Iron in PDB 6w0s: Crystal Structure of Substrate Free Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053
Protein crystallography data
The structure of Crystal Structure of Substrate Free Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053, PDB code: 6w0s
was solved by
Z.Luo,
X.Jia,
C.Sun,
X.Qu,
B.Kobe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.06 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
42.208,
91.325,
98.275,
90.00,
96.41,
90.00
|
R / Rfree (%)
|
18.6 /
22
|
Other elements in 6w0s:
The structure of Crystal Structure of Substrate Free Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Substrate Free Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053
(pdb code 6w0s). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the
Crystal Structure of Substrate Free Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053, PDB code: 6w0s:
Jump to Iron binding site number:
1;
2;
Iron binding site 1 out
of 2 in 6w0s
Go back to
Iron Binding Sites List in 6w0s
Iron binding site 1 out
of 2 in the Crystal Structure of Substrate Free Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053
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 Substrate Free Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe409
b:12.8
occ:1.00
|
FE
|
A:HEM409
|
0.0
|
12.8
|
1.0
|
NA
|
A:HEM409
|
2.0
|
11.0
|
1.0
|
NB
|
A:HEM409
|
2.0
|
11.5
|
1.0
|
ND
|
A:HEM409
|
2.0
|
12.2
|
1.0
|
NC
|
A:HEM409
|
2.0
|
9.3
|
1.0
|
O
|
A:HOH525
|
2.3
|
19.0
|
1.0
|
SG
|
A:CYS348
|
2.3
|
13.2
|
1.0
|
C4C
|
A:HEM409
|
3.0
|
15.6
|
1.0
|
C1A
|
A:HEM409
|
3.0
|
11.1
|
1.0
|
C4A
|
A:HEM409
|
3.0
|
14.0
|
1.0
|
C4B
|
A:HEM409
|
3.0
|
10.5
|
1.0
|
C1C
|
A:HEM409
|
3.0
|
10.0
|
1.0
|
C1D
|
A:HEM409
|
3.1
|
12.4
|
1.0
|
C1B
|
A:HEM409
|
3.1
|
14.7
|
1.0
|
C4D
|
A:HEM409
|
3.1
|
11.4
|
1.0
|
HB2
|
A:CYS348
|
3.1
|
10.3
|
1.0
|
CB
|
A:CYS348
|
3.4
|
8.6
|
1.0
|
CHD
|
A:HEM409
|
3.4
|
14.5
|
1.0
|
CHA
|
A:HEM409
|
3.4
|
12.3
|
1.0
|
CHC
|
A:HEM409
|
3.4
|
14.1
|
1.0
|
CHB
|
A:HEM409
|
3.4
|
16.3
|
1.0
|
H
|
A:GLY350
|
3.9
|
14.3
|
1.0
|
HA
|
A:CYS348
|
3.9
|
13.9
|
1.0
|
HD2
|
A:PRO349
|
4.0
|
16.1
|
1.0
|
HB1
|
A:ALA237
|
4.1
|
21.8
|
1.0
|
HB3
|
A:CYS348
|
4.1
|
10.3
|
1.0
|
O
|
A:ALA237
|
4.2
|
17.0
|
1.0
|
C3C
|
A:HEM409
|
4.2
|
10.8
|
1.0
|
CA
|
A:CYS348
|
4.2
|
11.6
|
1.0
|
C3A
|
A:HEM409
|
4.2
|
12.4
|
1.0
|
C2A
|
A:HEM409
|
4.2
|
13.9
|
1.0
|
C2C
|
A:HEM409
|
4.2
|
12.8
|
1.0
|
C2B
|
A:HEM409
|
4.3
|
10.3
|
1.0
|
C3B
|
A:HEM409
|
4.3
|
14.1
|
1.0
|
C2D
|
A:HEM409
|
4.3
|
14.2
|
1.0
|
HO3
|
A:GOL401
|
4.3
|
42.7
|
1.0
|
HA3
|
A:GLY350
|
4.3
|
15.2
|
1.0
|
C3D
|
A:HEM409
|
4.3
|
13.8
|
1.0
|
O3
|
A:GOL401
|
4.3
|
35.6
|
1.0
|
HHA
|
A:HEM409
|
4.4
|
14.7
|
1.0
|
HHC
|
A:HEM409
|
4.4
|
16.9
|
1.0
|
HHB
|
A:HEM409
|
4.4
|
19.5
|
1.0
|
HG21
|
A:THR241
|
4.5
|
18.3
|
1.0
|
H31
|
A:GOL401
|
4.6
|
33.5
|
1.0
|
HD1
|
A:PHE341
|
4.6
|
15.7
|
1.0
|
N
|
A:GLY350
|
4.7
|
11.9
|
1.0
|
HG1
|
A:THR241
|
4.7
|
17.7
|
1.0
|
C
|
A:CYS348
|
4.9
|
14.8
|
1.0
|
CD
|
A:PRO349
|
4.9
|
13.5
|
1.0
|
CA
|
A:GLY350
|
4.9
|
12.7
|
1.0
|
C3
|
A:GOL401
|
5.0
|
27.9
|
1.0
|
|
Iron binding site 2 out
of 2 in 6w0s
Go back to
Iron Binding Sites List in 6w0s
Iron binding site 2 out
of 2 in the Crystal Structure of Substrate Free Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053
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 Substrate Free Cytochrome P450 NASF5053 From Streptomyces Sp. Nrrl F-5053 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe406
b:12.2
occ:1.00
|
FE
|
B:HEM406
|
0.0
|
12.2
|
1.0
|
NB
|
B:HEM406
|
2.0
|
10.4
|
1.0
|
NA
|
B:HEM406
|
2.0
|
8.4
|
1.0
|
NC
|
B:HEM406
|
2.0
|
6.9
|
1.0
|
ND
|
B:HEM406
|
2.0
|
13.0
|
1.0
|
O
|
B:HOH593
|
2.3
|
19.2
|
1.0
|
SG
|
B:CYS348
|
2.3
|
12.5
|
1.0
|
C4B
|
B:HEM406
|
3.0
|
10.4
|
1.0
|
C1C
|
B:HEM406
|
3.0
|
10.7
|
1.0
|
C1A
|
B:HEM406
|
3.0
|
12.8
|
1.0
|
C4C
|
B:HEM406
|
3.0
|
13.5
|
1.0
|
C4A
|
B:HEM406
|
3.0
|
13.0
|
1.0
|
C1B
|
B:HEM406
|
3.0
|
10.9
|
1.0
|
C4D
|
B:HEM406
|
3.1
|
10.2
|
1.0
|
C1D
|
B:HEM406
|
3.1
|
12.2
|
1.0
|
HB2
|
B:CYS348
|
3.2
|
9.5
|
1.0
|
CHC
|
B:HEM406
|
3.4
|
11.9
|
1.0
|
CB
|
B:CYS348
|
3.4
|
8.0
|
1.0
|
CHA
|
B:HEM406
|
3.4
|
11.2
|
1.0
|
CHD
|
B:HEM406
|
3.5
|
15.9
|
1.0
|
CHB
|
B:HEM406
|
3.5
|
14.5
|
1.0
|
HA
|
B:CYS348
|
3.9
|
14.3
|
1.0
|
H
|
B:GLY350
|
3.9
|
13.3
|
1.0
|
HD2
|
B:PRO349
|
4.1
|
18.6
|
1.0
|
HB3
|
B:CYS348
|
4.2
|
9.5
|
1.0
|
O
|
B:ALA237
|
4.2
|
16.3
|
1.0
|
HB1
|
B:ALA237
|
4.2
|
21.2
|
1.0
|
CA
|
B:CYS348
|
4.2
|
12.0
|
1.0
|
C3C
|
B:HEM406
|
4.2
|
10.8
|
1.0
|
C2C
|
B:HEM406
|
4.2
|
9.5
|
1.0
|
C3B
|
B:HEM406
|
4.2
|
14.4
|
1.0
|
C2B
|
B:HEM406
|
4.2
|
12.3
|
1.0
|
C2A
|
B:HEM406
|
4.2
|
15.3
|
1.0
|
C3A
|
B:HEM406
|
4.2
|
13.7
|
1.0
|
C2D
|
B:HEM406
|
4.3
|
14.5
|
1.0
|
C3D
|
B:HEM406
|
4.3
|
13.5
|
1.0
|
HA3
|
B:GLY350
|
4.3
|
19.4
|
1.0
|
HHC
|
B:HEM406
|
4.3
|
14.2
|
1.0
|
HHA
|
B:HEM406
|
4.4
|
13.5
|
1.0
|
HHD
|
B:HEM406
|
4.4
|
19.1
|
1.0
|
HHB
|
B:HEM406
|
4.4
|
17.4
|
1.0
|
O
|
B:HOH808
|
4.5
|
28.5
|
1.0
|
HD1
|
B:PHE341
|
4.6
|
15.6
|
1.0
|
N
|
B:GLY350
|
4.7
|
11.1
|
1.0
|
C
|
B:CYS348
|
4.9
|
12.6
|
1.0
|
CA
|
B:GLY350
|
4.9
|
16.2
|
1.0
|
CD
|
B:PRO349
|
5.0
|
15.5
|
1.0
|
|
Reference:
C.Sun,
Z.Luo,
W.Zhang,
Z.Deng,
M.Mobli,
B.Kobe,
X.Jia,
X.Qu.
Molecular Basis of Regio- and Stereo-Specificity in Biosynthesis of Bacterial Heterodimeric Diketopiperazines To Be Published.
Page generated: Wed Aug 7 13:47:54 2024
|