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Iron in PDB 3jcu: Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution

Other elements in 3jcu:

The structure of Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 206 atoms
Manganese (Mn) 8 atoms
Calcium (Ca) 2 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution (pdb code 3jcu). 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution, PDB code: 3jcu:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3jcu

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Iron binding site 1 out of 4 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:26.9
occ:1.00
NE2 D:HIS214 2.0 41.2 1.0
NE2 A:HIS272 2.1 54.7 1.0
NE2 D:HIS268 2.1 48.8 1.0
NE2 A:HIS215 2.2 46.6 1.0
O2 D:BCT401 2.3 32.5 1.0
O3 D:BCT401 2.3 35.7 1.0
C D:BCT401 2.6 41.5 1.0
CE1 D:HIS214 3.0 43.8 1.0
CD2 D:HIS214 3.0 39.5 1.0
CD2 A:HIS272 3.1 49.7 1.0
CE1 D:HIS268 3.1 51.5 1.0
CE1 A:HIS215 3.1 50.2 1.0
CE1 A:HIS272 3.1 60.4 1.0
CD2 D:HIS268 3.2 45.9 1.0
CD2 A:HIS215 3.2 47.2 1.0
O1 D:BCT401 3.9 51.6 1.0
ND1 D:HIS214 4.1 41.4 1.0
CG D:HIS214 4.1 40.0 1.0
ND1 D:HIS268 4.2 45.8 1.0
CG A:HIS272 4.2 51.5 1.0
ND1 A:HIS272 4.2 56.0 1.0
ND1 A:HIS215 4.2 48.0 1.0
CG D:HIS268 4.3 42.8 1.0
CG A:HIS215 4.3 45.9 1.0
OH A:TYR246 4.5 0.8 1.0
CG2 A:VAL219 4.7 72.6 1.0
CG2 D:VAL218 4.7 58.3 1.0
OH D:TYR244 4.7 71.0 1.0

Iron binding site 2 out of 4 in 3jcu

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Iron binding site 2 out of 4 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:0.6
occ:1.00
FE F:HEM101 0.0 0.6 1.0
NC F:HEM101 2.0 0.0 1.0
NA F:HEM101 2.0 0.6 1.0
NB F:HEM101 2.0 0.0 1.0
ND F:HEM101 2.1 0.7 1.0
NE2 F:HIS24 2.5 0.4 1.0
NE2 E:HIS23 2.6 0.5 1.0
C1C F:HEM101 3.0 0.8 1.0
C4C F:HEM101 3.0 0.7 1.0
C1A F:HEM101 3.0 0.0 1.0
C4A F:HEM101 3.0 0.8 1.0
C1B F:HEM101 3.1 0.9 1.0
C4B F:HEM101 3.1 0.2 1.0
C1D F:HEM101 3.1 0.8 1.0
C4D F:HEM101 3.1 0.8 1.0
CD2 E:HIS23 3.2 0.3 1.0
CE1 F:HIS24 3.2 0.3 1.0
CD2 F:HIS24 3.4 0.6 1.0
CE1 E:HIS23 3.4 0.5 1.0
CHD F:HEM101 3.4 0.4 1.0
CHA F:HEM101 3.4 0.8 1.0
CHC F:HEM101 3.4 99.9 1.0
CHB F:HEM101 3.4 0.9 1.0
CG E:HIS23 4.2 0.2 1.0
C2C F:HEM101 4.2 0.7 1.0
C2A F:HEM101 4.2 0.4 1.0
C3A F:HEM101 4.2 0.7 1.0
C3C F:HEM101 4.2 0.5 1.0
ND1 E:HIS23 4.2 0.3 1.0
ND1 F:HIS24 4.3 0.7 1.0
C2B F:HEM101 4.3 1.0 1.0
C3B F:HEM101 4.3 0.5 1.0
C2D F:HEM101 4.3 0.2 1.0
C3D F:HEM101 4.3 0.5 1.0
CG F:HIS24 4.4 0.3 1.0

Iron binding site 3 out of 4 in 3jcu

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Iron binding site 3 out of 4 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe402

b:26.9
occ:1.00
NE2 d:HIS214 2.0 41.2 1.0
NE2 a:HIS272 2.1 54.7 1.0
NE2 d:HIS268 2.1 48.8 1.0
NE2 a:HIS215 2.2 46.6 1.0
O2 d:BCT401 2.3 32.5 1.0
O3 d:BCT401 2.3 35.7 1.0
C d:BCT401 2.6 41.5 1.0
CE1 d:HIS214 3.0 43.8 1.0
CD2 d:HIS214 3.0 39.5 1.0
CD2 a:HIS272 3.1 49.7 1.0
CE1 d:HIS268 3.1 51.5 1.0
CE1 a:HIS215 3.1 50.2 1.0
CE1 a:HIS272 3.1 60.4 1.0
CD2 d:HIS268 3.2 45.9 1.0
CD2 a:HIS215 3.2 47.2 1.0
O1 d:BCT401 3.9 51.6 1.0
ND1 d:HIS214 4.1 41.4 1.0
CG d:HIS214 4.1 40.0 1.0
ND1 d:HIS268 4.2 45.8 1.0
CG a:HIS272 4.2 51.5 1.0
ND1 a:HIS272 4.2 56.0 1.0
ND1 a:HIS215 4.2 48.0 1.0
CG d:HIS268 4.3 42.8 1.0
CG a:HIS215 4.3 45.9 1.0
OH a:TYR246 4.5 0.8 1.0
CG2 a:VAL219 4.7 72.6 1.0
CG2 d:VAL218 4.7 58.3 1.0
OH d:TYR244 4.7 71.0 1.0

Iron binding site 4 out of 4 in 3jcu

Go back to Iron Binding Sites List in 3jcu
Iron binding site 4 out of 4 in the Cryo-Em Structure of Spinach Psii-Lhcii Supercomplex at 3.2 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 Spinach Psii-Lhcii Supercomplex at 3.2 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Fe101

b:0.6
occ:1.00
FE f:HEM101 0.0 0.6 1.0
NC f:HEM101 2.0 0.0 1.0
NA f:HEM101 2.0 0.6 1.0
NB f:HEM101 2.0 0.0 1.0
ND f:HEM101 2.1 0.7 1.0
NE2 f:HIS24 2.5 0.4 1.0
NE2 e:HIS23 2.6 0.5 1.0
C1C f:HEM101 3.0 0.8 1.0
C4C f:HEM101 3.0 0.7 1.0
C1A f:HEM101 3.0 0.0 1.0
C4A f:HEM101 3.0 0.8 1.0
C1B f:HEM101 3.1 0.9 1.0
C4B f:HEM101 3.1 0.2 1.0
C1D f:HEM101 3.1 0.8 1.0
C4D f:HEM101 3.1 0.8 1.0
CE1 f:HIS24 3.2 0.3 1.0
CD2 e:HIS23 3.2 0.3 1.0
CD2 f:HIS24 3.4 0.6 1.0
CE1 e:HIS23 3.4 0.5 1.0
CHD f:HEM101 3.4 0.4 1.0
CHA f:HEM101 3.4 0.8 1.0
CHC f:HEM101 3.4 99.9 1.0
CHB f:HEM101 3.4 0.9 1.0
CG e:HIS23 4.2 0.2 1.0
C2C f:HEM101 4.2 0.7 1.0
C2A f:HEM101 4.2 0.4 1.0
C3A f:HEM101 4.2 0.7 1.0
C3C f:HEM101 4.2 0.5 1.0
ND1 e:HIS23 4.2 0.3 1.0
ND1 f:HIS24 4.3 0.7 1.0
C2B f:HEM101 4.3 1.0 1.0
C3B f:HEM101 4.3 0.5 1.0
C2D f:HEM101 4.3 0.2 1.0
C3D f:HEM101 4.3 0.5 1.0
CG f:HIS24 4.4 0.3 1.0

Reference:

X.P.Wei, X.D.Su, P.Cao, X.Y.Liu, W.R.Chang, M.Li, X.Z.Zhang, Z.F.Liu. Structure of Spinach Photosystem II-Lhcii Supercomplex at 3.2 A Resolution Nature V. 534 69 2016.
ISSN: ISSN 0028-0836
DOI: 10.1038/NATURE18020
Page generated: Sun Dec 13 15:09:42 2020

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