Magnesium in PDB 7cji: Photosystem II Structure in the S1 State

All present enzymatic activity of Photosystem II Structure in the S1 State:
1.10.3.9;

The structure of Photosystem II Structure in the S1 State, PDB code: 7cji 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)	39.93 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	126.02, 231.7, 288.32, 90, 90, 90
R / Rfree (%)	16 / 20.8

The structure of Photosystem II Structure in the S1 State also contains other interesting chemical elements:

Calcium	(Ca)	9 atoms
Iron	(Fe)	6 atoms
Chlorine	(Cl)	4 atoms
Manganese	(Mn)	8 atoms

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 S1 State (pdb code 7cji). 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 S1 State, PDB code: 7cji:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 72 in the Photosystem II Structure in the S1 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 S1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:41.6 occ:1.00 MG A:CLA404 0.0 41.6 1.0 NB A:CLA404 2.0 40.3 1.0 ND A:CLA404 2.0 51.5 1.0 NA A:CLA404 2.1 46.2 1.0 NC A:CLA404 2.1 42.8 1.0 NE2 A:HIS198 2.2 41.1 1.0 C4D A:CLA404 3.0 40.4 1.0 C4B A:CLA404 3.0 40.2 1.0 C1C A:CLA404 3.0 40.0 1.0 C4A A:CLA404 3.0 40.7 1.0 C1B A:CLA404 3.0 45.8 1.0 C1A A:CLA404 3.0 40.6 1.0 CE1 A:HIS198 3.1 44.7 1.0 C4C A:CLA404 3.2 41.8 1.0 C1D A:CLA404 3.3 40.2 1.0 CD2 A:HIS198 3.3 45.4 1.0 CHC A:CLA404 3.4 40.1 1.0 CHB A:CLA404 3.4 40.6 1.0 CHA A:CLA404 3.5 40.6 1.0 CHD A:CLA404 3.7 40.1 1.0 CE A:MET183 4.1 39.3 1.0 ND1 A:HIS198 4.2 44.8 1.0 C3D A:CLA404 4.3 40.5 1.0 C3B A:CLA404 4.3 42.2 1.0 CG A:HIS198 4.4 48.1 1.0 C2B A:CLA404 4.4 40.5 1.0 C2A A:CLA404 4.4 43.5 1.0 C3A A:CLA404 4.4 42.5 1.0 C2C A:CLA404 4.4 44.2 1.0 C3C A:CLA404 4.5 39.9 1.0 CAB D:CLA405 4.5 39.5 1.0 C2D A:CLA404 4.5 40.3 1.0 CBD A:CLA404 4.9 46.5 1.0

Magnesium binding site 2 out of 72 in the Photosystem II Structure in the S1 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 S1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:44.6 occ:1.00 MG A:CLA405 0.0 44.6 1.0 ND A:CLA405 2.0 44.2 1.0 NB A:CLA405 2.1 39.4 1.0 NC A:CLA405 2.1 46.1 1.0 NA A:CLA405 2.1 49.0 1.0 O A:HOH606 2.2 41.3 1.0 C4D A:CLA405 3.0 44.7 1.0 C1C A:CLA405 3.0 42.9 1.0 C4A A:CLA405 3.0 46.5 1.0 C1B A:CLA405 3.0 42.8 1.0 C4B A:CLA405 3.0 39.6 1.0 C1A A:CLA405 3.1 42.3 1.0 C4C A:CLA405 3.1 39.2 1.0 C1D A:CLA405 3.3 42.0 1.0 CHB A:CLA405 3.4 38.8 1.0 CHC A:CLA405 3.4 39.6 1.0 CHA A:CLA405 3.5 43.4 1.0 CHD A:CLA405 3.7 46.6 1.0 CBB A:PHO407 4.0 41.8 1.0 O A:HOH576 4.2 41.6 1.0 C3D A:CLA405 4.3 38.3 1.0 C2B A:CLA405 4.4 41.1 1.0 C3B A:CLA405 4.4 43.3 1.0 C2C A:CLA405 4.4 46.3 1.0 C3A A:CLA405 4.4 46.7 1.0 C2A A:CLA405 4.4 44.4 1.0 C3C A:CLA405 4.4 45.5 1.0 C2D A:CLA405 4.5 41.8 1.0 CG2 A:THR179 4.6 38.6 1.0 OG1 A:THR179 4.7 39.3 1.0 C19 A:PHO407 4.7 38.8 1.0 CBA A:CLA405 4.7 44.0 1.0 CBD A:CLA405 4.9 50.1 1.0

Magnesium binding site 3 out of 72 in the Photosystem II Structure in the S1 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 S1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:45.7 occ:1.00 MG A:CLA406 0.0 45.7 1.0 ND A:CLA406 2.0 44.8 1.0 NB A:CLA406 2.0 43.3 1.0 NA A:CLA406 2.1 45.8 1.0 NC A:CLA406 2.1 45.8 1.0 O A:HOH635 2.2 49.4 1.0 C4D A:CLA406 3.0 46.1 1.0 C4A A:CLA406 3.0 47.1 1.0 C1C A:CLA406 3.0 42.2 1.0 C1B A:CLA406 3.0 43.9 1.0 C4B A:CLA406 3.0 43.2 1.0 C1A A:CLA406 3.1 47.9 1.0 C4C A:CLA406 3.1 41.7 1.0 C1D A:CLA406 3.2 41.8 1.0 CHB A:CLA406 3.4 46.5 1.0 CHC A:CLA406 3.4 44.4 1.0 CHA A:CLA406 3.5 47.1 1.0 CHD A:CLA406 3.7 41.5 1.0 CBB D:PHO402 4.0 45.4 1.0 O A:HOH608 4.3 51.5 1.0 C3D A:CLA406 4.3 43.5 1.0 C2B A:CLA406 4.4 47.3 1.0 C3B A:CLA406 4.4 52.5 1.0 C2C A:CLA406 4.4 45.1 1.0 C3A A:CLA406 4.4 49.0 1.0 C2A A:CLA406 4.4 47.7 1.0 C3C A:CLA406 4.4 46.4 1.0 C2D A:CLA406 4.5 41.8 1.0 C20 D:PHO402 4.6 44.1 1.0 CG2 D:ILE178 4.8 41.9 1.0 CBA A:CLA406 4.8 56.2 1.0 CBD A:CLA406 4.9 48.7 1.0 CE1 A:PHE206 5.0 46.1 1.0

Magnesium binding site 4 out of 72 in the Photosystem II Structure in the S1 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 S1 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:46.8 occ:1.00 MG A:CLA408 0.0 46.8 1.0 ND A:CLA408 2.0 48.7 1.0 NB A:CLA408 2.0 48.2 1.0 NC A:CLA408 2.1 45.8 1.0 NA A:CLA408 2.1 55.6 1.0 NE2 A:HIS118 2.2 44.7 1.0 C4D A:CLA408 3.0 49.2 1.0 CE1 A:HIS118 3.0 50.4 1.0 C4B A:CLA408 3.0 46.4 1.0 C1C A:CLA408 3.0 46.0 1.0 C4A A:CLA408 3.0 54.1 1.0 C1A A:CLA408 3.1 54.5 1.0 C1B A:CLA408 3.1 47.6 1.0 C4C A:CLA408 3.2 45.6 1.0 C1D A:CLA408 3.3 45.3 1.0 CD2 A:HIS118 3.4 47.6 1.0 CHC A:CLA408 3.4 48.0 1.0 CHB A:CLA408 3.4 51.4 1.0 CHA A:CLA408 3.4 51.1 1.0 CHD A:CLA408 3.7 45.3 1.0 ND1 A:HIS118 4.2 43.8 1.0 C3D A:CLA408 4.2 46.9 1.0 C3B A:CLA408 4.3 48.9 1.0 C2B A:CLA408 4.4 46.9 1.0 C2C A:CLA408 4.4 49.7 1.0 CG A:HIS118 4.4 43.8 1.0 C3A A:CLA408 4.4 55.2 1.0 C2A A:CLA408 4.4 51.1 1.0 C3C A:CLA408 4.4 50.1 1.0 C2D A:CLA408 4.5 45.1 1.0 CG1 I:VAL8 4.5 51.3 1.0 CG2 I:VAL12 4.6 55.4 1.0 CBD A:CLA408 4.9 47.8 1.0

Magnesium binding site 5 out of 72 in the Photosystem II Structure in the S1 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 S1 State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:69.3 occ:1.00 MG B:CLA601 0.0 69.3 1.0 NB B:CLA601 2.0 65.4 1.0 ND B:CLA601 2.0 78.1 1.0 NC B:CLA601 2.1 68.6 1.0 NA B:CLA601 2.1 76.9 1.0 O B:HOH832 2.2 56.5 1.0 C4D B:CLA601 3.0 75.7 1.0 C1C B:CLA601 3.0 62.2 1.0 C4B B:CLA601 3.0 62.2 1.0 C4A B:CLA601 3.0 75.1 1.0 C1B B:CLA601 3.0 61.6 1.0 C1A B:CLA601 3.1 76.6 1.0 C4C B:CLA601 3.2 61.7 1.0 C1D B:CLA601 3.3 75.2 1.0 CHC B:CLA601 3.4 61.8 1.0 CHB B:CLA601 3.4 66.7 1.0 CHA B:CLA601 3.5 75.4 1.0 CHD B:CLA601 3.7 65.6 1.0 C12 B:CLA601 3.9 90.9 1.0 C11 B:CLA601 4.1 87.5 1.0 C10 B:CLA601 4.2 86.8 1.0 C3D B:CLA601 4.3 76.3 1.0 C3B B:CLA601 4.3 59.5 1.0 C2C B:CLA601 4.4 62.6 1.0 C2B B:CLA601 4.4 59.5 1.0 O B:TRP185 4.4 60.3 1.0 C2A B:CLA601 4.4 79.5 1.0 C3A B:CLA601 4.4 73.8 1.0 C3C B:CLA601 4.4 61.2 1.0 CE2 B:PHE190 4.5 60.4 1.0 C2D B:CLA601 4.5 76.7 1.0 CZ B:PHE190 4.9 61.5 1.0 C13 B:CLA601 4.9 94.3 1.0 CBD B:CLA601 4.9 81.4 1.0 CBA B:CLA601 5.0 92.0 1.0

Magnesium binding site 6 out of 72 in the Photosystem II Structure in the S1 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 S1 State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:53.7 occ:1.00 MG B:CLA602 0.0 53.7 1.0 ND B:CLA602 2.0 53.5 1.0 NB B:CLA602 2.0 54.5 1.0 NC B:CLA602 2.1 53.4 1.0 NA B:CLA602 2.1 57.9 1.0 ND1 B:HIS201 2.2 58.1 1.0 C4D B:CLA602 3.0 49.1 1.0 C1C B:CLA602 3.0 59.5 1.0 C1B B:CLA602 3.0 57.0 1.0 C4B B:CLA602 3.0 56.0 1.0 C4A B:CLA602 3.0 56.8 1.0 C1A B:CLA602 3.1 52.7 1.0 CE1 B:HIS201 3.1 55.6 1.0 C4C B:CLA602 3.1 52.7 1.0 C1D B:CLA602 3.3 51.8 1.0 CG B:HIS201 3.3 54.0 1.0 CHC B:CLA602 3.4 52.9 1.0 CHB B:CLA602 3.4 50.9 1.0 CHA B:CLA602 3.5 50.1 1.0 CB B:HIS201 3.7 50.4 1.0 CHD B:CLA602 3.7 52.8 1.0 CZ H:PHE41 3.9 67.7 1.0 NE2 B:HIS201 4.2 54.4 1.0 C3D B:CLA602 4.3 50.0 1.0 CA B:HIS201 4.3 51.4 1.0 C2B B:CLA602 4.4 61.0 1.0 C3B B:CLA602 4.4 60.0 1.0 CD2 B:HIS201 4.4 55.9 1.0 C2C B:CLA602 4.4 55.9 1.0 C3A B:CLA602 4.4 56.7 1.0 C2A B:CLA602 4.4 50.5 1.0 C3C B:CLA602 4.4 52.5 1.0 C2D B:CLA602 4.5 49.1 1.0 CE2 H:PHE41 4.5 64.3 1.0 CE1 B:PHE190 4.9 52.9 1.0 CBD B:CLA602 4.9 53.1 1.0 CE1 H:PHE41 4.9 62.6 1.0 O B:HIS201 5.0 54.5 1.0

Magnesium binding site 7 out of 72 in the Photosystem II Structure in the S1 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 S1 State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:54.9 occ:1.00 MG B:CLA603 0.0 54.9 1.0 NB B:CLA603 2.0 53.7 1.0 ND B:CLA603 2.0 52.7 1.0 NC B:CLA603 2.1 51.6 1.0 NA B:CLA603 2.1 51.8 1.0 NE2 B:HIS202 2.2 47.9 1.0 C4D B:CLA603 3.0 48.6 1.0 C4B B:CLA603 3.0 53.7 1.0 C1B B:CLA603 3.0 54.1 1.0 C1C B:CLA603 3.0 53.0 1.0 C4A B:CLA603 3.0 52.2 1.0 C1A B:CLA603 3.1 52.1 1.0 C4C B:CLA603 3.1 51.0 1.0 CD2 B:HIS202 3.1 48.6 1.0 CE1 B:HIS202 3.2 48.0 1.0 C1D B:CLA603 3.3 51.7 1.0 CHB B:CLA603 3.4 54.0 1.0 CHC B:CLA603 3.4 50.8 1.0 CHA B:CLA603 3.5 51.2 1.0 CHD B:CLA603 3.7 48.4 1.0 C6 B:CLA605 4.3 61.6 1.0 ND1 B:HIS202 4.3 52.5 1.0 C3D B:CLA603 4.3 49.8 1.0 CG B:HIS202 4.3 53.4 1.0 C3B B:CLA603 4.3 54.1 1.0 C2B B:CLA603 4.4 55.2 1.0 C2C B:CLA603 4.4 48.8 1.0 C2A B:CLA603 4.4 48.4 1.0 C3A B:CLA603 4.4 48.5 1.0 C3C B:CLA603 4.4 47.9 1.0 C2D B:CLA603 4.5 54.5 1.0 C7 B:CLA605 4.8 60.6 1.0 NE2 B:HIS201 4.9 54.4 1.0 C9 B:CLA605 4.9 52.1 1.0 CD2 B:HIS201 4.9 55.9 1.0 C4 B:CLA605 5.0 58.5 1.0 CBD B:CLA603 5.0 54.0 1.0

Magnesium binding site 8 out of 72 in the Photosystem II Structure in the S1 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 S1 State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:40.5 occ:1.00 MG B:CLA604 0.0 40.5 1.0 NB B:CLA604 2.0 39.9 1.0 ND B:CLA604 2.0 41.3 1.0 NC B:CLA604 2.1 40.6 1.0 NA B:CLA604 2.1 43.2 1.0 NE2 B:HIS455 2.2 49.5 1.0 C4D B:CLA604 3.0 41.7 1.0 C4B B:CLA604 3.0 42.9 1.0 C1B B:CLA604 3.0 43.6 1.0 C1C B:CLA604 3.0 40.8 1.0 C4A B:CLA604 3.1 41.9 1.0 CD2 B:HIS455 3.1 48.3 1.0 C1A B:CLA604 3.1 42.7 1.0 C4C B:CLA604 3.2 41.0 1.0 C1D B:CLA604 3.2 41.9 1.0 CE1 B:HIS455 3.3 46.6 1.0 CHB B:CLA604 3.4 45.2 1.0 CHC B:CLA604 3.4 42.5 1.0 CHA B:CLA604 3.5 41.6 1.0 CHD B:CLA604 3.7 41.6 1.0 C14 B:CLA612 4.1 54.9 1.0 C3D B:CLA604 4.3 45.1 1.0 CG B:HIS455 4.3 49.8 1.0 ND1 B:HIS455 4.3 46.2 1.0 C3B B:CLA604 4.3 42.6 1.0 C2B B:CLA604 4.4 42.0 1.0 C2C B:CLA604 4.4 40.5 1.0 C3A B:CLA604 4.4 47.3 1.0 C3C B:CLA604 4.5 41.0 1.0 C2A B:CLA604 4.5 47.6 1.0 C2D B:CLA604 4.5 42.3 1.0 C15 B:CLA612 4.5 58.0 1.0 C13 B:CLA612 4.8 60.0 1.0 CBD B:CLA604 5.0 44.3 1.0

Magnesium binding site 9 out of 72 in the Photosystem II Structure in the S1 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 S1 State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:48.6 occ:1.00 MG B:CLA605 0.0 48.6 1.0 ND B:CLA605 2.0 46.2 1.0 NB B:CLA605 2.1 43.7 1.0 NC B:CLA605 2.1 44.8 1.0 NA B:CLA605 2.1 45.1 1.0 NE2 B:HIS100 2.2 50.0 1.0 C4D B:CLA605 3.0 41.7 1.0 C1C B:CLA605 3.0 45.0 1.0 C4B B:CLA605 3.0 44.0 1.0 C1B B:CLA605 3.1 44.1 1.0 C4A B:CLA605 3.1 44.7 1.0 C1A B:CLA605 3.1 46.0 1.0 CE1 B:HIS100 3.1 45.6 1.0 C4C B:CLA605 3.2 42.3 1.0 CD2 B:HIS100 3.2 44.8 1.0 C1D B:CLA605 3.3 43.5 1.0 CHB B:CLA605 3.4 43.9 1.0 CHC B:CLA605 3.4 43.8 1.0 CHA B:CLA605 3.5 41.8 1.0 CHD B:CLA605 3.7 43.2 1.0 C1 B:CLA604 4.1 61.3 1.0 C3D B:CLA605 4.3 41.2 1.0 ND1 B:HIS100 4.3 43.2 1.0 CG B:HIS100 4.4 47.9 1.0 C3B B:CLA605 4.4 44.8 1.0 C2C B:CLA605 4.4 44.5 1.0 C2B B:CLA605 4.4 45.2 1.0 C3A B:CLA605 4.4 43.3 1.0 C2A B:CLA605 4.4 44.5 1.0 C3C B:CLA605 4.5 51.3 1.0 C2D B:CLA605 4.5 46.7 1.0 C4 B:CLA606 4.7 47.5 1.0 C2 B:CLA604 4.8 67.7 1.0 CBD B:CLA605 4.9 44.4 1.0

Magnesium binding site 10 out of 72 in the Photosystem II Structure in the S1 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 S1 State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:55.4 occ:1.00 MG B:CLA606 0.0 55.4 1.0 ND B:CLA606 2.0 61.1 1.0 NB B:CLA606 2.0 46.9 1.0 NC B:CLA606 2.1 53.0 1.0 NA B:CLA606 2.1 56.1 1.0 ND1 B:HIS157 2.2 53.6 1.0 CE1 B:HIS157 2.9 58.9 1.0 C4D B:CLA606 3.0 56.0 1.0 C1C B:CLA606 3.0 51.7 1.0 C1B B:CLA606 3.0 55.5 1.0 C4B B:CLA606 3.0 51.5 1.0 C4A B:CLA606 3.1 52.2 1.0 C1A B:CLA606 3.1 48.9 1.0 C4C B:CLA606 3.1 49.4 1.0 C1D B:CLA606 3.3 56.2 1.0 CHB B:CLA606 3.4 45.6 1.0 CHC B:CLA606 3.4 51.0 1.0 CG B:HIS157 3.4 53.9 1.0 CHA B:CLA606 3.5 48.4 1.0 CHD B:CLA606 3.7 52.2 1.0 CB B:HIS157 4.0 53.6 1.0 C16 B:UNL625 4.0 59.0 1.0 NE2 B:HIS157 4.1 50.9 1.0 C3D B:CLA606 4.2 60.4 1.0 C15 B:UNL625 4.3 67.3 1.0 C3B B:CLA606 4.4 51.7 1.0 C2C B:CLA606 4.4 52.3 1.0 C2B B:CLA606 4.4 46.0 1.0 CD2 B:HIS157 4.4 47.9 1.0 C3C B:CLA606 4.4 52.0 1.0 C3A B:CLA606 4.5 45.1 1.0 C2A B:CLA606 4.5 51.0 1.0 C2D B:CLA606 4.5 57.9 1.0 C14 B:UNL625 4.9 70.5 1.0 CBD B:CLA606 4.9 58.8 1.0 CD B:PRO164 5.0 56.1 1.0

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