Magnesium in PDB 5gth: Native Xfel Structure of Photosystem II (Dark Dataset)

All present enzymatic activity of Native Xfel Structure of Photosystem II (Dark Dataset):
1.10.3.9;

The structure of Native Xfel Structure of Photosystem II (Dark Dataset), PDB code: 5gth 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)	19.98 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	126.520, 231.230, 287.460, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 18.6

The structure of Native Xfel Structure of Photosystem II (Dark Dataset) also contains other interesting chemical elements:

Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Calcium	(Ca)	8 atoms
Chlorine	(Cl)	4 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 Native Xfel Structure of Photosystem II (Dark Dataset) (pdb code 5gth). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 72 binding sites of Magnesium where determined in the Native Xfel Structure of Photosystem II (Dark Dataset), PDB code: 5gth:
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 Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:24.1 occ:1.00 MG A:CLA404 0.0 24.1 1.0 ND A:CLA404 2.0 30.5 1.0 NB A:CLA404 2.0 21.9 1.0 NA A:CLA404 2.1 31.8 1.0 NC A:CLA404 2.1 21.6 1.0 NE2 A:HIS198 2.2 29.1 1.0 C4D A:CLA404 3.0 21.9 1.0 C4B A:CLA404 3.0 23.1 1.0 C4A A:CLA404 3.0 25.0 1.0 C1C A:CLA404 3.0 24.1 1.0 C1A A:CLA404 3.0 22.2 1.0 C1B A:CLA404 3.1 22.1 1.0 CE1 A:HIS198 3.1 32.8 1.0 C4C A:CLA404 3.2 21.5 1.0 CD2 A:HIS198 3.3 27.3 1.0 C1D A:CLA404 3.3 21.7 1.0 CHB A:CLA404 3.4 22.2 1.0 CHC A:CLA404 3.4 21.6 1.0 CHA A:CLA404 3.5 22.1 1.0 CHD A:CLA404 3.7 21.6 1.0 CE A:MET183 4.0 25.7 1.0 C3D A:CLA404 4.3 22.5 1.0 ND1 A:HIS198 4.3 23.1 1.0 C3B A:CLA404 4.3 22.4 1.0 CG A:HIS198 4.4 28.0 1.0 C2B A:CLA404 4.4 22.1 1.0 C2A A:CLA404 4.4 22.4 1.0 C2C A:CLA404 4.4 28.6 1.0 C3A A:CLA404 4.4 24.5 1.0 CAB D:CLA404 4.4 21.2 1.0 C3C A:CLA404 4.5 25.2 1.0 C2D A:CLA404 4.5 23.4 1.0 CBD A:CLA404 4.9 24.4 1.0

Magnesium binding site 2 out of 72 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:29.1 occ:1.00 MG A:CLA405 0.0 29.1 1.0 ND A:CLA405 2.0 22.0 1.0 NB A:CLA405 2.0 20.9 1.0 NC A:CLA405 2.1 24.5 1.0 NA A:CLA405 2.1 47.2 1.0 O A:HOH594 2.2 22.2 1.0 C4D A:CLA405 3.0 23.2 1.0 C1C A:CLA405 3.0 21.2 1.0 C1B A:CLA405 3.0 23.6 1.0 C4A A:CLA405 3.0 29.2 1.0 C4B A:CLA405 3.0 23.6 1.0 C1A A:CLA405 3.1 20.1 1.0 C4C A:CLA405 3.1 20.9 1.0 C1D A:CLA405 3.3 20.7 1.0 CHB A:CLA405 3.4 22.3 1.0 CHC A:CLA405 3.4 21.3 1.0 CHA A:CLA405 3.5 27.7 1.0 CHD A:CLA405 3.7 20.6 1.0 CBB D:PHO401 3.9 23.9 1.0 O A:HOH599 3.9 23.0 1.0 C3D A:CLA405 4.3 20.0 1.0 C3B A:CLA405 4.4 21.4 1.0 C2B A:CLA405 4.4 25.2 1.0 C2C A:CLA405 4.4 37.1 1.0 C2A A:CLA405 4.4 39.3 1.0 C3C A:CLA405 4.4 27.7 1.0 C3A A:CLA405 4.4 31.2 1.0 CG2 A:THR179 4.5 20.2 1.0 C2D A:CLA405 4.5 22.6 1.0 OG1 A:THR179 4.7 20.1 1.0 C19 D:PHO401 4.8 24.6 1.0 CBA A:CLA405 4.9 20.6 1.0 CBD A:CLA405 4.9 27.6 1.0

Magnesium binding site 3 out of 72 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:24.4 occ:1.00 MG A:CLA406 0.0 24.4 1.0 ND A:CLA406 2.0 24.9 1.0 NB A:CLA406 2.0 24.9 1.0 NC A:CLA406 2.1 25.7 1.0 NA A:CLA406 2.1 25.9 1.0 O A:HOH606 2.2 31.9 1.0 C1C A:CLA406 3.0 23.8 1.0 C4D A:CLA406 3.0 24.1 1.0 C4A A:CLA406 3.0 29.2 1.0 C4B A:CLA406 3.0 24.8 1.0 C1B A:CLA406 3.0 25.5 1.0 C1A A:CLA406 3.1 30.6 1.0 C4C A:CLA406 3.1 23.3 1.0 C1D A:CLA406 3.3 23.4 1.0 CHB A:CLA406 3.4 28.8 1.0 CHC A:CLA406 3.4 24.3 1.0 CHA A:CLA406 3.5 33.2 1.0 CHD A:CLA406 3.7 35.6 1.0 CBB A:PHO407 3.8 32.8 1.0 C3D A:CLA406 4.3 23.8 1.0 C3B A:CLA406 4.3 25.4 1.0 C2C A:CLA406 4.3 23.3 1.0 C2B A:CLA406 4.4 25.8 1.0 C3A A:CLA406 4.4 26.0 1.0 C2A A:CLA406 4.4 27.4 1.0 O A:HOH583 4.4 36.9 1.0 C3C A:CLA406 4.4 32.2 1.0 C2D A:CLA406 4.5 23.3 1.0 C20 A:PHO407 4.5 30.6 1.0 CG2 D:ILE178 4.8 23.4 1.0 CBD A:CLA406 4.9 27.2 1.0 CBA A:CLA406 5.0 41.1 1.0 CE1 A:PHE206 5.0 26.1 1.0

Magnesium binding site 4 out of 72 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:30.7 occ:1.00 MG A:CLA408 0.0 30.7 1.0 ND A:CLA408 2.0 27.2 1.0 NB A:CLA408 2.0 37.4 1.0 NC A:CLA408 2.1 27.5 1.0 NA A:CLA408 2.1 45.5 1.0 NE2 A:HIS118 2.2 26.8 1.0 C4D A:CLA408 3.0 32.0 1.0 C1C A:CLA408 3.0 27.8 1.0 CE1 A:HIS118 3.0 31.2 1.0 C4B A:CLA408 3.0 33.5 1.0 C1B A:CLA408 3.0 31.1 1.0 C4A A:CLA408 3.0 39.1 1.0 C1A A:CLA408 3.1 45.1 1.0 C4C A:CLA408 3.2 27.4 1.0 C1D A:CLA408 3.3 31.5 1.0 CD2 A:HIS118 3.3 34.8 1.0 CHC A:CLA408 3.4 46.4 1.0 CHB A:CLA408 3.4 28.0 1.0 CHA A:CLA408 3.4 34.3 1.0 CHD A:CLA408 3.7 29.1 1.0 ND1 A:HIS118 4.2 26.8 1.0 C3D A:CLA408 4.2 35.8 1.0 C3B A:CLA408 4.3 36.6 1.0 C2C A:CLA408 4.4 36.7 1.0 C2B A:CLA408 4.4 29.1 1.0 CG A:HIS118 4.4 25.6 1.0 C3A A:CLA408 4.4 36.1 1.0 C2A A:CLA408 4.4 45.4 1.0 C3C A:CLA408 4.4 27.7 1.0 CG1 I:VAL8 4.5 29.2 1.0 C2D A:CLA408 4.5 26.9 1.0 CG2 I:VAL12 4.7 29.9 1.0 CBD A:CLA408 4.9 26.9 1.0

Magnesium binding site 5 out of 72 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:57.0 occ:1.00 MG B:CLA601 0.0 57.0 1.0 NB B:CLA601 2.0 41.5 1.0 ND B:CLA601 2.0 43.7 1.0 NC B:CLA601 2.1 46.5 1.0 NA B:CLA601 2.1 71.3 1.0 O B:HOH809 2.2 44.4 1.0 C4D B:CLA601 3.0 45.1 1.0 C1C B:CLA601 3.0 47.6 1.0 C4B B:CLA601 3.0 50.2 1.0 C4A B:CLA601 3.0 68.1 1.0 C1B B:CLA601 3.0 46.2 1.0 C1A B:CLA601 3.1 62.6 1.0 C4C B:CLA601 3.1 52.5 1.0 C1D B:CLA601 3.3 53.3 1.0 CHC B:CLA601 3.4 52.5 1.0 CHB B:CLA601 3.4 56.3 1.0 CHA B:CLA601 3.5 54.5 1.0 C10 B:CLA601 3.7 55.4 1.0 CHD B:CLA601 3.7 39.5 1.0 C3D B:CLA601 4.3 50.2 1.0 C12 B:CLA601 4.3 54.0 1.0 C3B B:CLA601 4.4 42.6 1.0 C2C B:CLA601 4.4 52.5 1.0 O B:TRP185 4.4 44.4 1.0 C2B B:CLA601 4.4 40.5 1.0 C3A B:CLA601 4.4 64.2 1.0 C2A B:CLA601 4.4 59.0 1.0 C3C B:CLA601 4.4 49.4 1.0 CBB B:CLA602 4.5 55.0 1.0 C2D B:CLA601 4.5 60.0 1.0 CE2 B:PHE190 4.5 38.2 1.0 C11 B:CLA601 4.6 49.1 1.0 O B:HOH703 4.7 86.2 1.0 C8 B:CLA601 4.7 58.1 1.0 C7 B:CLA601 4.8 59.4 1.0 CZ B:PHE190 4.8 35.9 1.0 CBD B:CLA601 4.9 52.9 1.0

Magnesium binding site 6 out of 72 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:37.6 occ:1.00 MG B:CLA602 0.0 37.6 1.0 ND B:CLA602 2.0 34.0 1.0 NB B:CLA602 2.0 43.2 1.0 NC B:CLA602 2.1 42.9 1.0 NA B:CLA602 2.1 41.1 1.0 ND1 B:HIS201 2.2 40.1 1.0 CE1 B:HIS201 3.0 39.6 1.0 C4D B:CLA602 3.0 31.1 1.0 C1C B:CLA602 3.0 46.6 1.0 C4B B:CLA602 3.0 36.9 1.0 C4A B:CLA602 3.0 42.6 1.0 C1B B:CLA602 3.1 42.5 1.0 C1A B:CLA602 3.1 36.0 1.0 C4C B:CLA602 3.2 36.0 1.0 C1D B:CLA602 3.3 34.8 1.0 CG B:HIS201 3.3 42.6 1.0 CHC B:CLA602 3.4 42.7 1.0 CHB B:CLA602 3.4 32.9 1.0 CHA B:CLA602 3.5 36.4 1.0 CHD B:CLA602 3.7 32.9 1.0 CB B:HIS201 3.8 34.2 1.0 CZ H:PHE41 3.9 46.8 1.0 NE2 B:HIS201 4.1 37.8 1.0 C3D B:CLA602 4.3 37.1 1.0 CD2 B:HIS201 4.3 31.4 1.0 C3B B:CLA602 4.3 37.9 1.0 C2C B:CLA602 4.4 46.6 1.0 C2B B:CLA602 4.4 34.7 1.0 C3A B:CLA602 4.4 38.2 1.0 C2A B:CLA602 4.4 33.1 1.0 CE2 H:PHE41 4.4 43.8 1.0 C3C B:CLA602 4.4 34.4 1.0 CA B:HIS201 4.5 38.6 1.0 C2D B:CLA602 4.5 33.3 1.0 CE1 B:PHE190 4.9 44.8 1.0 CBD B:CLA602 4.9 37.7 1.0

Magnesium binding site 7 out of 72 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:30.2 occ:1.00 MG B:CLA603 0.0 30.2 1.0 ND B:CLA603 2.0 30.9 1.0 NB B:CLA603 2.0 41.7 1.0 NC B:CLA603 2.1 49.5 1.0 NA B:CLA603 2.1 38.7 1.0 NE2 B:HIS202 2.2 29.9 1.0 C4D B:CLA603 3.0 38.7 1.0 C1C B:CLA603 3.0 35.3 1.0 C4B B:CLA603 3.0 39.8 1.0 C1B B:CLA603 3.0 33.9 1.0 C4A B:CLA603 3.0 38.2 1.0 C1A B:CLA603 3.1 32.8 1.0 CD2 B:HIS202 3.1 33.1 1.0 C4C B:CLA603 3.2 29.3 1.0 CE1 B:HIS202 3.2 44.7 1.0 C1D B:CLA603 3.3 52.0 1.0 CHB B:CLA603 3.4 41.1 1.0 CHC B:CLA603 3.4 33.3 1.0 CHA B:CLA603 3.5 41.9 1.0 CHD B:CLA603 3.7 54.8 1.0 C3D B:CLA603 4.3 36.3 1.0 CG B:HIS202 4.3 34.1 1.0 C6 B:CLA605 4.3 36.6 1.0 ND1 B:HIS202 4.3 30.8 1.0 C3B B:CLA603 4.3 38.9 1.0 C2B B:CLA603 4.4 46.5 1.0 C2C B:CLA603 4.4 30.0 1.0 C2A B:CLA603 4.4 44.7 1.0 C3A B:CLA603 4.4 33.1 1.0 C3C B:CLA603 4.4 40.0 1.0 C2D B:CLA603 4.5 46.3 1.0 C7 B:CLA605 4.8 45.7 1.0 C4 B:CLA605 4.9 48.3 1.0 CBD B:CLA603 4.9 45.9 1.0 CBA B:CLA603 5.0 26.7 1.0 NE2 B:HIS201 5.0 37.8 1.0

Magnesium binding site 8 out of 72 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:22.8 occ:1.00 MG B:CLA604 0.0 22.8 1.0 ND B:CLA604 2.0 23.5 1.0 NB B:CLA604 2.0 22.0 1.0 NC B:CLA604 2.1 41.3 1.0 NA B:CLA604 2.1 24.9 1.0 NE2 B:HIS455 2.2 26.2 1.0 C4D B:CLA604 3.0 23.8 1.0 C4B B:CLA604 3.0 22.8 1.0 C1B B:CLA604 3.0 21.8 1.0 C4A B:CLA604 3.0 27.9 1.0 C1C B:CLA604 3.0 22.4 1.0 C1A B:CLA604 3.1 26.7 1.0 CE1 B:HIS455 3.1 30.1 1.0 C4C B:CLA604 3.2 23.2 1.0 CD2 B:HIS455 3.2 27.5 1.0 C1D B:CLA604 3.2 23.9 1.0 CHB B:CLA604 3.4 22.6 1.0 CHC B:CLA604 3.4 22.0 1.0 CHA B:CLA604 3.5 23.7 1.0 CHD B:CLA604 3.7 33.4 1.0 C14 B:CLA612 4.1 28.6 1.0 C3D B:CLA604 4.2 24.4 1.0 ND1 B:HIS455 4.3 23.8 1.0 CG B:HIS455 4.3 28.9 1.0 C3B B:CLA604 4.3 25.1 1.0 C2B B:CLA604 4.4 21.3 1.0 C2C B:CLA604 4.4 22.6 1.0 C3A B:CLA604 4.4 32.7 1.0 C2A B:CLA604 4.4 36.2 1.0 C3C B:CLA604 4.4 31.4 1.0 C2D B:CLA604 4.5 26.9 1.0 C15 B:CLA612 4.6 30.6 1.0 C13 B:CLA612 4.8 35.1 1.0 CE1 B:PHE451 4.9 24.4 1.0 CBD B:CLA604 4.9 34.2 1.0

Magnesium binding site 9 out of 72 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:32.5 occ:1.00 MG B:CLA605 0.0 32.5 1.0 ND B:CLA605 2.0 24.1 1.0 NB B:CLA605 2.1 25.8 1.0 NC B:CLA605 2.1 31.1 1.0 NA B:CLA605 2.1 25.3 1.0 NE2 B:HIS100 2.2 32.5 1.0 C4D B:CLA605 3.0 23.8 1.0 C1C B:CLA605 3.0 25.4 1.0 C4B B:CLA605 3.0 26.2 1.0 C1A B:CLA605 3.1 28.0 1.0 C4A B:CLA605 3.1 27.9 1.0 C1B B:CLA605 3.1 42.3 1.0 C4C B:CLA605 3.1 28.3 1.0 CE1 B:HIS100 3.2 25.0 1.0 CD2 B:HIS100 3.2 27.4 1.0 C1D B:CLA605 3.3 43.1 1.0 CHC B:CLA605 3.4 26.4 1.0 CHB B:CLA605 3.4 26.0 1.0 CHA B:CLA605 3.5 32.3 1.0 CHD B:CLA605 3.7 23.9 1.0 C1 B:CLA604 4.0 26.1 1.0 ND1 B:HIS100 4.3 32.2 1.0 C3D B:CLA605 4.3 39.8 1.0 CG B:HIS100 4.3 26.4 1.0 C3B B:CLA605 4.3 31.7 1.0 C2C B:CLA605 4.4 27.2 1.0 C2B B:CLA605 4.4 26.9 1.0 C2A B:CLA605 4.4 29.5 1.0 C3A B:CLA605 4.4 29.2 1.0 C3C B:CLA605 4.4 24.7 1.0 C2D B:CLA605 4.5 28.2 1.0 C2 B:CLA604 4.7 44.6 1.0 CBD B:CLA605 4.9 26.7 1.0

Magnesium binding site 10 out of 72 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:32.7 occ:1.00 MG B:CLA606 0.0 32.7 1.0 ND B:CLA606 2.0 35.0 1.0 NB B:CLA606 2.0 28.9 1.0 NC B:CLA606 2.1 32.5 1.0 NA B:CLA606 2.1 28.4 1.0 ND1 B:HIS157 2.2 43.8 1.0 CE1 B:HIS157 2.7 46.2 1.0 C4D B:CLA606 3.0 38.1 1.0 C1C B:CLA606 3.0 30.7 1.0 C1B B:CLA606 3.0 40.9 1.0 C4B B:CLA606 3.0 29.2 1.0 C4A B:CLA606 3.1 33.8 1.0 C1A B:CLA606 3.1 32.0 1.0 C4C B:CLA606 3.1 36.0 1.0 C1D B:CLA606 3.3 36.0 1.0 CHB B:CLA606 3.4 27.6 1.0 CHC B:CLA606 3.4 30.1 1.0 CHA B:CLA606 3.5 33.5 1.0 CG B:HIS157 3.5 41.6 1.0 CHD B:CLA606 3.7 32.3 1.0 NE2 B:HIS157 4.0 31.0 1.0 C15 B:UNL628 4.1 41.4 1.0 C16 B:UNL628 4.1 29.7 1.0 CB B:HIS157 4.2 37.5 1.0 C3D B:CLA606 4.3 41.5 1.0 C3B B:CLA606 4.4 37.9 1.0 C2B B:CLA606 4.4 27.9 1.0 CD2 B:HIS157 4.4 29.8 1.0 C2C B:CLA606 4.4 40.6 1.0 C3C B:CLA606 4.4 32.1 1.0 C3A B:CLA606 4.4 27.1 1.0 C2A B:CLA606 4.4 31.9 1.0 C2D B:CLA606 4.5 38.7 1.0 C14 B:UNL628 4.6 36.8 1.0 CBD B:CLA606 4.9 37.1 1.0 C17 B:UNL628 5.0 44.7 1.0

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