Iron in PDB 7yl8: Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature
Protein crystallography data
The structure of Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature, PDB code: 7yl8
was solved by
M.Unno,
K.Wada,
K.Kobayashi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
N/A /
1.45
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.43,
37.91,
33.01,
90,
105.96,
90
|
|
R / Rfree (%)
|
16.2 /
18.4
|
Iron Binding Sites:
The binding sites of Iron atom in the Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature
(pdb code 7yl8). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature, PDB code: 7yl8:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 7yl8
Go back to
Iron Binding Sites List in 7yl8
Iron binding site 1 out
of 4 in the Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:17.1
occ:0.90
|
FE1
|
A:SF4101
|
0.0
|
17.1
|
0.9
|
|
S4
|
A:SF4101
|
2.2
|
16.8
|
0.9
|
|
S2
|
A:SF4101
|
2.3
|
16.9
|
0.9
|
|
S3
|
A:SF4101
|
2.3
|
18.0
|
0.9
|
|
SG
|
A:CYS61
|
2.3
|
18.5
|
1.0
|
|
FE2
|
A:SF4101
|
2.7
|
17.8
|
0.9
|
|
FE4
|
A:SF4101
|
2.7
|
19.3
|
0.9
|
|
FE3
|
A:SF4101
|
2.7
|
17.0
|
0.9
|
|
HB2
|
A:SER65
|
3.2
|
19.6
|
1.0
|
|
HD2
|
A:PRO62
|
3.2
|
22.4
|
1.0
|
|
HB2
|
A:CYS61
|
3.3
|
21.4
|
1.0
|
|
CB
|
A:CYS61
|
3.3
|
17.9
|
1.0
|
|
HA
|
A:CYS61
|
3.5
|
21.9
|
1.0
|
|
HG13
|
A:ILE66
|
3.6
|
21.6
|
1.0
|
|
S1
|
A:SF4101
|
3.8
|
19.4
|
1.0
|
|
HD13
|
A:ILE66
|
4.0
|
24.5
|
1.0
|
|
CA
|
A:CYS61
|
4.0
|
18.2
|
1.0
|
|
D
|
A:SER65
|
4.1
|
20.7
|
0.9
|
|
H
|
A:SER65
|
4.1
|
20.7
|
0.1
|
|
D
|
A:THR63
|
4.1
|
20.9
|
0.8
|
|
H
|
A:THR63
|
4.1
|
20.9
|
0.2
|
|
CB
|
A:SER65
|
4.2
|
16.3
|
1.0
|
|
CD
|
A:PRO62
|
4.2
|
18.7
|
1.0
|
|
HB3
|
A:CYS61
|
4.3
|
21.4
|
1.0
|
|
HB3
|
A:CYS17
|
4.3
|
20.2
|
1.0
|
|
HA
|
A:CYS11
|
4.3
|
22.2
|
1.0
|
|
HG
|
A:SER65
|
4.3
|
23.1
|
0.5
|
|
DG
|
A:SER65
|
4.4
|
23.1
|
0.6
|
|
OG1
|
A:THR63
|
4.4
|
24.8
|
1.0
|
|
D
|
A:ILE66
|
4.5
|
17.4
|
0.8
|
|
H
|
A:ILE66
|
4.5
|
17.4
|
0.1
|
|
HD11
|
A:ILE66
|
4.5
|
24.5
|
1.0
|
|
CD1
|
A:ILE66
|
4.6
|
20.4
|
1.0
|
|
CG1
|
A:ILE66
|
4.6
|
18.0
|
1.0
|
|
OG
|
A:SER65
|
4.6
|
19.2
|
1.0
|
|
SG
|
A:CYS14
|
4.6
|
23.5
|
1.0
|
|
C
|
A:CYS61
|
4.6
|
18.2
|
1.0
|
|
HG2
|
A:PRO62
|
4.6
|
23.4
|
1.0
|
|
D2
|
A:HOH237
|
4.6
|
30.3
|
1.0
|
|
D
|
A:ILE12
|
4.6
|
26.6
|
0.9
|
|
H
|
A:ILE12
|
4.6
|
26.6
|
0.1
|
|
N
|
A:PRO62
|
4.7
|
16.8
|
1.0
|
|
HG1
|
A:THR63
|
4.7
|
29.8
|
0.1
|
|
DG1
|
A:THR63
|
4.7
|
29.8
|
0.9
|
|
HB3
|
A:SER65
|
4.8
|
19.6
|
1.0
|
|
SG
|
A:CYS17
|
4.8
|
18.6
|
1.0
|
|
HD3
|
A:PRO62
|
4.8
|
22.4
|
1.0
|
|
SG
|
A:CYS11
|
4.9
|
20.3
|
1.0
|
|
HB2
|
A:CYS11
|
4.9
|
21.9
|
1.0
|
|
N
|
A:SER65
|
4.9
|
17.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 7yl8
Go back to
Iron Binding Sites List in 7yl8
Iron binding site 2 out
of 4 in the Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:17.8
occ:0.93
|
FE2
|
A:SF4101
|
0.0
|
17.8
|
0.9
|
|
S3
|
A:SF4101
|
2.2
|
18.0
|
0.9
|
|
S4
|
A:SF4101
|
2.3
|
16.8
|
0.9
|
|
S1
|
A:SF4101
|
2.3
|
19.4
|
1.0
|
|
SG
|
A:CYS11
|
2.3
|
20.3
|
1.0
|
|
FE1
|
A:SF4101
|
2.7
|
17.1
|
0.9
|
|
FE4
|
A:SF4101
|
2.7
|
19.3
|
0.9
|
|
FE3
|
A:SF4101
|
2.7
|
17.0
|
0.9
|
|
D
|
A:ALA13
|
3.2
|
26.1
|
0.8
|
|
H
|
A:ALA13
|
3.2
|
26.1
|
0.2
|
|
HA
|
A:CYS11
|
3.3
|
22.2
|
1.0
|
|
CB
|
A:CYS11
|
3.3
|
18.3
|
1.0
|
|
HB2
|
A:CYS11
|
3.3
|
21.9
|
1.0
|
|
D
|
A:ILE12
|
3.4
|
26.6
|
0.9
|
|
H
|
A:ILE12
|
3.4
|
26.6
|
0.1
|
|
HB3
|
A:ALA33
|
3.4
|
22.9
|
1.0
|
|
H
|
A:CYS14
|
3.7
|
31.2
|
0.1
|
|
D
|
A:CYS14
|
3.7
|
31.2
|
0.9
|
|
CA
|
A:CYS11
|
3.8
|
18.5
|
1.0
|
|
H
|
A:ALA33
|
3.8
|
25.6
|
0.2
|
|
D
|
A:ALA33
|
3.8
|
25.6
|
0.8
|
|
S2
|
A:SF4101
|
3.8
|
16.9
|
0.9
|
|
HB2
|
A:ALA33
|
3.9
|
22.9
|
1.0
|
|
N
|
A:ILE12
|
4.0
|
22.2
|
1.0
|
|
N
|
A:ALA13
|
4.0
|
21.7
|
1.0
|
|
HB2
|
A:SER65
|
4.0
|
19.6
|
1.0
|
|
HA
|
A:ALA13
|
4.1
|
30.0
|
1.0
|
|
HE1
|
A:TYR27
|
4.1
|
24.4
|
0.3
|
|
CB
|
A:ALA33
|
4.2
|
19.1
|
1.0
|
|
C
|
A:CYS11
|
4.3
|
22.8
|
1.0
|
|
HB3
|
A:CYS11
|
4.3
|
21.9
|
1.0
|
|
HG13
|
A:VAL6
|
4.6
|
21.1
|
1.0
|
|
N
|
A:CYS14
|
4.6
|
26.0
|
1.0
|
|
CA
|
A:ALA13
|
4.6
|
25.0
|
1.0
|
|
N
|
A:ALA33
|
4.7
|
21.3
|
1.0
|
|
HG12
|
A:VAL6
|
4.8
|
21.1
|
1.0
|
|
SG
|
A:CYS61
|
4.8
|
18.5
|
1.0
|
|
H
|
A:GLY15
|
4.8
|
31.8
|
0.3
|
|
D
|
A:GLY15
|
4.8
|
31.8
|
0.7
|
|
CB
|
A:SER65
|
4.8
|
16.3
|
1.0
|
|
SG
|
A:CYS17
|
4.8
|
18.6
|
1.0
|
|
HB3
|
A:SER65
|
4.8
|
19.6
|
1.0
|
|
HG12
|
A:ILE12
|
4.9
|
30.7
|
1.0
|
|
C
|
A:ILE12
|
4.9
|
27.5
|
1.0
|
|
SG
|
A:CYS14
|
4.9
|
23.5
|
1.0
|
|
HB1
|
A:ALA33
|
4.9
|
22.9
|
1.0
|
|
HG13
|
A:ILE12
|
4.9
|
30.7
|
1.0
|
|
OG
|
A:SER65
|
5.0
|
19.2
|
1.0
|
|
HA
|
A:ILE32
|
5.0
|
28.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 7yl8
Go back to
Iron Binding Sites List in 7yl8
Iron binding site 3 out
of 4 in the Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:17.0
occ:0.89
|
FE3
|
A:SF4101
|
0.0
|
17.0
|
0.9
|
|
S4
|
A:SF4101
|
2.2
|
16.8
|
0.9
|
|
S2
|
A:SF4101
|
2.3
|
16.9
|
0.9
|
|
SG
|
A:CYS17
|
2.3
|
18.6
|
1.0
|
|
S1
|
A:SF4101
|
2.3
|
19.4
|
1.0
|
|
FE1
|
A:SF4101
|
2.7
|
17.1
|
0.9
|
|
FE2
|
A:SF4101
|
2.7
|
17.8
|
0.9
|
|
FE4
|
A:SF4101
|
2.8
|
19.3
|
0.9
|
|
HB3
|
A:CYS17
|
3.0
|
20.2
|
1.0
|
|
D
|
A:CYS17
|
3.1
|
24.2
|
0.9
|
|
H
|
A:CYS17
|
3.1
|
24.2
|
0.1
|
|
HB2
|
A:ALA33
|
3.2
|
22.9
|
1.0
|
|
CB
|
A:CYS17
|
3.2
|
16.8
|
1.0
|
|
HD13
|
A:ILE66
|
3.3
|
24.5
|
1.0
|
|
HB3
|
A:ALA33
|
3.5
|
22.9
|
1.0
|
|
HE1
|
A:TYR27
|
3.7
|
24.4
|
0.3
|
|
CB
|
A:ALA33
|
3.7
|
19.1
|
1.0
|
|
S3
|
A:SF4101
|
3.9
|
18.0
|
0.9
|
|
N
|
A:CYS17
|
3.9
|
20.2
|
1.0
|
|
HE1
|
A:TYR27
|
3.9
|
25.0
|
0.7
|
|
HB1
|
A:ALA33
|
4.0
|
22.9
|
1.0
|
|
HB2
|
A:CYS17
|
4.0
|
20.2
|
1.0
|
|
OH
|
A:TYR27
|
4.0
|
23.9
|
0.3
|
|
HG13
|
A:ILE66
|
4.2
|
21.6
|
1.0
|
|
CA
|
A:CYS17
|
4.2
|
20.9
|
1.0
|
|
CD1
|
A:ILE66
|
4.3
|
20.4
|
1.0
|
|
D
|
A:ALA16
|
4.4
|
26.4
|
0.8
|
|
H
|
A:ALA16
|
4.4
|
26.4
|
0.2
|
|
H
|
A:GLY15
|
4.5
|
31.8
|
0.3
|
|
D
|
A:GLY15
|
4.5
|
31.8
|
0.7
|
|
CE1
|
A:TYR27
|
4.5
|
20.3
|
0.3
|
|
HB2
|
A:ALA16
|
4.6
|
30.2
|
1.0
|
|
D2
|
A:HOH237
|
4.6
|
30.3
|
1.0
|
|
HB2
|
A:CYS61
|
4.7
|
21.4
|
1.0
|
|
HD11
|
A:ILE66
|
4.7
|
24.5
|
1.0
|
|
SG
|
A:CYS11
|
4.7
|
20.3
|
1.0
|
|
SG
|
A:CYS14
|
4.7
|
23.5
|
1.0
|
|
D
|
A:CYS14
|
4.7
|
31.2
|
0.9
|
|
H
|
A:CYS14
|
4.7
|
31.2
|
0.1
|
|
H
|
A:GLY18
|
4.7
|
22.9
|
0.2
|
|
D
|
A:GLY18
|
4.7
|
22.9
|
0.8
|
|
CG1
|
A:ILE66
|
4.8
|
18.0
|
1.0
|
|
CZ
|
A:TYR27
|
4.8
|
17.3
|
0.3
|
|
DH
|
A:TYR27
|
4.8
|
28.7
|
0.3
|
|
SG
|
A:CYS61
|
4.8
|
18.5
|
1.0
|
|
D
|
A:ALA33
|
4.9
|
25.6
|
0.8
|
|
H
|
A:ALA33
|
4.9
|
25.6
|
0.2
|
|
N
|
A:ALA16
|
4.9
|
22.0
|
1.0
|
|
HA
|
A:CYS17
|
4.9
|
25.1
|
1.0
|
|
HG12
|
A:ILE66
|
5.0
|
21.6
|
1.0
|
|
HD2
|
A:PRO62
|
5.0
|
22.4
|
1.0
|
|
CE1
|
A:TYR27
|
5.0
|
20.8
|
0.7
|
|
HD12
|
A:ILE66
|
5.0
|
24.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 7yl8
Go back to
Iron Binding Sites List in 7yl8
Iron binding site 4 out
of 4 in the Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Neutron Structure of Bacillus Thermoproteolyticus Ferredoxin at Room Temperature within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:19.3
occ:0.88
|
FE4
|
A:SF4101
|
0.0
|
19.3
|
0.9
|
|
S1
|
A:SF4101
|
2.3
|
19.4
|
1.0
|
|
S3
|
A:SF4101
|
2.3
|
18.0
|
0.9
|
|
SG
|
A:CYS14
|
2.3
|
23.5
|
1.0
|
|
S2
|
A:SF4101
|
2.3
|
16.9
|
0.9
|
|
D
|
A:CYS14
|
2.7
|
31.2
|
0.9
|
|
H
|
A:CYS14
|
2.7
|
31.2
|
0.1
|
|
FE1
|
A:SF4101
|
2.7
|
17.1
|
0.9
|
|
FE2
|
A:SF4101
|
2.7
|
17.8
|
0.9
|
|
FE3
|
A:SF4101
|
2.8
|
17.0
|
0.9
|
|
HD2
|
A:PRO62
|
3.2
|
22.4
|
1.0
|
|
H
|
A:ALA16
|
3.4
|
26.4
|
0.2
|
|
D
|
A:ALA16
|
3.4
|
26.4
|
0.8
|
|
CB
|
A:CYS14
|
3.4
|
26.7
|
1.0
|
|
HB3
|
A:CYS14
|
3.5
|
32.0
|
1.0
|
|
H
|
A:GLY15
|
3.5
|
31.8
|
0.3
|
|
D
|
A:GLY15
|
3.5
|
31.8
|
0.7
|
|
N
|
A:CYS14
|
3.5
|
26.0
|
1.0
|
|
HB2
|
A:ALA16
|
3.8
|
30.2
|
1.0
|
|
S4
|
A:SF4101
|
3.8
|
16.8
|
0.9
|
|
CA
|
A:CYS14
|
3.9
|
28.5
|
1.0
|
|
D
|
A:CYS17
|
4.0
|
24.2
|
0.9
|
|
H
|
A:CYS17
|
4.0
|
24.2
|
0.1
|
|
N
|
A:GLY15
|
4.0
|
26.5
|
1.0
|
|
CD
|
A:PRO62
|
4.2
|
18.7
|
1.0
|
|
HG13
|
A:ILE12
|
4.3
|
30.7
|
1.0
|
|
C
|
A:CYS14
|
4.3
|
34.2
|
1.0
|
|
N
|
A:ALA16
|
4.3
|
22.0
|
1.0
|
|
HG2
|
A:PRO62
|
4.3
|
23.4
|
1.0
|
|
H
|
A:ILE12
|
4.3
|
26.6
|
0.1
|
|
D
|
A:ILE12
|
4.3
|
26.6
|
0.9
|
|
D
|
A:ALA13
|
4.3
|
26.1
|
0.8
|
|
H
|
A:ALA13
|
4.3
|
26.1
|
0.2
|
|
HB2
|
A:CYS14
|
4.3
|
32.0
|
1.0
|
|
HA
|
A:CYS61
|
4.4
|
21.9
|
1.0
|
|
HD3
|
A:PRO62
|
4.5
|
22.4
|
1.0
|
|
HE1
|
A:TYR27
|
4.6
|
24.4
|
0.3
|
|
CG
|
A:PRO62
|
4.6
|
19.4
|
1.0
|
|
HG3
|
A:PRO62
|
4.6
|
23.4
|
1.0
|
|
N
|
A:ALA13
|
4.7
|
21.7
|
1.0
|
|
SG
|
A:CYS61
|
4.7
|
18.5
|
1.0
|
|
C
|
A:ALA13
|
4.7
|
28.9
|
1.0
|
|
HA
|
A:ALA13
|
4.7
|
30.0
|
1.0
|
|
HG12
|
A:ILE12
|
4.7
|
30.7
|
1.0
|
|
SG
|
A:CYS17
|
4.7
|
18.6
|
1.0
|
|
SG
|
A:CYS11
|
4.7
|
20.3
|
1.0
|
|
CB
|
A:ALA16
|
4.8
|
25.1
|
1.0
|
|
N
|
A:CYS17
|
4.9
|
20.2
|
1.0
|
|
HB3
|
A:CYS17
|
4.9
|
20.2
|
1.0
|
|
D2
|
A:HOH237
|
4.9
|
30.3
|
1.0
|
|
HA
|
A:CYS14
|
4.9
|
34.2
|
1.0
|
|
CA
|
A:ALA13
|
5.0
|
25.0
|
1.0
|
|
Reference:
K.Wada,
K.Kobayashi,
I.Era,
Y.Isobe,
T.Kamimura,
M.Murakawa,
M.Sugishima,
K.Kusaka,
N.Yano,
K.Fukuyama,
M.Mishima,
Y.Kitagawa,
M.Unno.
Protonation/Deprotonation-Driven Switch For the Redox Stability of the Low-Potential [4FE-4S] Ferredoxin To Be Published.
Page generated: Fri Aug 9 12:22:32 2024
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