Magnesium in PDB 7cjj: Photosystem II Structure in the S2 State

Enzymatic activity of Photosystem II Structure in the S2 State

All present enzymatic activity of Photosystem II Structure in the S2 State:
1.10.3.9;

Protein crystallography data

The structure of Photosystem II Structure in the S2 State, PDB code: 7cjj was solved by H.Li, J.-R.Shen, M.Suga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.90 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.75, 231.63, 288.4, 90, 90, 90
R / Rfree (%) 16.8 / 21.8

Other elements in 7cjj:

The structure of Photosystem II Structure in the S2 State also contains other interesting chemical elements:

Calcium (Ca) 11 atoms
Iron (Fe) 8 atoms
Chlorine (Cl) 4 atoms
Manganese (Mn) 16 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 72;

Binding sites:

The binding sites of Magnesium atom in the Photosystem II Structure in the S2 State (pdb code 7cjj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 72 binding sites of Magnesium where determined in the Photosystem II Structure in the S2 State, PDB code: 7cjj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 72 in 7cjj

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Magnesium binding site 1 out of 72 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Photosystem II Structure in the S2 State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:35.9
occ:1.00
MG A:CLA403 0.0 35.9 1.0
NB A:CLA403 2.0 34.5 1.0
ND A:CLA403 2.0 45.1 1.0
NA A:CLA403 2.1 42.8 1.0
NC A:CLA403 2.1 42.5 1.0
NE2 A:HIS198 2.2 38.6 1.0
C4B A:CLA403 3.0 34.4 1.0
C4D A:CLA403 3.0 38.5 1.0
C1A A:CLA403 3.0 34.8 1.0
C4A A:CLA403 3.0 38.0 1.0
C1C A:CLA403 3.0 36.9 1.0
C1B A:CLA403 3.0 40.5 1.0
CE1 A:HIS198 3.1 38.9 1.0
C4C A:CLA403 3.2 34.3 1.0
CD2 A:HIS198 3.3 37.5 1.0
C1D A:CLA403 3.3 34.5 1.0
CHC A:CLA403 3.4 34.3 1.0
CHB A:CLA403 3.4 34.8 1.0
CHA A:CLA403 3.4 34.8 1.0
CHD A:CLA403 3.7 34.4 1.0
CE A:MET183 4.1 33.6 1.0
ND1 A:HIS198 4.3 41.1 1.0
C3D A:CLA403 4.3 34.7 1.0
C3B A:CLA403 4.3 34.5 1.0
C2A A:CLA403 4.4 36.7 1.0
C2B A:CLA403 4.4 34.7 1.0
CG A:HIS198 4.4 45.6 1.0
C3A A:CLA403 4.4 35.1 1.0
C2C A:CLA403 4.4 38.6 1.0
C3C A:CLA403 4.4 34.2 1.0
CAB D:CLA403 4.5 34.6 1.0
C2D A:CLA403 4.5 34.6 1.0
CBD A:CLA403 4.9 44.4 1.0

Magnesium binding site 2 out of 72 in 7cjj

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Magnesium binding site 2 out of 72 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Photosystem II Structure in the S2 State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:38.7
occ:1.00
MG A:CLA404 0.0 38.7 1.0
NB A:CLA404 2.0 35.9 1.0
ND A:CLA404 2.0 39.1 1.0
NA A:CLA404 2.1 40.0 1.0
NC A:CLA404 2.1 39.8 1.0
O A:HOH581 2.2 36.6 1.0
C4D A:CLA404 3.0 37.1 1.0
C1C A:CLA404 3.0 38.1 1.0
C4A A:CLA404 3.0 39.7 1.0
C4B A:CLA404 3.0 36.6 1.0
C1B A:CLA404 3.0 36.9 1.0
C1A A:CLA404 3.1 37.0 1.0
C4C A:CLA404 3.1 36.5 1.0
C1D A:CLA404 3.3 36.1 1.0
CHB A:CLA404 3.4 33.1 1.0
CHC A:CLA404 3.4 33.9 1.0
CHA A:CLA404 3.5 39.3 1.0
CHD A:CLA404 3.7 37.7 1.0
CBB A:PHO406 3.9 44.7 1.0
O A:HOH604 4.1 41.5 1.0
C3D A:CLA404 4.3 34.3 1.0
C3B A:CLA404 4.3 42.6 1.0
C2C A:CLA404 4.4 42.3 1.0
C2B A:CLA404 4.4 43.8 1.0
C3A A:CLA404 4.4 42.7 1.0
C2A A:CLA404 4.4 40.1 1.0
C3C A:CLA404 4.4 37.5 1.0
C2D A:CLA404 4.5 33.9 1.0
OG1 A:THR179 4.6 40.4 1.0
CG2 A:THR179 4.6 36.1 1.0
CBA A:CLA404 4.7 41.4 1.0
C19 A:PHO406 4.8 33.2 1.0
CBD A:CLA404 4.9 40.7 1.0

Magnesium binding site 3 out of 72 in 7cjj

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Magnesium binding site 3 out of 72 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Photosystem II Structure in the S2 State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:40.6
occ:1.00
MG A:CLA405 0.0 40.6 1.0
ND A:CLA405 2.0 40.1 1.0
NB A:CLA405 2.0 37.3 1.0
NA A:CLA405 2.1 40.9 1.0
NC A:CLA405 2.1 38.8 1.0
O A:HOH632 2.2 43.6 1.0
C4D A:CLA405 3.0 41.2 1.0
C4A A:CLA405 3.0 46.5 1.0
C1B A:CLA405 3.0 38.4 1.0
C1C A:CLA405 3.0 36.6 1.0
C4B A:CLA405 3.0 38.4 1.0
C1A A:CLA405 3.0 45.3 1.0
C4C A:CLA405 3.1 36.5 1.0
C1D A:CLA405 3.2 36.0 1.0
CHB A:CLA405 3.4 38.1 1.0
CHC A:CLA405 3.4 39.1 1.0
CHA A:CLA405 3.5 44.3 1.0
CHD A:CLA405 3.7 36.0 1.0
CBB A:PHO415 4.0 45.4 1.0
C3D A:CLA405 4.3 40.4 1.0
O A:HOH608 4.3 45.3 1.0
C2B A:CLA405 4.4 38.5 1.0
C3B A:CLA405 4.4 43.5 1.0
C2C A:CLA405 4.4 39.4 1.0
C3A A:CLA405 4.4 45.3 1.0
C2A A:CLA405 4.4 47.9 1.0
C3C A:CLA405 4.4 37.5 1.0
C2D A:CLA405 4.5 40.2 1.0
C20 A:PHO415 4.7 38.1 1.0
CG2 D:ILE178 4.7 36.1 1.0
CBA A:CLA405 4.8 51.3 1.0
CBD A:CLA405 4.9 48.2 1.0

Magnesium binding site 4 out of 72 in 7cjj

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Magnesium binding site 4 out of 72 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Photosystem II Structure in the S2 State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:44.3
occ:1.00
MG A:CLA407 0.0 44.3 1.0
ND A:CLA407 2.0 44.6 1.0
NB A:CLA407 2.1 43.5 1.0
NA A:CLA407 2.1 48.0 1.0
NC A:CLA407 2.1 45.0 1.0
NE2 A:HIS118 2.2 42.6 1.0
C4D A:CLA407 3.0 47.6 1.0
C4B A:CLA407 3.0 44.7 1.0
C1C A:CLA407 3.0 41.6 1.0
C4A A:CLA407 3.0 45.3 1.0
CE1 A:HIS118 3.1 48.3 1.0
C1A A:CLA407 3.1 50.4 1.0
C1B A:CLA407 3.1 40.4 1.0
C4C A:CLA407 3.1 41.4 1.0
C1D A:CLA407 3.3 42.8 1.0
CD2 A:HIS118 3.3 40.4 1.0
CHC A:CLA407 3.4 42.3 1.0
CHB A:CLA407 3.4 40.5 1.0
CHA A:CLA407 3.5 50.2 1.0
CHD A:CLA407 3.7 44.9 1.0
ND1 A:HIS118 4.2 37.9 1.0
C3D A:CLA407 4.2 42.8 1.0
C3B A:CLA407 4.4 45.6 1.0
C2B A:CLA407 4.4 40.8 1.0
CG A:HIS118 4.4 41.9 1.0
C2C A:CLA407 4.4 46.6 1.0
CG1 I:VAL8 4.4 50.0 1.0
C3A A:CLA407 4.4 47.6 1.0
C2A A:CLA407 4.4 50.1 1.0
C3C A:CLA407 4.4 44.6 1.0
C2D A:CLA407 4.5 42.2 1.0
CG2 I:VAL12 4.5 49.6 1.0
CBD A:CLA407 4.9 47.9 1.0

Magnesium binding site 5 out of 72 in 7cjj

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Magnesium binding site 5 out of 72 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Photosystem II Structure in the S2 State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:66.2
occ:1.00
MG B:CLA601 0.0 66.2 1.0
NB B:CLA601 2.0 60.7 1.0
ND B:CLA601 2.0 72.0 1.0
NC B:CLA601 2.1 64.0 1.0
NA B:CLA601 2.1 72.4 1.0
O B:HOH861 2.2 50.1 1.0
C4D B:CLA601 3.0 71.4 1.0
C1C B:CLA601 3.0 57.6 1.0
C4A B:CLA601 3.0 69.2 1.0
C1B B:CLA601 3.0 55.8 1.0
C4B B:CLA601 3.0 58.9 1.0
C1A B:CLA601 3.1 70.8 1.0
C4C B:CLA601 3.1 60.2 1.0
C1D B:CLA601 3.3 70.0 1.0
CHB B:CLA601 3.4 62.1 1.0
CHC B:CLA601 3.4 59.8 1.0
CHA B:CLA601 3.5 70.9 1.0
CHD B:CLA601 3.7 62.6 1.0
C12 B:CLA601 3.7 82.8 1.0
C11 B:CLA601 4.1 80.8 1.0
C10 B:CLA601 4.2 79.5 1.0
C3D B:CLA601 4.3 73.4 1.0
C3B B:CLA601 4.4 54.8 1.0
C2C B:CLA601 4.4 62.5 1.0
C2B B:CLA601 4.4 60.3 1.0
C3A B:CLA601 4.4 67.3 1.0
C2A B:CLA601 4.4 74.8 1.0
C3C B:CLA601 4.4 60.8 1.0
O B:TRP185 4.5 61.3 1.0
C2D B:CLA601 4.5 73.9 1.0
CE2 B:PHE190 4.5 53.4 1.0
O B:HOH783 4.7 88.9 1.0
C13 B:CLA601 4.8 85.9 1.0
CZ B:PHE190 4.9 50.9 1.0
CBD B:CLA601 5.0 78.1 1.0
CBA B:CLA601 5.0 90.9 1.0
C15 B:CLA601 5.0 80.8 1.0

Magnesium binding site 6 out of 72 in 7cjj

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Magnesium binding site 6 out of 72 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Photosystem II Structure in the S2 State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:50.3
occ:1.00
MG B:CLA602 0.0 50.3 1.0
ND B:CLA602 2.0 43.7 1.0
NB B:CLA602 2.0 50.1 1.0
NC B:CLA602 2.1 47.4 1.0
NA B:CLA602 2.1 53.9 1.0
ND1 B:HIS201 2.2 52.5 1.0
C4D B:CLA602 3.0 45.5 1.0
C1B B:CLA602 3.0 52.8 1.0
C1C B:CLA602 3.0 51.1 1.0
CE1 B:HIS201 3.0 54.3 1.0
C4B B:CLA602 3.0 52.5 1.0
C4A B:CLA602 3.1 54.2 1.0
C1A B:CLA602 3.1 50.4 1.0
C4C B:CLA602 3.2 50.4 1.0
C1D B:CLA602 3.3 46.6 1.0
CG B:HIS201 3.3 49.0 1.0
CHC B:CLA602 3.4 49.5 1.0
CHB B:CLA602 3.4 48.4 1.0
CHA B:CLA602 3.5 48.0 1.0
CHD B:CLA602 3.7 44.4 1.0
CB B:HIS201 3.7 50.7 1.0
CZ H:PHE41 4.0 62.0 1.0
NE2 B:HIS201 4.2 49.1 1.0
C3D B:CLA602 4.3 46.9 1.0
C3B B:CLA602 4.3 55.7 1.0
C2B B:CLA602 4.3 56.6 1.0
CA B:HIS201 4.3 49.0 1.0
CD2 B:HIS201 4.4 52.4 1.0
C2C B:CLA602 4.4 52.9 1.0
C3A B:CLA602 4.4 57.0 1.0
C2A B:CLA602 4.4 51.9 1.0
C3C B:CLA602 4.4 49.3 1.0
C2D B:CLA602 4.5 43.0 1.0
CE2 H:PHE41 4.5 59.1 1.0
CE1 B:PHE190 4.8 47.4 1.0
CBD B:CLA602 4.9 51.3 1.0
CE1 H:PHE41 5.0 59.0 1.0

Magnesium binding site 7 out of 72 in 7cjj

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Magnesium binding site 7 out of 72 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Photosystem II Structure in the S2 State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:48.8
occ:1.00
MG B:CLA603 0.0 48.8 1.0
NB B:CLA603 2.0 46.7 1.0
ND B:CLA603 2.0 51.1 1.0
NC B:CLA603 2.1 45.2 1.0
NA B:CLA603 2.1 47.1 1.0
NE2 B:HIS202 2.2 45.7 1.0
C4D B:CLA603 3.0 45.2 1.0
C1B B:CLA603 3.0 46.1 1.0
C4A B:CLA603 3.0 44.6 1.0
C4B B:CLA603 3.0 50.1 1.0
C1C B:CLA603 3.0 47.9 1.0
C1A B:CLA603 3.1 47.1 1.0
C4C B:CLA603 3.1 45.0 1.0
CD2 B:HIS202 3.1 42.6 1.0
CE1 B:HIS202 3.2 44.9 1.0
C1D B:CLA603 3.2 48.2 1.0
CHB B:CLA603 3.4 45.6 1.0
CHC B:CLA603 3.4 42.8 1.0
CHA B:CLA603 3.5 47.1 1.0
CHD B:CLA603 3.7 42.2 1.0
C6 B:CLA605 4.1 51.7 1.0
C3D B:CLA603 4.3 48.6 1.0
ND1 B:HIS202 4.3 44.6 1.0
CG B:HIS202 4.3 46.3 1.0
C3B B:CLA603 4.3 50.5 1.0
C2B B:CLA603 4.4 47.5 1.0
C2C B:CLA603 4.4 41.8 1.0
C2A B:CLA603 4.4 45.2 1.0
C3A B:CLA603 4.4 41.1 1.0
C3C B:CLA603 4.4 41.5 1.0
C2D B:CLA603 4.5 52.9 1.0
C9 B:CLA605 4.6 51.6 1.0
C5 B:CLA605 4.9 53.2 1.0
NE2 B:HIS201 4.9 49.1 1.0
C4 B:CLA605 4.9 60.8 1.0
CD2 B:HIS201 4.9 52.4 1.0
CBD B:CLA603 5.0 53.0 1.0

Magnesium binding site 8 out of 72 in 7cjj

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Magnesium binding site 8 out of 72 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Photosystem II Structure in the S2 State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:36.2
occ:1.00
MG B:CLA604 0.0 36.2 1.0
NB B:CLA604 2.0 37.9 1.0
ND B:CLA604 2.0 35.6 1.0
NC B:CLA604 2.1 35.0 1.0
NA B:CLA604 2.1 40.6 1.0
NE2 B:HIS455 2.2 45.4 1.0
C4D B:CLA604 3.0 36.0 1.0
C4B B:CLA604 3.0 39.8 1.0
C1B B:CLA604 3.0 41.5 1.0
C1C B:CLA604 3.1 40.2 1.0
C4A B:CLA604 3.1 41.0 1.0
CD2 B:HIS455 3.1 45.1 1.0
C1A B:CLA604 3.1 39.4 1.0
C4C B:CLA604 3.2 35.3 1.0
CE1 B:HIS455 3.2 44.5 1.0
C1D B:CLA604 3.3 36.0 1.0
CHB B:CLA604 3.4 41.9 1.0
CHC B:CLA604 3.4 34.6 1.0
CHA B:CLA604 3.5 37.7 1.0
CHD B:CLA604 3.7 37.7 1.0
C14 B:CLA612 4.1 49.4 1.0
C3D B:CLA604 4.3 39.7 1.0
CG B:HIS455 4.3 44.5 1.0
ND1 B:HIS455 4.3 42.5 1.0
C3B B:CLA604 4.3 37.5 1.0
C2B B:CLA604 4.3 40.7 1.0
C2C B:CLA604 4.4 35.5 1.0
C3A B:CLA604 4.5 44.3 1.0
C3C B:CLA604 4.5 35.3 1.0
C2A B:CLA604 4.5 43.2 1.0
C2D B:CLA604 4.5 37.1 1.0
C15 B:CLA612 4.6 55.5 1.0
C13 B:CLA612 4.8 56.2 1.0
CBD B:CLA604 5.0 40.1 1.0
CE1 B:PHE451 5.0 45.2 1.0

Magnesium binding site 9 out of 72 in 7cjj

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Magnesium binding site 9 out of 72 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Photosystem II Structure in the S2 State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:43.8
occ:1.00
MG B:CLA605 0.0 43.8 1.0
ND B:CLA605 2.0 42.3 1.0
NB B:CLA605 2.0 37.9 1.0
NC B:CLA605 2.1 43.1 1.0
NA B:CLA605 2.1 39.3 1.0
NE2 B:HIS100 2.2 47.0 1.0
C4D B:CLA605 3.0 39.1 1.0
C1B B:CLA605 3.0 38.3 1.0
C1C B:CLA605 3.0 43.3 1.0
C4A B:CLA605 3.0 41.8 1.0
C4B B:CLA605 3.0 41.5 1.0
C1A B:CLA605 3.1 42.9 1.0
CE1 B:HIS100 3.1 44.4 1.0
C4C B:CLA605 3.2 39.8 1.0
CD2 B:HIS100 3.3 42.3 1.0
C1D B:CLA605 3.3 43.0 1.0
CHB B:CLA605 3.4 38.1 1.0
CHC B:CLA605 3.4 42.0 1.0
CHA B:CLA605 3.5 44.4 1.0
CHD B:CLA605 3.7 41.6 1.0
C1 B:CLA604 4.1 56.6 1.0
C3D B:CLA605 4.3 40.0 1.0
ND1 B:HIS100 4.3 38.2 1.0
C3B B:CLA605 4.4 42.1 1.0
C2B B:CLA605 4.4 46.2 1.0
CG B:HIS100 4.4 41.1 1.0
C2C B:CLA605 4.4 42.9 1.0
C3A B:CLA605 4.4 39.5 1.0
C2A B:CLA605 4.4 37.7 1.0
C3C B:CLA605 4.4 47.3 1.0
C2D B:CLA605 4.5 41.8 1.0
C2 B:CLA604 4.7 66.9 1.0
C4 B:CLA606 4.8 45.5 1.0
CBD B:CLA605 4.9 40.3 1.0

Magnesium binding site 10 out of 72 in 7cjj

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Magnesium binding site 10 out of 72 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Photosystem II Structure in the S2 State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg606

b:51.6
occ:1.00
MG B:CLA606 0.0 51.6 1.0
ND B:CLA606 2.0 55.7 1.0
NB B:CLA606 2.0 41.9 1.0
NC B:CLA606 2.1 45.7 1.0
NA B:CLA606 2.1 51.8 1.0
ND1 B:HIS157 2.2 46.8 1.0
CE1 B:HIS157 2.9 53.7 1.0
C4D B:CLA606 3.0 50.9 1.0
C1C B:CLA606 3.0 48.5 1.0
C1B B:CLA606 3.0 47.2 1.0
C4B B:CLA606 3.0 46.8 1.0
C4A B:CLA606 3.1 46.8 1.0
C1A B:CLA606 3.1 41.1 1.0
C4C B:CLA606 3.1 46.7 1.0
C1D B:CLA606 3.3 53.8 1.0
CHB B:CLA606 3.4 41.4 1.0
CG B:HIS157 3.4 45.9 1.0
CHC B:CLA606 3.4 44.9 1.0
CHA B:CLA606 3.5 46.7 1.0
CHD B:CLA606 3.7 54.2 1.0
C16 B:UNL625 3.9 56.4 1.0
CB B:HIS157 4.0 46.5 1.0
NE2 B:HIS157 4.1 45.0 1.0
C3D B:CLA606 4.3 56.0 1.0
C3B B:CLA606 4.4 50.1 1.0
C2C B:CLA606 4.4 49.6 1.0
C2B B:CLA606 4.4 45.3 1.0
CD2 B:HIS157 4.4 45.8 1.0
C15 B:UNL625 4.4 61.5 1.0
C3C B:CLA606 4.4 46.3 1.0
C2A B:CLA606 4.5 42.2 1.0
C3A B:CLA606 4.5 39.7 1.0
C2D B:CLA606 4.5 55.6 1.0
CBD B:CLA606 4.9 55.2 1.0
C14 B:UNL625 4.9 57.5 1.0
CD B:PRO164 5.0 52.0 1.0

Reference:

H.Li, Y.Nakajima, T.Nomura, M.Sugahara, S.Yonekura, S.K.Chan, T.Nakane, T.Yamane, Y.Umena, M.Suzuki, T.Masuda, T.Motomura, H.Naitow, Y.Matsuura, T.Kimura, K.Tono, S.Owada, Y.Joti, R.Tanaka, E.Nango, F.Akita, M.Kubo, S.Iwata, J.-R.Shen, M.Suga. Capturing Structural Changes of the S1 to S2 Transition of Photosystem II Using Time-Resolved Serial Femtosecond Crystallography Iucrj 2021.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252521002177
Page generated: Sun Jul 11 16:16:25 2021

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