Iron in PDB 8c29: Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution
Enzymatic activity of Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution
All present enzymatic activity of Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution:
1.10.3.9;
Other elements in 8c29:
The structure of Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution
(pdb code 8c29). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution, PDB code: 8c29:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 8c29
Go back to
Iron Binding Sites List in 8c29
Iron binding site 1 out
of 4 in the Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:75.2
occ:1.00
|
O2
|
D:BCT401
|
2.1
|
56.0
|
1.0
|
O3
|
D:BCT401
|
2.1
|
50.7
|
1.0
|
NE2
|
A:HIS215
|
2.2
|
25.7
|
1.0
|
NE2
|
D:HIS215
|
2.3
|
22.0
|
1.0
|
NE2
|
D:HIS269
|
2.4
|
19.7
|
1.0
|
NE2
|
A:HIS272
|
2.4
|
21.9
|
1.0
|
C
|
D:BCT401
|
2.5
|
52.7
|
1.0
|
CD2
|
D:HIS215
|
3.2
|
16.4
|
1.0
|
CE1
|
A:HIS215
|
3.2
|
30.7
|
1.0
|
CD2
|
A:HIS215
|
3.2
|
24.0
|
1.0
|
CE1
|
D:HIS269
|
3.2
|
20.5
|
1.0
|
CE1
|
D:HIS215
|
3.3
|
21.2
|
1.0
|
CE1
|
A:HIS272
|
3.3
|
25.4
|
1.0
|
CD2
|
A:HIS272
|
3.4
|
26.8
|
1.0
|
CD2
|
D:HIS269
|
3.5
|
24.6
|
1.0
|
O1
|
D:BCT401
|
3.7
|
46.1
|
1.0
|
ND1
|
A:HIS215
|
4.3
|
30.5
|
1.0
|
CG
|
A:HIS215
|
4.3
|
27.7
|
1.0
|
CG
|
D:HIS215
|
4.4
|
14.2
|
1.0
|
ND1
|
D:HIS215
|
4.4
|
25.2
|
1.0
|
ND1
|
D:HIS269
|
4.4
|
26.1
|
1.0
|
ND1
|
A:HIS272
|
4.5
|
26.9
|
1.0
|
CG
|
A:HIS272
|
4.6
|
29.7
|
1.0
|
CG
|
D:HIS269
|
4.6
|
22.1
|
1.0
|
CG2
|
D:VAL219
|
4.8
|
21.8
|
1.0
|
OH
|
D:TYR245
|
4.9
|
44.2
|
1.0
|
CG2
|
A:VAL219
|
4.9
|
30.9
|
1.0
|
|
Iron binding site 2 out
of 4 in 8c29
Go back to
Iron Binding Sites List in 8c29
Iron binding site 2 out
of 4 in the Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe501
b:109.2
occ:1.00
|
FE
|
F:HEM501
|
0.0
|
109.2
|
1.0
|
ND
|
F:HEM501
|
2.0
|
97.8
|
1.0
|
NC
|
F:HEM501
|
2.0
|
98.6
|
1.0
|
NB
|
F:HEM501
|
2.0
|
99.3
|
1.0
|
NA
|
F:HEM501
|
2.1
|
99.6
|
1.0
|
NE2
|
F:HIS18
|
2.8
|
87.3
|
1.0
|
NE2
|
E:HIS23
|
2.9
|
90.1
|
1.0
|
CE1
|
F:HIS18
|
3.0
|
85.9
|
1.0
|
C1C
|
F:HEM501
|
3.1
|
97.1
|
1.0
|
C4D
|
F:HEM501
|
3.1
|
97.2
|
1.0
|
C1D
|
F:HEM501
|
3.1
|
100.0
|
1.0
|
C4C
|
F:HEM501
|
3.1
|
96.5
|
1.0
|
C4B
|
F:HEM501
|
3.1
|
97.8
|
1.0
|
C1A
|
F:HEM501
|
3.1
|
99.5
|
1.0
|
C4A
|
F:HEM501
|
3.1
|
98.1
|
1.0
|
C1B
|
F:HEM501
|
3.1
|
98.7
|
1.0
|
CE1
|
E:HIS23
|
3.1
|
87.8
|
1.0
|
CHA
|
F:HEM501
|
3.4
|
96.9
|
1.0
|
CHC
|
F:HEM501
|
3.4
|
97.8
|
1.0
|
CHD
|
F:HEM501
|
3.4
|
97.8
|
1.0
|
CHB
|
F:HEM501
|
3.4
|
98.0
|
1.0
|
CD2
|
F:HIS18
|
3.9
|
81.5
|
1.0
|
CD2
|
E:HIS23
|
4.0
|
86.4
|
1.0
|
ND1
|
F:HIS18
|
4.1
|
82.3
|
1.0
|
ND1
|
E:HIS23
|
4.2
|
87.2
|
1.0
|
C2C
|
F:HEM501
|
4.3
|
95.6
|
1.0
|
C3D
|
F:HEM501
|
4.3
|
99.7
|
1.0
|
C2D
|
F:HEM501
|
4.3
|
100.4
|
1.0
|
C3C
|
F:HEM501
|
4.3
|
97.3
|
1.0
|
C3A
|
F:HEM501
|
4.3
|
99.6
|
1.0
|
C2A
|
F:HEM501
|
4.3
|
100.4
|
1.0
|
C2B
|
F:HEM501
|
4.3
|
100.0
|
1.0
|
C3B
|
F:HEM501
|
4.3
|
99.9
|
1.0
|
CG
|
F:HIS18
|
4.6
|
82.1
|
1.0
|
CG
|
E:HIS23
|
4.6
|
87.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 8c29
Go back to
Iron Binding Sites List in 8c29
Iron binding site 3 out
of 4 in the Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe402
b:78.0
occ:1.00
|
O2
|
d:BCT401
|
2.1
|
51.9
|
1.0
|
O3
|
d:BCT401
|
2.1
|
48.3
|
1.0
|
NE2
|
a:HIS215
|
2.2
|
25.7
|
1.0
|
NE2
|
d:HIS215
|
2.3
|
16.2
|
1.0
|
NE2
|
a:HIS272
|
2.4
|
20.9
|
1.0
|
NE2
|
d:HIS269
|
2.4
|
20.1
|
1.0
|
C
|
d:BCT401
|
2.5
|
50.6
|
1.0
|
CD2
|
d:HIS215
|
3.2
|
12.3
|
1.0
|
CE1
|
a:HIS215
|
3.2
|
29.9
|
1.0
|
CD2
|
a:HIS215
|
3.2
|
29.6
|
1.0
|
CE1
|
d:HIS269
|
3.2
|
21.7
|
1.0
|
CE1
|
d:HIS215
|
3.3
|
20.5
|
1.0
|
CE1
|
a:HIS272
|
3.3
|
21.9
|
1.0
|
CD2
|
a:HIS272
|
3.4
|
28.3
|
1.0
|
CD2
|
d:HIS269
|
3.5
|
27.4
|
1.0
|
O1
|
d:BCT401
|
3.7
|
45.3
|
1.0
|
ND1
|
a:HIS215
|
4.3
|
29.7
|
1.0
|
CG
|
a:HIS215
|
4.3
|
28.5
|
1.0
|
CG
|
d:HIS215
|
4.4
|
9.2
|
1.0
|
ND1
|
d:HIS215
|
4.4
|
23.9
|
1.0
|
ND1
|
d:HIS269
|
4.4
|
29.8
|
1.0
|
ND1
|
a:HIS272
|
4.5
|
26.0
|
1.0
|
CG
|
a:HIS272
|
4.6
|
28.4
|
1.0
|
CG
|
d:HIS269
|
4.6
|
25.2
|
1.0
|
CG2
|
d:VAL219
|
4.8
|
21.6
|
1.0
|
CG2
|
a:VAL219
|
4.9
|
33.0
|
1.0
|
OH
|
d:TYR245
|
5.0
|
42.0
|
1.0
|
|
Iron binding site 4 out
of 4 in 8c29
Go back to
Iron Binding Sites List in 8c29
Iron binding site 4 out
of 4 in the Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Cryo-Em Structure of Photosystem II C2S2 Supercomplex From Norway Spruce (Picea Abies) at 2.8 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
f:Fe501
b:104.8
occ:1.00
|
FE
|
f:HEM501
|
0.0
|
104.8
|
1.0
|
NB
|
f:HEM501
|
2.1
|
95.7
|
1.0
|
NA
|
f:HEM501
|
2.1
|
96.4
|
1.0
|
NC
|
f:HEM501
|
2.1
|
94.4
|
1.0
|
ND
|
f:HEM501
|
2.1
|
94.9
|
1.0
|
NE2
|
f:HIS18
|
2.6
|
85.2
|
1.0
|
NE2
|
e:HIS23
|
2.8
|
91.0
|
1.0
|
CE1
|
e:HIS23
|
3.0
|
88.0
|
1.0
|
C4A
|
f:HEM501
|
3.1
|
95.1
|
1.0
|
C1B
|
f:HEM501
|
3.1
|
95.9
|
1.0
|
C1A
|
f:HEM501
|
3.1
|
96.2
|
1.0
|
C4B
|
f:HEM501
|
3.1
|
93.5
|
1.0
|
C1C
|
f:HEM501
|
3.1
|
93.8
|
1.0
|
C4C
|
f:HEM501
|
3.1
|
91.5
|
1.0
|
C1D
|
f:HEM501
|
3.1
|
96.7
|
1.0
|
C4D
|
f:HEM501
|
3.1
|
92.9
|
1.0
|
CD2
|
f:HIS18
|
3.4
|
82.1
|
1.0
|
CHB
|
f:HEM501
|
3.4
|
94.7
|
1.0
|
CHC
|
f:HEM501
|
3.4
|
93.1
|
1.0
|
CHA
|
f:HEM501
|
3.4
|
92.8
|
1.0
|
CHD
|
f:HEM501
|
3.5
|
93.5
|
1.0
|
CE1
|
f:HIS18
|
3.6
|
83.7
|
1.0
|
CD2
|
e:HIS23
|
3.8
|
88.3
|
1.0
|
ND1
|
e:HIS23
|
4.1
|
88.6
|
1.0
|
C3A
|
f:HEM501
|
4.3
|
95.9
|
1.0
|
C2A
|
f:HEM501
|
4.3
|
97.2
|
1.0
|
C2B
|
f:HEM501
|
4.3
|
96.8
|
1.0
|
C2C
|
f:HEM501
|
4.3
|
92.8
|
1.0
|
C3B
|
f:HEM501
|
4.3
|
96.6
|
1.0
|
C3C
|
f:HEM501
|
4.3
|
94.4
|
1.0
|
C2D
|
f:HEM501
|
4.3
|
97.7
|
1.0
|
C3D
|
f:HEM501
|
4.3
|
96.5
|
1.0
|
CG
|
e:HIS23
|
4.5
|
88.7
|
1.0
|
CG
|
f:HIS18
|
4.6
|
80.4
|
1.0
|
ND1
|
f:HIS18
|
4.7
|
82.7
|
1.0
|
|
Reference:
M.Opatikova,
D.A.Semchonok,
D.Kopecny,
P.Ilik,
P.Pospisil,
I.Ilikova,
P.Roudnicky,
S.C.Zeljkovic,
P.Tarkowski,
F.L.Kyrilis,
F.Hamdi,
P.L.Kastritis,
R.Kouril.
Cryo-Em Structure of A Plant Photosystem II Supercomplex with Light-Harvesting Protein LHCB8 and Alpha-Tocopherol Nat.Plants 2023.
ISSN: ESSN 2055-0278
DOI: 10.1038/S41477-023-01483-0
Page generated: Fri Aug 9 20:24:02 2024
|