Iron in PDB 7xxf: Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis
Other elements in 7xxf:
The structure of Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis
(pdb code 7xxf). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis, PDB code: 7xxf:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 7xxf
Go back to
Iron Binding Sites List in 7xxf
Iron binding site 1 out
of 5 in the Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe401
b:58.2
occ:1.00
|
FE
|
C:HEC401
|
0.0
|
58.2
|
1.0
|
ND
|
C:HEC401
|
1.9
|
47.2
|
1.0
|
NE2
|
C:HIS115
|
2.0
|
45.9
|
1.0
|
NA
|
C:HEC401
|
2.0
|
46.3
|
1.0
|
NC
|
C:HEC401
|
2.1
|
40.9
|
1.0
|
NB
|
C:HEC401
|
2.1
|
44.0
|
1.0
|
SD
|
C:MET98
|
2.1
|
47.9
|
1.0
|
CD2
|
C:HIS115
|
2.8
|
41.6
|
1.0
|
C4D
|
C:HEC401
|
2.9
|
40.4
|
1.0
|
C1D
|
C:HEC401
|
2.9
|
39.1
|
1.0
|
C1A
|
C:HEC401
|
3.0
|
45.2
|
1.0
|
C4C
|
C:HEC401
|
3.0
|
38.3
|
1.0
|
C4A
|
C:HEC401
|
3.0
|
44.7
|
1.0
|
CE1
|
C:HIS115
|
3.1
|
43.5
|
1.0
|
C4B
|
C:HEC401
|
3.1
|
42.8
|
1.0
|
C1B
|
C:HEC401
|
3.1
|
41.9
|
1.0
|
C1C
|
C:HEC401
|
3.1
|
40.6
|
1.0
|
CE
|
C:MET98
|
3.3
|
40.1
|
1.0
|
CHA
|
C:HEC401
|
3.3
|
44.3
|
1.0
|
CHD
|
C:HEC401
|
3.4
|
37.8
|
1.0
|
CHB
|
C:HEC401
|
3.5
|
42.0
|
1.0
|
CHC
|
C:HEC401
|
3.5
|
41.9
|
1.0
|
CG
|
C:MET98
|
3.5
|
39.5
|
1.0
|
CG
|
C:HIS115
|
4.0
|
41.8
|
1.0
|
ND1
|
C:HIS115
|
4.1
|
41.7
|
1.0
|
C3D
|
C:HEC401
|
4.1
|
41.3
|
1.0
|
C2D
|
C:HEC401
|
4.1
|
39.9
|
1.0
|
C2A
|
C:HEC401
|
4.2
|
44.4
|
1.0
|
C3A
|
C:HEC401
|
4.2
|
46.1
|
1.0
|
C3C
|
C:HEC401
|
4.3
|
44.4
|
1.0
|
C2C
|
C:HEC401
|
4.3
|
41.4
|
1.0
|
C2B
|
C:HEC401
|
4.3
|
44.9
|
1.0
|
C3B
|
C:HEC401
|
4.3
|
44.5
|
1.0
|
CB
|
C:MET98
|
4.4
|
37.7
|
1.0
|
|
Iron binding site 2 out
of 5 in 7xxf
Go back to
Iron Binding Sites List in 7xxf
Iron binding site 2 out
of 5 in the Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe402
b:45.0
occ:1.00
|
FE
|
C:HEC402
|
0.0
|
45.0
|
1.0
|
ND
|
C:HEC402
|
1.9
|
30.8
|
1.0
|
NA
|
C:HEC402
|
2.0
|
31.0
|
1.0
|
NE2
|
C:HIS163
|
2.0
|
21.7
|
1.0
|
SD
|
C:MET134
|
2.1
|
33.2
|
1.0
|
NC
|
C:HEC402
|
2.1
|
27.2
|
1.0
|
NB
|
C:HEC402
|
2.1
|
32.6
|
1.0
|
C4D
|
C:HEC402
|
2.9
|
25.4
|
1.0
|
CE1
|
C:HIS163
|
2.9
|
23.3
|
1.0
|
C1D
|
C:HEC402
|
2.9
|
23.8
|
1.0
|
C1A
|
C:HEC402
|
3.0
|
25.7
|
1.0
|
C4C
|
C:HEC402
|
3.0
|
24.4
|
1.0
|
C4A
|
C:HEC402
|
3.1
|
28.3
|
1.0
|
C4B
|
C:HEC402
|
3.1
|
25.5
|
1.0
|
C1B
|
C:HEC402
|
3.1
|
26.2
|
1.0
|
C1C
|
C:HEC402
|
3.1
|
26.2
|
1.0
|
CD2
|
C:HIS163
|
3.2
|
20.6
|
1.0
|
CG
|
C:MET134
|
3.3
|
29.3
|
1.0
|
CE
|
C:MET134
|
3.3
|
23.6
|
1.0
|
CHA
|
C:HEC402
|
3.3
|
24.4
|
1.0
|
CHD
|
C:HEC402
|
3.4
|
23.6
|
1.0
|
CHB
|
C:HEC402
|
3.5
|
25.7
|
1.0
|
CHC
|
C:HEC402
|
3.5
|
22.5
|
1.0
|
ND1
|
C:HIS163
|
4.0
|
24.5
|
1.0
|
CB
|
C:MET134
|
4.1
|
23.6
|
1.0
|
C3D
|
C:HEC402
|
4.1
|
28.2
|
1.0
|
C2D
|
C:HEC402
|
4.1
|
27.1
|
1.0
|
C2A
|
C:HEC402
|
4.2
|
26.7
|
1.0
|
CG
|
C:HIS163
|
4.2
|
22.6
|
1.0
|
C3A
|
C:HEC402
|
4.2
|
27.4
|
1.0
|
C3C
|
C:HEC402
|
4.3
|
26.6
|
1.0
|
C2C
|
C:HEC402
|
4.3
|
24.6
|
1.0
|
C2B
|
C:HEC402
|
4.3
|
27.3
|
1.0
|
C3B
|
C:HEC402
|
4.3
|
28.7
|
1.0
|
|
Iron binding site 3 out
of 5 in 7xxf
Go back to
Iron Binding Sites List in 7xxf
Iron binding site 3 out
of 5 in the Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe403
b:33.3
occ:1.00
|
FE
|
C:HEC403
|
0.0
|
33.3
|
1.0
|
ND
|
C:HEC403
|
1.9
|
20.2
|
1.0
|
NA
|
C:HEC403
|
2.0
|
18.9
|
1.0
|
NE2
|
C:HIS260
|
2.0
|
21.9
|
1.0
|
NC
|
C:HEC403
|
2.1
|
11.7
|
1.0
|
NB
|
C:HEC403
|
2.1
|
18.0
|
1.0
|
SD
|
C:MET245
|
2.1
|
20.7
|
1.0
|
C4D
|
C:HEC403
|
2.9
|
14.6
|
1.0
|
CD2
|
C:HIS260
|
2.9
|
7.7
|
1.0
|
C1D
|
C:HEC403
|
2.9
|
9.9
|
1.0
|
C1A
|
C:HEC403
|
3.0
|
17.9
|
1.0
|
CE1
|
C:HIS260
|
3.0
|
4.5
|
1.0
|
C4C
|
C:HEC403
|
3.0
|
13.6
|
1.0
|
C4A
|
C:HEC403
|
3.0
|
12.4
|
1.0
|
C4B
|
C:HEC403
|
3.1
|
11.2
|
1.0
|
C1B
|
C:HEC403
|
3.1
|
16.2
|
1.0
|
C1C
|
C:HEC403
|
3.1
|
11.6
|
1.0
|
CG
|
C:MET245
|
3.3
|
8.0
|
1.0
|
CHA
|
C:HEC403
|
3.3
|
12.3
|
1.0
|
CE
|
C:MET245
|
3.4
|
11.3
|
1.0
|
CHD
|
C:HEC403
|
3.4
|
11.3
|
1.0
|
CHB
|
C:HEC403
|
3.5
|
9.9
|
1.0
|
CHC
|
C:HEC403
|
3.5
|
11.3
|
1.0
|
CG
|
C:HIS260
|
4.0
|
14.8
|
1.0
|
ND1
|
C:HIS260
|
4.0
|
10.8
|
1.0
|
C3D
|
C:HEC403
|
4.1
|
18.3
|
1.0
|
C2D
|
C:HEC403
|
4.1
|
16.9
|
1.0
|
C2A
|
C:HEC403
|
4.2
|
17.9
|
1.0
|
CB
|
C:MET245
|
4.2
|
11.8
|
1.0
|
C3A
|
C:HEC403
|
4.2
|
14.2
|
1.0
|
C3C
|
C:HEC403
|
4.3
|
17.9
|
1.0
|
C2C
|
C:HEC403
|
4.3
|
14.2
|
1.0
|
C2B
|
C:HEC403
|
4.3
|
13.2
|
1.0
|
C3B
|
C:HEC403
|
4.3
|
15.0
|
1.0
|
|
Iron binding site 4 out
of 5 in 7xxf
Go back to
Iron Binding Sites List in 7xxf
Iron binding site 4 out
of 5 in the Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe404
b:33.4
occ:1.00
|
FE
|
C:HEC404
|
0.0
|
33.4
|
1.0
|
ND
|
C:HEC404
|
1.9
|
21.8
|
1.0
|
NA
|
C:HEC404
|
2.0
|
22.0
|
1.0
|
NE2
|
C:HIS320
|
2.0
|
17.0
|
1.0
|
NE2
|
C:HIS148
|
2.0
|
17.2
|
1.0
|
NC
|
C:HEC404
|
2.1
|
24.1
|
1.0
|
NB
|
C:HEC404
|
2.1
|
21.7
|
1.0
|
CE1
|
C:HIS148
|
2.7
|
17.2
|
1.0
|
CE1
|
C:HIS320
|
2.8
|
9.6
|
1.0
|
C4D
|
C:HEC404
|
2.9
|
17.1
|
1.0
|
C1D
|
C:HEC404
|
2.9
|
17.0
|
1.0
|
C1A
|
C:HEC404
|
3.0
|
11.8
|
1.0
|
C4C
|
C:HEC404
|
3.0
|
21.8
|
1.0
|
C4A
|
C:HEC404
|
3.0
|
19.2
|
1.0
|
C1B
|
C:HEC404
|
3.1
|
13.2
|
1.0
|
C4B
|
C:HEC404
|
3.1
|
13.8
|
1.0
|
CD2
|
C:HIS320
|
3.1
|
16.3
|
1.0
|
C1C
|
C:HEC404
|
3.1
|
18.1
|
1.0
|
CD2
|
C:HIS148
|
3.2
|
17.6
|
1.0
|
CHA
|
C:HEC404
|
3.3
|
16.2
|
1.0
|
CHD
|
C:HEC404
|
3.4
|
17.8
|
1.0
|
CHB
|
C:HEC404
|
3.5
|
16.1
|
1.0
|
CHC
|
C:HEC404
|
3.5
|
17.9
|
1.0
|
ND1
|
C:HIS148
|
3.9
|
15.3
|
1.0
|
ND1
|
C:HIS320
|
4.0
|
10.5
|
1.0
|
C3D
|
C:HEC404
|
4.1
|
22.2
|
1.0
|
C2D
|
C:HEC404
|
4.1
|
20.2
|
1.0
|
CG
|
C:HIS148
|
4.2
|
15.3
|
1.0
|
CG
|
C:HIS320
|
4.2
|
16.3
|
1.0
|
C2A
|
C:HEC404
|
4.2
|
18.6
|
1.0
|
C3A
|
C:HEC404
|
4.2
|
19.4
|
1.0
|
C3C
|
C:HEC404
|
4.3
|
22.3
|
1.0
|
C2C
|
C:HEC404
|
4.3
|
21.0
|
1.0
|
C2B
|
C:HEC404
|
4.3
|
18.0
|
1.0
|
C3B
|
C:HEC404
|
4.3
|
18.1
|
1.0
|
|
Iron binding site 5 out
of 5 in 7xxf
Go back to
Iron Binding Sites List in 7xxf
Iron binding site 5 out
of 5 in the Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Structure of Photosynthetic LH1-Rc Super-Complex of Rhodopila Globiformis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe401
b:42.6
occ:1.00
|
OE2
|
M:GLU234
|
2.0
|
36.1
|
1.0
|
NE2
|
L:HIS191
|
2.1
|
23.8
|
1.0
|
OE1
|
M:GLU234
|
2.1
|
40.7
|
1.0
|
NE2
|
M:HIS219
|
2.2
|
23.7
|
1.0
|
NE2
|
M:HIS266
|
2.2
|
27.4
|
1.0
|
NE2
|
L:HIS231
|
2.2
|
22.0
|
1.0
|
CD
|
M:GLU234
|
2.3
|
29.5
|
1.0
|
CE1
|
L:HIS191
|
2.8
|
16.5
|
1.0
|
CE1
|
M:HIS219
|
3.1
|
15.7
|
1.0
|
CE1
|
L:HIS231
|
3.1
|
14.2
|
1.0
|
CE1
|
M:HIS266
|
3.1
|
14.6
|
1.0
|
CD2
|
M:HIS266
|
3.2
|
13.9
|
1.0
|
CD2
|
L:HIS191
|
3.2
|
17.0
|
1.0
|
CD2
|
M:HIS219
|
3.3
|
12.9
|
1.0
|
CD2
|
L:HIS231
|
3.3
|
9.7
|
1.0
|
CG
|
M:GLU234
|
3.8
|
26.0
|
1.0
|
ND1
|
L:HIS191
|
4.0
|
19.6
|
1.0
|
ND1
|
M:HIS219
|
4.2
|
12.1
|
1.0
|
CG
|
L:HIS191
|
4.2
|
21.5
|
1.0
|
ND1
|
M:HIS266
|
4.3
|
20.1
|
1.0
|
ND1
|
L:HIS231
|
4.3
|
24.4
|
1.0
|
CG
|
M:HIS266
|
4.3
|
20.6
|
1.0
|
CG
|
M:HIS219
|
4.4
|
15.5
|
1.0
|
CG
|
L:HIS231
|
4.4
|
21.2
|
1.0
|
CG1
|
L:ILE195
|
4.4
|
22.5
|
1.0
|
CG2
|
M:VAL223
|
4.5
|
17.1
|
1.0
|
O
|
M:HOH529
|
4.6
|
33.3
|
1.0
|
CB
|
M:GLU234
|
4.7
|
28.6
|
1.0
|
|
Reference:
K.Tani,
R.Kanno,
K.Kurosawa,
S.Takaichi,
K.V.P.Nagashima,
M.Hall,
L.J.Yu,
Y.Kimura,
M.T.Madigan,
A.Mizoguchi,
B.M.Humbel,
Z.Y.Wang-Otomo.
An LH1-Rc Photocomplex From An Extremophilic Phototroph Provides Insight Into Origins of Two Photosynthesis Proteins. Commun Biol V. 5 1197 2022.
ISSN: ESSN 2399-3642
PubMed: 36344631
DOI: 10.1038/S42003-022-04174-2
Page generated: Fri Aug 9 11:10:03 2024
|