Iron in PDB 8zk2: Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum
Other elements in 8zk2:
The structure of Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum
(pdb code 8zk2). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum, PDB code: 8zk2:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 8zk2
Go back to
Iron Binding Sites List in 8zk2
Iron binding site 1 out
of 5 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum
![](/pictures/FE/pdb/zk/8zk2-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/zk/8zk2-FE-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:46.9
occ:1.00
|
FE
|
C:HEC501
|
0.0
|
46.9
|
1.0
|
NE2
|
C:HIS134
|
2.1
|
50.2
|
1.0
|
NA
|
C:HEC501
|
2.1
|
46.9
|
1.0
|
NC
|
C:HEC501
|
2.1
|
46.9
|
1.0
|
NB
|
C:HEC501
|
2.1
|
46.9
|
1.0
|
ND
|
C:HEC501
|
2.1
|
46.9
|
1.0
|
SD
|
C:MET117
|
2.3
|
42.9
|
1.0
|
CD2
|
C:HIS134
|
3.0
|
50.2
|
1.0
|
C1D
|
C:HEC501
|
3.1
|
46.9
|
1.0
|
CE1
|
C:HIS134
|
3.1
|
50.2
|
1.0
|
C4C
|
C:HEC501
|
3.1
|
46.9
|
1.0
|
C1B
|
C:HEC501
|
3.1
|
46.9
|
1.0
|
C4A
|
C:HEC501
|
3.1
|
46.9
|
1.0
|
C1A
|
C:HEC501
|
3.1
|
46.9
|
1.0
|
C4D
|
C:HEC501
|
3.1
|
46.9
|
1.0
|
C4B
|
C:HEC501
|
3.1
|
46.9
|
1.0
|
C1C
|
C:HEC501
|
3.1
|
46.9
|
1.0
|
CHD
|
C:HEC501
|
3.4
|
46.9
|
1.0
|
CHB
|
C:HEC501
|
3.4
|
46.9
|
1.0
|
CHA
|
C:HEC501
|
3.4
|
46.9
|
1.0
|
CHC
|
C:HEC501
|
3.5
|
46.9
|
1.0
|
CG
|
C:MET117
|
3.5
|
42.9
|
1.0
|
CE
|
C:MET117
|
3.9
|
42.9
|
1.0
|
ND1
|
C:HIS134
|
4.2
|
50.2
|
1.0
|
CG
|
C:HIS134
|
4.2
|
50.2
|
1.0
|
CB
|
C:MET117
|
4.2
|
42.9
|
1.0
|
C2B
|
C:HEC501
|
4.3
|
46.9
|
1.0
|
C3B
|
C:HEC501
|
4.3
|
46.9
|
1.0
|
C2D
|
C:HEC501
|
4.3
|
46.9
|
1.0
|
C3A
|
C:HEC501
|
4.3
|
46.9
|
1.0
|
C3D
|
C:HEC501
|
4.3
|
46.9
|
1.0
|
C2A
|
C:HEC501
|
4.3
|
46.9
|
1.0
|
C3C
|
C:HEC501
|
4.3
|
46.9
|
1.0
|
C2C
|
C:HEC501
|
4.3
|
46.9
|
1.0
|
CA
|
C:MET117
|
5.0
|
42.9
|
1.0
|
|
Iron binding site 2 out
of 5 in 8zk2
Go back to
Iron Binding Sites List in 8zk2
Iron binding site 2 out
of 5 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum
![](/pictures/FE/pdb/zk/8zk2-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/zk/8zk2-FE-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe502
b:34.0
occ:1.00
|
FE
|
C:HEC502
|
0.0
|
34.0
|
1.0
|
NC
|
C:HEC502
|
2.1
|
34.0
|
1.0
|
NE2
|
C:HIS179
|
2.1
|
32.4
|
1.0
|
NB
|
C:HEC502
|
2.1
|
34.0
|
1.0
|
NA
|
C:HEC502
|
2.2
|
34.0
|
1.0
|
ND
|
C:HEC502
|
2.2
|
34.0
|
1.0
|
CE
|
C:MET153
|
2.3
|
34.7
|
1.0
|
SD
|
C:MET153
|
2.4
|
34.7
|
1.0
|
CG
|
C:MET153
|
2.7
|
34.7
|
1.0
|
CE1
|
C:HIS179
|
2.8
|
32.4
|
1.0
|
C1C
|
C:HEC502
|
3.1
|
34.0
|
1.0
|
C4C
|
C:HEC502
|
3.1
|
34.0
|
1.0
|
C4B
|
C:HEC502
|
3.1
|
34.0
|
1.0
|
C1B
|
C:HEC502
|
3.1
|
34.0
|
1.0
|
C1D
|
C:HEC502
|
3.2
|
34.0
|
1.0
|
C4A
|
C:HEC502
|
3.2
|
34.0
|
1.0
|
C1A
|
C:HEC502
|
3.2
|
34.0
|
1.0
|
C4D
|
C:HEC502
|
3.2
|
34.0
|
1.0
|
CD2
|
C:HIS179
|
3.3
|
32.4
|
1.0
|
CHC
|
C:HEC502
|
3.4
|
34.0
|
1.0
|
CHD
|
C:HEC502
|
3.5
|
34.0
|
1.0
|
CHB
|
C:HEC502
|
3.5
|
34.0
|
1.0
|
CHA
|
C:HEC502
|
3.6
|
34.0
|
1.0
|
CB
|
C:MET153
|
3.8
|
34.7
|
1.0
|
ND1
|
C:HIS179
|
4.1
|
32.4
|
1.0
|
C2C
|
C:HEC502
|
4.3
|
34.0
|
1.0
|
CG
|
C:HIS179
|
4.3
|
32.4
|
1.0
|
C3B
|
C:HEC502
|
4.3
|
34.0
|
1.0
|
C3C
|
C:HEC502
|
4.3
|
34.0
|
1.0
|
C2B
|
C:HEC502
|
4.3
|
34.0
|
1.0
|
C3A
|
C:HEC502
|
4.4
|
34.0
|
1.0
|
C2D
|
C:HEC502
|
4.4
|
34.0
|
1.0
|
C2A
|
C:HEC502
|
4.4
|
34.0
|
1.0
|
C3D
|
C:HEC502
|
4.4
|
34.0
|
1.0
|
CA
|
C:MET153
|
4.8
|
34.7
|
1.0
|
CE
|
C:MET156
|
4.9
|
33.3
|
1.0
|
|
Iron binding site 3 out
of 5 in 8zk2
Go back to
Iron Binding Sites List in 8zk2
Iron binding site 3 out
of 5 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum
![](/pictures/FE/pdb/zk/8zk2-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/zk/8zk2-FE-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe503
b:32.8
occ:1.00
|
FE
|
C:HEC503
|
0.0
|
32.8
|
1.0
|
NE2
|
C:HIS278
|
2.1
|
23.2
|
1.0
|
NC
|
C:HEC503
|
2.1
|
32.8
|
1.0
|
NA
|
C:HEC503
|
2.1
|
32.8
|
1.0
|
NB
|
C:HEC503
|
2.1
|
32.8
|
1.0
|
ND
|
C:HEC503
|
2.1
|
32.8
|
1.0
|
SD
|
C:MET263
|
2.3
|
23.4
|
1.0
|
CE
|
C:MET263
|
2.8
|
23.4
|
1.0
|
CD2
|
C:HIS278
|
3.0
|
23.2
|
1.0
|
C1D
|
C:HEC503
|
3.1
|
32.8
|
1.0
|
CE1
|
C:HIS278
|
3.1
|
23.2
|
1.0
|
C4C
|
C:HEC503
|
3.1
|
32.8
|
1.0
|
C4A
|
C:HEC503
|
3.1
|
32.8
|
1.0
|
C1B
|
C:HEC503
|
3.1
|
32.8
|
1.0
|
C4D
|
C:HEC503
|
3.1
|
32.8
|
1.0
|
C1C
|
C:HEC503
|
3.1
|
32.8
|
1.0
|
C4B
|
C:HEC503
|
3.1
|
32.8
|
1.0
|
C1A
|
C:HEC503
|
3.1
|
32.8
|
1.0
|
CG
|
C:MET263
|
3.3
|
23.4
|
1.0
|
CHD
|
C:HEC503
|
3.4
|
32.8
|
1.0
|
CHB
|
C:HEC503
|
3.5
|
32.8
|
1.0
|
CHA
|
C:HEC503
|
3.5
|
32.8
|
1.0
|
CHC
|
C:HEC503
|
3.5
|
32.8
|
1.0
|
CG
|
C:HIS278
|
4.1
|
23.2
|
1.0
|
ND1
|
C:HIS278
|
4.1
|
23.2
|
1.0
|
CB
|
C:MET263
|
4.2
|
23.4
|
1.0
|
C2D
|
C:HEC503
|
4.3
|
32.8
|
1.0
|
C2B
|
C:HEC503
|
4.3
|
32.8
|
1.0
|
C3D
|
C:HEC503
|
4.3
|
32.8
|
1.0
|
C3A
|
C:HEC503
|
4.3
|
32.8
|
1.0
|
C3B
|
C:HEC503
|
4.3
|
32.8
|
1.0
|
C2C
|
C:HEC503
|
4.3
|
32.8
|
1.0
|
C3C
|
C:HEC503
|
4.3
|
32.8
|
1.0
|
C2A
|
C:HEC503
|
4.3
|
32.8
|
1.0
|
|
Iron binding site 4 out
of 5 in 8zk2
Go back to
Iron Binding Sites List in 8zk2
Iron binding site 4 out
of 5 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum
![](/pictures/FE/pdb/zk/8zk2-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/zk/8zk2-FE-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe504
b:32.8
occ:1.00
|
FE
|
C:HEC504
|
0.0
|
32.8
|
1.0
|
NA
|
C:HEC504
|
2.0
|
32.8
|
1.0
|
NE2
|
C:HIS167
|
2.0
|
27.2
|
1.0
|
NE2
|
C:HIS338
|
2.0
|
25.5
|
1.0
|
NC
|
C:HEC504
|
2.1
|
32.8
|
1.0
|
NB
|
C:HEC504
|
2.1
|
32.8
|
1.0
|
ND
|
C:HEC504
|
2.1
|
32.8
|
1.0
|
CE1
|
C:HIS338
|
2.8
|
25.5
|
1.0
|
CE1
|
C:HIS167
|
2.8
|
27.2
|
1.0
|
C1A
|
C:HEC504
|
3.1
|
32.8
|
1.0
|
C4C
|
C:HEC504
|
3.1
|
32.8
|
1.0
|
C1D
|
C:HEC504
|
3.1
|
32.8
|
1.0
|
C4A
|
C:HEC504
|
3.1
|
32.8
|
1.0
|
C4D
|
C:HEC504
|
3.1
|
32.8
|
1.0
|
C1C
|
C:HEC504
|
3.1
|
32.8
|
1.0
|
C4B
|
C:HEC504
|
3.1
|
32.8
|
1.0
|
C1B
|
C:HEC504
|
3.1
|
32.8
|
1.0
|
CD2
|
C:HIS167
|
3.2
|
27.2
|
1.0
|
CD2
|
C:HIS338
|
3.2
|
25.5
|
1.0
|
CHA
|
C:HEC504
|
3.4
|
32.8
|
1.0
|
CHD
|
C:HEC504
|
3.4
|
32.8
|
1.0
|
CHC
|
C:HEC504
|
3.5
|
32.8
|
1.0
|
CHB
|
C:HEC504
|
3.5
|
32.8
|
1.0
|
ND1
|
C:HIS167
|
4.0
|
27.2
|
1.0
|
ND1
|
C:HIS338
|
4.0
|
25.5
|
1.0
|
CG
|
C:HIS167
|
4.2
|
27.2
|
1.0
|
CG
|
C:HIS338
|
4.2
|
25.5
|
1.0
|
C2A
|
C:HEC504
|
4.3
|
32.8
|
1.0
|
C3A
|
C:HEC504
|
4.3
|
32.8
|
1.0
|
C3C
|
C:HEC504
|
4.3
|
32.8
|
1.0
|
C2C
|
C:HEC504
|
4.3
|
32.8
|
1.0
|
C3B
|
C:HEC504
|
4.3
|
32.8
|
1.0
|
C2B
|
C:HEC504
|
4.3
|
32.8
|
1.0
|
C2D
|
C:HEC504
|
4.3
|
32.8
|
1.0
|
C3D
|
C:HEC504
|
4.3
|
32.8
|
1.0
|
CD
|
C:PRO344
|
4.9
|
26.2
|
1.0
|
|
Iron binding site 5 out
of 5 in 8zk2
Go back to
Iron Binding Sites List in 8zk2
Iron binding site 5 out
of 5 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum
![](/pictures/FE/pdb/zk/8zk2-FE-sphere_05.jpg) Mono view
![](/pictures/FE/pdb/zk/8zk2-FE-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Fe401
b:40.2
occ:1.00
|
NE2
|
L:HIS192
|
2.1
|
32.1
|
1.0
|
NE2
|
M:HIS220
|
2.1
|
27.1
|
1.0
|
NE2
|
L:HIS232
|
2.2
|
32.4
|
1.0
|
OE2
|
M:GLU235
|
2.2
|
33.3
|
1.0
|
OE1
|
M:GLU235
|
2.2
|
33.3
|
1.0
|
NE2
|
M:HIS267
|
2.4
|
28.3
|
1.0
|
CD
|
M:GLU235
|
2.5
|
33.3
|
1.0
|
CD2
|
M:HIS220
|
3.0
|
27.1
|
1.0
|
CE1
|
L:HIS192
|
3.0
|
32.1
|
1.0
|
CE1
|
L:HIS232
|
3.1
|
32.4
|
1.0
|
CD2
|
L:HIS232
|
3.1
|
32.4
|
1.0
|
CD2
|
L:HIS192
|
3.2
|
32.1
|
1.0
|
CE1
|
M:HIS220
|
3.2
|
27.1
|
1.0
|
CE1
|
M:HIS267
|
3.3
|
28.3
|
1.0
|
CD2
|
M:HIS267
|
3.4
|
28.3
|
1.0
|
CG
|
M:GLU235
|
4.0
|
33.3
|
1.0
|
ND1
|
L:HIS192
|
4.2
|
32.1
|
1.0
|
CG
|
M:HIS220
|
4.2
|
27.1
|
1.0
|
ND1
|
L:HIS232
|
4.2
|
32.4
|
1.0
|
CG
|
L:HIS232
|
4.3
|
32.4
|
1.0
|
ND1
|
M:HIS220
|
4.3
|
27.1
|
1.0
|
CG
|
L:HIS192
|
4.3
|
32.1
|
1.0
|
ND1
|
M:HIS267
|
4.4
|
28.3
|
1.0
|
CG1
|
M:ILE224
|
4.4
|
27.4
|
1.0
|
CG
|
M:HIS267
|
4.5
|
28.3
|
1.0
|
CG1
|
L:ILE196
|
4.5
|
30.1
|
1.0
|
C25
|
L:PGV410
|
4.7
|
42.6
|
1.0
|
CD1
|
L:ILE196
|
4.7
|
30.1
|
1.0
|
CB
|
M:GLU235
|
4.8
|
33.3
|
1.0
|
C26
|
L:PGV410
|
4.9
|
42.6
|
1.0
|
CD1
|
M:ILE224
|
4.9
|
27.4
|
1.0
|
|
Reference:
X.P.Wang,
G.L.Wang,
Y.Fu,
A.Minamino,
M.J.Zou,
F.Ma,
B.Xu,
Z.Y.Wang-Otomo,
Y.Kimura,
M.T.Madigan,
J.Overmann,
L.J.Yu.
Insights Into the Divergence of the Photosynthetic LH1 Complex Obtained From Structural Analysis of the Unusual Photocomplexes of Roseospirillum Parvum. Commun Biol V. 7 1658 2024.
ISSN: ESSN 2399-3642
PubMed: 39702771
DOI: 10.1038/S42003-024-07354-4
Page generated: Sat Feb 8 18:45:09 2025
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