
D:HEM501
|
3.2
|
32.2
|
1.0
|
C9
|
D:EGM502
|
3.2
|
21.5
|
1.0
|
CB
|
D:CYS358
|
3.3
|
31.6
|
1.0
|
CHA
|
D:HEM501
|
3.4
|
29.1
|
1.0
|
CHB
|
D:HEM501
|
3.4
|
30.2
|
1.0
|
CHD
|
D:HEM501
|
3.4
|
31.8
|
1.0
|
CHC
|
D:HEM501
|
3.5
|
30.7
|
1.0
|
CA
|
D:CYS358
|
3.9
|
31.5
|
1.0
|
C3A
|
D:HEM501
|
4.2
|
28.8
|
1.0
|
C3D
|
D:HEM501
|
4.2
|
29.3
|
1.0
|
C2D
|
D:HEM501
|
4.2
|
29.5
|
1.0
|
C2A
|
D:HEM501
|
4.2
|
28.7
|
1.0
|
C3B
|
D:HEM501
|
4.3
|
29.9
|
1.0
|
C2B
|
D:HEM501
|
4.3
|
29.4
|
1.0
|
C3C
|
D:HEM501
|
4.4
|
33.2
|
1.0
|
C2C
|
D:HEM501
|
4.4
|
32.9
|
1.0
|
C
|
D:CYS358
|
4.7
|
31.6
|
1.0
|
C8
|
D:EGM502
|
4.7
|
20.3
|
1.0
|
CB
|
D:ALA248
|
4.7
|
31.9
|
1.0
|
N
|
D:GLY360
|
4.8
|
33.5
|
1.0
|
N
|
D:VAL359
|
4.9
|
31.9
|
1.0
|
|
Reference:
S.G.Bell,
R.M.Zhou,
W.Yang,
A.B.H.Tan,
A.S.Gentleman,
L.-L.Wong,
W.Zhou.
Investigation of the Substrate Range of CYP199A4: Modification of the Partition Between Hydroxylation and Desaturation Activities By Substrate and Protein Engineering Chemistry V. 18 16677 2012.
ISSN: ISSN 0947-6539
PubMed: 23135838
DOI: 10.1002/CHEM.201202776
Page generated: Mon Aug 5 01:31:58 2024
|