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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:

Magnesium (Mg) 206 atoms

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

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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

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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

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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

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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: Thu Dec 28 05:49:31 2023

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