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Iron in PDB 5ws6: Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset

Enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset

All present enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset:
1.10.3.9;

Protein crystallography data

The structure of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset, PDB code: 5ws6 was solved by M.Suga, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.960, 230.220, 286.020, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 17.5

Other elements in 5ws6:

The structure of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Manganese (Mn) 16 atoms
Calcium (Ca) 12 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset (pdb code 5ws6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset, PDB code: 5ws6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5ws6

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Iron binding site 1 out of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:62.6
occ:0.20
FE A:FE2401 0.0 62.6 0.2
FE A:FE2401 0.2 60.9 0.8
NE2 A:HIS215 2.1 53.0 0.8
NE2 D:HIS214 2.1 45.1 0.2
NE2 A:HIS215 2.1 50.2 0.2
NE2 D:HIS214 2.1 46.0 0.8
NE2 D:HIS268 2.2 51.5 1.0
O2 A:BCT403 2.2 58.2 0.2
O1 A:BCT403 2.2 60.5 0.2
NE2 A:HIS272 2.2 56.5 0.2
NE2 A:HIS272 2.4 59.1 0.8
O2 A:BCT403 2.4 55.3 0.8
O1 A:BCT403 2.5 61.5 0.8
C A:BCT403 2.5 60.7 0.2
C A:BCT403 2.8 62.5 0.8
CE1 A:HIS215 2.9 47.0 0.8
CE1 A:HIS215 2.9 48.6 0.2
CE1 D:HIS214 3.0 43.9 0.2
CE1 A:HIS272 3.0 54.8 0.2
CE1 D:HIS214 3.1 44.5 0.8
CD2 D:HIS268 3.1 41.8 1.0
CD2 D:HIS214 3.1 44.7 0.8
CE1 D:HIS268 3.1 48.3 1.0
CD2 A:HIS215 3.2 47.0 0.8
CD2 D:HIS214 3.2 44.0 0.2
CD2 A:HIS215 3.2 48.6 0.2
CE1 A:HIS272 3.3 53.3 0.8
CD2 A:HIS272 3.3 54.4 0.2
CD2 A:HIS272 3.4 53.5 0.8
O3 A:BCT403 3.8 69.1 0.2
ND1 A:HIS215 4.1 46.7 0.8
O3 A:BCT403 4.1 78.3 0.8
ND1 A:HIS215 4.1 47.6 0.2
ND1 D:HIS214 4.1 42.0 0.2
ND1 A:HIS272 4.2 53.0 0.2
ND1 D:HIS214 4.2 41.0 0.8
ND1 D:HIS268 4.2 48.0 1.0
CG A:HIS215 4.3 48.4 0.8
CG D:HIS268 4.3 47.1 1.0
CG D:HIS214 4.3 42.5 0.8
CG D:HIS214 4.3 42.3 0.2
CG A:HIS215 4.3 47.9 0.2
CG A:HIS272 4.4 54.1 0.2
ND1 A:HIS272 4.5 51.4 0.8
CG A:HIS272 4.5 55.4 0.8
CG2 A:VAL219 4.6 48.1 1.0
OH D:TYR244 4.8 52.4 1.0
CG2 D:VAL218 4.9 43.1 1.0

Iron binding site 2 out of 8 in 5ws6

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Iron binding site 2 out of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:60.9
occ:0.80
FE A:FE2401 0.0 60.9 0.8
FE A:FE2401 0.2 62.6 0.2
NE2 D:HIS214 2.1 45.1 0.2
NE2 A:HIS272 2.1 56.5 0.2
O2 A:BCT403 2.1 58.2 0.2
NE2 D:HIS214 2.1 46.0 0.8
NE2 A:HIS215 2.2 53.0 0.8
O1 A:BCT403 2.2 60.5 0.2
NE2 A:HIS215 2.2 50.2 0.2
NE2 A:HIS272 2.3 59.1 0.8
NE2 D:HIS268 2.3 51.5 1.0
O2 A:BCT403 2.3 55.3 0.8
C A:BCT403 2.4 60.7 0.2
O1 A:BCT403 2.4 61.5 0.8
C A:BCT403 2.7 62.5 0.8
CE1 A:HIS272 2.9 54.8 0.2
CE1 D:HIS214 2.9 43.9 0.2
CE1 A:HIS215 3.0 47.0 0.8
CE1 A:HIS215 3.0 48.6 0.2
CE1 D:HIS214 3.0 44.5 0.8
CD2 D:HIS214 3.1 44.7 0.8
CD2 D:HIS214 3.2 44.0 0.2
CE1 A:HIS272 3.2 53.3 0.8
CD2 A:HIS272 3.2 54.4 0.2
CE1 D:HIS268 3.2 48.3 1.0
CD2 D:HIS268 3.3 41.8 1.0
CD2 A:HIS272 3.3 53.5 0.8
CD2 A:HIS215 3.3 47.0 0.8
CD2 A:HIS215 3.3 48.6 0.2
O3 A:BCT403 3.8 69.1 0.2
O3 A:BCT403 4.0 78.3 0.8
ND1 A:HIS272 4.1 53.0 0.2
ND1 D:HIS214 4.1 42.0 0.2
ND1 D:HIS214 4.2 41.0 0.8
ND1 A:HIS215 4.2 46.7 0.8
ND1 A:HIS215 4.2 47.6 0.2
CG D:HIS214 4.2 42.5 0.8
CG D:HIS214 4.3 42.3 0.2
CG A:HIS272 4.3 54.1 0.2
ND1 A:HIS272 4.3 51.4 0.8
CG A:HIS215 4.3 48.4 0.8
ND1 D:HIS268 4.4 48.0 1.0
CG A:HIS215 4.4 47.9 0.2
CG A:HIS272 4.4 55.4 0.8
CG D:HIS268 4.4 47.1 1.0
CG2 A:VAL219 4.7 48.1 1.0
OH D:TYR244 4.7 52.4 1.0
CG2 D:VAL218 4.7 43.1 1.0

Iron binding site 3 out of 8 in 5ws6

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Iron binding site 3 out of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe103

b:77.5
occ:1.00
FE E:HEM103 0.0 77.5 1.0
ND E:HEM103 2.0 66.3 1.0
NA E:HEM103 2.0 80.2 1.0
NC E:HEM103 2.1 68.4 1.0
NE2 F:HIS24 2.1 70.6 1.0
NE2 E:HIS23 2.1 70.6 1.0
NB E:HEM103 2.1 64.2 1.0
CD2 F:HIS24 2.9 63.3 1.0
C4D E:HEM103 2.9 72.3 1.0
C1A E:HEM103 3.0 74.3 1.0
C1D E:HEM103 3.0 60.1 1.0
CD2 E:HIS23 3.0 70.4 1.0
C4C E:HEM103 3.1 64.1 1.0
C4A E:HEM103 3.1 74.8 1.0
C1B E:HEM103 3.1 71.4 1.0
C4B E:HEM103 3.1 63.3 1.0
C1C E:HEM103 3.1 64.1 1.0
CE1 E:HIS23 3.1 66.3 1.0
CE1 F:HIS24 3.2 74.8 1.0
CHA E:HEM103 3.3 69.7 1.0
CHD E:HEM103 3.4 62.7 1.0
CHB E:HEM103 3.5 73.3 1.0
CHC E:HEM103 3.5 61.3 1.0
CG F:HIS24 4.1 72.0 1.0
C2A E:HEM103 4.2 75.0 1.0
C3D E:HEM103 4.2 71.8 1.0
C2D E:HEM103 4.2 64.8 1.0
CG E:HIS23 4.2 65.4 1.0
ND1 E:HIS23 4.2 69.1 1.0
C3A E:HEM103 4.2 78.5 1.0
ND1 F:HIS24 4.2 76.9 1.0
C3C E:HEM103 4.3 65.7 1.0
C2C E:HEM103 4.3 61.0 1.0
C2B E:HEM103 4.3 73.0 1.0
C3B E:HEM103 4.3 73.9 1.0
CE2 E:TYR19 4.9 70.8 1.0
NE1 F:TRP20 5.0 84.7 1.0

Iron binding site 4 out of 8 in 5ws6

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Iron binding site 4 out of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Fe203

b:57.5
occ:1.00
FE V:HEC203 0.0 57.5 1.0
ND V:HEC203 2.0 60.9 1.0
NA V:HEC203 2.0 53.4 1.0
NE2 V:HIS41 2.1 44.2 1.0
NE2 V:HIS92 2.1 44.2 1.0
NC V:HEC203 2.1 45.9 1.0
NB V:HEC203 2.1 54.5 1.0
C4D V:HEC203 2.9 49.5 1.0
C1D V:HEC203 3.0 46.6 1.0
C1A V:HEC203 3.0 57.3 1.0
CD2 V:HIS41 3.0 46.0 1.0
C4A V:HEC203 3.0 54.0 1.0
C4C V:HEC203 3.0 47.9 1.0
CE1 V:HIS92 3.0 46.7 1.0
C1B V:HEC203 3.1 50.2 1.0
CD2 V:HIS92 3.1 44.6 1.0
C4B V:HEC203 3.1 51.8 1.0
CE1 V:HIS41 3.1 52.7 1.0
C1C V:HEC203 3.1 55.5 1.0
CHA V:HEC203 3.4 52.8 1.0
CHD V:HEC203 3.4 52.9 1.0
CHB V:HEC203 3.5 56.5 1.0
CHC V:HEC203 3.5 55.7 1.0
ND1 V:HIS92 4.2 47.8 1.0
C3D V:HEC203 4.2 54.1 1.0
C2A V:HEC203 4.2 55.4 1.0
C2D V:HEC203 4.2 46.5 1.0
CG V:HIS41 4.2 53.1 1.0
ND1 V:HIS41 4.2 55.0 1.0
CG V:HIS92 4.2 53.2 1.0
C3A V:HEC203 4.2 50.6 1.0
C3C V:HEC203 4.3 56.6 1.0
C2B V:HEC203 4.3 52.3 1.0
C2C V:HEC203 4.3 58.1 1.0
C3B V:HEC203 4.3 52.9 1.0
CE1 V:TYR75 4.8 53.1 1.0

Iron binding site 5 out of 8 in 5ws6

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Iron binding site 5 out of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe401

b:61.0
occ:0.20
FE a:FE2401 0.0 61.0 0.2
FE a:FE2401 0.0 60.8 0.8
NE2 a:HIS215 2.1 55.7 0.2
NE2 a:HIS215 2.1 58.5 0.8
NE2 d:HIS214 2.2 49.9 0.2
O2 a:BCT420 2.2 63.8 0.2
NE2 d:HIS214 2.2 51.5 0.8
NE2 a:HIS272 2.2 52.4 0.2
O1 a:BCT420 2.3 58.8 0.2
NE2 d:HIS268 2.3 53.8 1.0
NE2 a:HIS272 2.3 52.7 0.8
O2 a:BCT420 2.3 63.8 0.8
O1 a:BCT420 2.4 54.7 0.8
C a:BCT420 2.5 63.8 0.2
C a:BCT420 2.7 64.1 0.8
CE1 a:HIS215 2.9 55.6 0.2
CE1 a:HIS215 3.0 54.0 0.8
CE1 a:HIS272 3.1 52.0 0.2
CE1 d:HIS214 3.1 51.8 0.2
CE1 d:HIS214 3.1 51.5 0.8
CD2 d:HIS214 3.2 43.4 0.8
CD2 d:HIS214 3.2 46.8 0.2
CE1 d:HIS268 3.2 61.8 1.0
CE1 a:HIS272 3.2 49.3 0.8
CD2 a:HIS215 3.2 54.4 0.2
CD2 a:HIS272 3.3 52.6 0.2
CD2 a:HIS215 3.3 53.2 0.8
CD2 a:HIS272 3.3 53.1 0.8
CD2 d:HIS268 3.3 54.1 1.0
O3 a:BCT420 3.8 68.9 0.2
O3 a:BCT420 4.0 72.8 0.8
ND1 a:HIS215 4.1 55.4 0.2
ND1 a:HIS215 4.1 57.1 0.8
ND1 d:HIS214 4.2 51.7 0.2
ND1 a:HIS272 4.2 54.4 0.2
ND1 d:HIS214 4.2 54.1 0.8
CG a:HIS215 4.3 53.3 0.2
CG d:HIS214 4.3 47.6 0.2
CG d:HIS214 4.3 47.6 0.8
CG a:HIS215 4.3 53.6 0.8
ND1 d:HIS268 4.3 51.5 1.0
ND1 a:HIS272 4.3 57.7 0.8
CG a:HIS272 4.4 53.1 0.2
CG a:HIS272 4.4 53.2 0.8
CG d:HIS268 4.4 51.2 1.0
CG2 a:VAL219 4.5 49.7 1.0
CG2 d:VAL218 4.8 46.1 1.0
OH d:TYR244 4.8 61.3 1.0

Iron binding site 6 out of 8 in 5ws6

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Iron binding site 6 out of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe401

b:60.8
occ:0.80
FE a:FE2401 0.0 60.8 0.8
FE a:FE2401 0.0 61.0 0.2
NE2 a:HIS215 2.1 55.7 0.2
NE2 a:HIS215 2.1 58.5 0.8
O2 a:BCT420 2.2 63.8 0.2
NE2 d:HIS214 2.2 49.9 0.2
NE2 d:HIS214 2.2 51.5 0.8
NE2 a:HIS272 2.2 52.4 0.2
NE2 d:HIS268 2.3 53.8 1.0
NE2 a:HIS272 2.3 52.7 0.8
O1 a:BCT420 2.3 58.8 0.2
O2 a:BCT420 2.3 63.8 0.8
O1 a:BCT420 2.4 54.7 0.8
C a:BCT420 2.5 63.8 0.2
C a:BCT420 2.7 64.1 0.8
CE1 a:HIS215 2.9 55.6 0.2
CE1 a:HIS215 2.9 54.0 0.8
CE1 a:HIS272 3.1 52.0 0.2
CE1 d:HIS214 3.1 51.8 0.2
CE1 d:HIS214 3.1 51.5 0.8
CD2 a:HIS215 3.2 54.4 0.2
CD2 d:HIS214 3.2 43.4 0.8
CD2 d:HIS214 3.2 46.8 0.2
CE1 d:HIS268 3.2 61.8 1.0
CE1 a:HIS272 3.2 49.3 0.8
CD2 a:HIS215 3.2 53.2 0.8
CD2 d:HIS268 3.3 54.1 1.0
CD2 a:HIS272 3.3 52.6 0.2
CD2 a:HIS272 3.3 53.1 0.8
O3 a:BCT420 3.9 68.9 0.2
ND1 a:HIS215 4.0 55.4 0.2
O3 a:BCT420 4.1 72.8 0.8
ND1 a:HIS215 4.1 57.1 0.8
CG a:HIS215 4.2 53.3 0.2
ND1 a:HIS272 4.2 54.4 0.2
ND1 d:HIS214 4.3 51.7 0.2
ND1 d:HIS214 4.3 54.1 0.8
CG a:HIS215 4.3 53.6 0.8
CG d:HIS214 4.3 47.6 0.2
CG d:HIS214 4.3 47.6 0.8
ND1 d:HIS268 4.3 51.5 1.0
ND1 a:HIS272 4.4 57.7 0.8
CG a:HIS272 4.4 53.1 0.2
CG d:HIS268 4.4 51.2 1.0
CG a:HIS272 4.4 53.2 0.8
CG2 a:VAL219 4.5 49.7 1.0
CG2 d:VAL218 4.8 46.1 1.0
OH d:TYR244 4.9 61.3 1.0

Iron binding site 7 out of 8 in 5ws6

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Iron binding site 7 out of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Fe102

b:89.2
occ:1.00
FE e:HEM102 0.0 89.2 1.0
ND e:HEM102 2.0 67.1 1.0
NA e:HEM102 2.0 0.1 1.0
NC e:HEM102 2.1 78.2 1.0
NE2 f:HIS24 2.1 79.3 1.0
NE2 e:HIS23 2.1 95.7 1.0
NB e:HEM102 2.1 84.1 1.0
CD2 f:HIS24 2.9 79.0 1.0
C4D e:HEM102 2.9 77.6 1.0
C1D e:HEM102 3.0 71.5 1.0
C1A e:HEM102 3.0 95.8 1.0
CD2 e:HIS23 3.0 93.0 1.0
C4C e:HEM102 3.0 72.5 1.0
C4A e:HEM102 3.1 0.6 1.0
CE1 e:HIS23 3.1 88.0 1.0
C1B e:HEM102 3.1 94.0 1.0
C4B e:HEM102 3.1 86.9 1.0
C1C e:HEM102 3.1 78.2 1.0
CE1 f:HIS24 3.2 87.4 1.0
CHA e:HEM102 3.4 80.8 1.0
CHD e:HEM102 3.4 71.2 1.0
CHB e:HEM102 3.5 95.2 1.0
CHC e:HEM102 3.5 81.1 1.0
CG f:HIS24 4.1 78.1 1.0
ND1 e:HIS23 4.1 90.7 1.0
CG e:HIS23 4.1 90.1 1.0
C3D e:HEM102 4.2 83.9 1.0
C2D e:HEM102 4.2 76.4 1.0
C2A e:HEM102 4.2 0.8 1.0
ND1 f:HIS24 4.2 89.7 1.0
C3A e:HEM102 4.2 0.8 1.0
C3C e:HEM102 4.2 81.8 1.0
C2C e:HEM102 4.3 81.0 1.0
C2B e:HEM102 4.3 94.1 1.0
C3B e:HEM102 4.3 95.6 1.0
CE2 e:TYR19 4.8 88.3 1.0

Iron binding site 8 out of 8 in 5ws6

Go back to Iron Binding Sites List in 5ws6
Iron binding site 8 out of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Fe203

b:66.7
occ:1.00
FE v:HEC203 0.0 66.7 1.0
ND v:HEC203 2.0 62.4 1.0
NA v:HEC203 2.0 62.5 1.0
NE2 v:HIS41 2.1 54.4 1.0
NE2 v:HIS92 2.1 64.6 1.0
NC v:HEC203 2.1 61.9 1.0
NB v:HEC203 2.1 68.0 1.0
C4D v:HEC203 2.9 61.5 1.0
C1D v:HEC203 2.9 59.0 1.0
C1A v:HEC203 2.9 58.7 1.0
CE1 v:HIS92 3.0 62.8 1.0
C4A v:HEC203 3.0 64.4 1.0
CD2 v:HIS41 3.0 56.9 1.0
C4C v:HEC203 3.0 66.4 1.0
C1B v:HEC203 3.1 64.6 1.0
C4B v:HEC203 3.1 64.1 1.0
CE1 v:HIS41 3.1 59.2 1.0
CD2 v:HIS92 3.1 61.9 1.0
C1C v:HEC203 3.1 63.6 1.0
CHA v:HEC203 3.3 52.2 1.0
CHD v:HEC203 3.4 54.9 1.0
CHB v:HEC203 3.5 62.8 1.0
CHC v:HEC203 3.5 71.3 1.0
ND1 v:HIS92 4.1 68.5 1.0
C2A v:HEC203 4.1 65.2 1.0
C3D v:HEC203 4.2 62.8 1.0
ND1 v:HIS41 4.2 57.8 1.0
CG v:HIS41 4.2 58.8 1.0
C2D v:HEC203 4.2 68.8 1.0
C3A v:HEC203 4.2 65.4 1.0
CG v:HIS92 4.2 63.0 1.0
C3C v:HEC203 4.3 69.6 1.0
C2B v:HEC203 4.3 60.5 1.0
C2C v:HEC203 4.3 65.0 1.0
C3B v:HEC203 4.3 66.3 1.0
CE1 v:TYR75 4.9 69.0 1.0

Reference:

M.Suga, F.Akita, M.Sugahara, M.Kubo, Y.Nakajima, T.Nakane, K.Yamashita, Y.Umena, M.Nakabayashi, T.Yamane, T.Nakano, M.Suzuki, T.Masuda, S.Inoue, T.Kimura, T.Nomura, S.Yonekura, L.J.Yu, T.Sakamoto, T.Motomura, J.H.Chen, Y.Kato, T.Noguchi, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, E.Nango, R.Tanaka, H.Naitow, Y.Matsuura, A.Yamashita, M.Yamamoto, O.Nureki, M.Yabashi, T.Ishikawa, S.Iwata, J.R.Shen. Light-Induced Structural Changes and the Site of O=O Bond Formation in Psii Caught By Xfel. Nature V. 543 131 2017.
ISSN: ESSN 1476-4687
PubMed: 28219079
DOI: 10.1038/NATURE21400
Page generated: Tue Aug 6 11:18:02 2024

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