Magnesium in PDB 5b5e: Crystal Structure Analysis of Photosystem II Complex

All present enzymatic activity of Crystal Structure Analysis of Photosystem II Complex:
1.10.3.9;

The structure of Crystal Structure Analysis of Photosystem II Complex, PDB code: 5b5e was solved by A.Tanaka, Y.Fukushima, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.98 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	121.404, 228.224, 286.429, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.2

The structure of Crystal Structure Analysis of Photosystem II Complex also contains other interesting chemical elements:

Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Calcium	(Ca)	7 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 Crystal Structure Analysis of Photosystem II Complex (pdb code 5b5e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 72 binding sites of Magnesium where determined in the Crystal Structure Analysis of Photosystem II Complex, PDB code: 5b5e:
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 Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:19.2 occ:1.00 MG A:CLA405 0.0 19.2 1.0 ND A:CLA405 1.9 17.0 1.0 NC A:CLA405 2.1 16.8 1.0 NA A:CLA405 2.1 17.6 1.0 NB A:CLA405 2.1 17.2 1.0 NE2 A:HIS198 2.1 18.9 1.0 C4D A:CLA405 2.9 17.3 1.0 C1A A:CLA405 3.1 16.6 1.0 C1C A:CLA405 3.1 14.7 1.0 C1D A:CLA405 3.1 16.2 1.0 C4A A:CLA405 3.1 17.4 1.0 CD2 A:HIS198 3.1 17.1 1.0 C4B A:CLA405 3.1 15.3 1.0 CE1 A:HIS198 3.1 16.7 1.0 C1B A:CLA405 3.1 16.4 1.0 C4C A:CLA405 3.2 14.8 1.0 CHA A:CLA405 3.4 16.7 1.0 CHC A:CLA405 3.5 15.3 1.0 CHB A:CLA405 3.5 16.2 1.0 CHD A:CLA405 3.6 15.2 1.0 CE A:MET183 4.1 15.9 1.0 C3D A:CLA405 4.1 15.5 1.0 ND1 A:HIS198 4.3 17.4 1.0 CG A:HIS198 4.3 17.3 1.0 C2D A:CLA405 4.3 16.2 1.0 C3A A:CLA405 4.4 17.9 1.0 C2C A:CLA405 4.4 14.5 1.0 C3B A:CLA405 4.4 15.1 1.0 C2A A:CLA405 4.4 18.5 1.0 C2B A:CLA405 4.4 16.9 1.0 CAB D:CLA403 4.5 18.2 1.0 C3C A:CLA405 4.5 14.4 1.0 CBD A:CLA405 4.9 18.1 1.0 CMA A:CLA405 4.9 19.3 1.0

Magnesium binding site 2 out of 72 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:20.2 occ:1.00 MG A:CLA406 0.0 20.2 1.0 NB A:CLA406 2.0 19.9 1.0 ND A:CLA406 2.0 20.8 1.0 NC A:CLA406 2.1 20.3 1.0 O A:HOH637 2.1 19.7 1.0 NA A:CLA406 2.2 18.8 1.0 C4D A:CLA406 2.9 18.7 1.0 C4B A:CLA406 3.0 19.0 1.0 C1B A:CLA406 3.0 18.8 1.0 C1C A:CLA406 3.1 19.0 1.0 C4C A:CLA406 3.1 18.9 1.0 C4A A:CLA406 3.1 19.6 1.0 C1D A:CLA406 3.1 18.8 1.0 C1A A:CLA406 3.2 18.8 1.0 CHB A:CLA406 3.4 18.4 1.0 CHC A:CLA406 3.4 18.0 1.0 CHD A:CLA406 3.5 18.5 1.0 CHA A:CLA406 3.6 18.5 1.0 CBB D:PHO402 3.9 17.7 1.0 O A:HOH621 4.1 20.1 1.0 C3D A:CLA406 4.2 18.2 1.0 C3B A:CLA406 4.3 20.0 1.0 C2B A:CLA406 4.3 18.7 1.0 C2D A:CLA406 4.3 19.1 1.0 C3C A:CLA406 4.4 19.7 1.0 C2C A:CLA406 4.4 19.0 1.0 C3A A:CLA406 4.4 18.9 1.0 C2A A:CLA406 4.5 20.2 1.0 CG2 D:ILE178 4.5 18.8 1.0 CE1 A:PHE206 4.7 18.9 1.0 C20 D:PHO402 4.9 19.9 1.0 CG1 D:ILE178 4.9 20.1 1.0 CBA A:CLA406 4.9 20.9 1.0 CBD A:CLA406 5.0 20.7 1.0 C19 D:PHO402 5.0 20.3 1.0

Magnesium binding site 3 out of 72 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:23.2 occ:1.00 MG A:CLA408 0.0 23.2 1.0 ND A:CLA408 1.9 21.4 1.0 NB A:CLA408 2.0 21.1 1.0 NC A:CLA408 2.1 22.8 1.0 NA A:CLA408 2.2 21.4 1.0 NE2 A:HIS118 2.2 19.0 1.0 C4D A:CLA408 2.9 21.5 1.0 C4A A:CLA408 3.1 21.0 1.0 C4B A:CLA408 3.1 20.4 1.0 CE1 A:HIS118 3.1 20.9 1.0 C1D A:CLA408 3.1 20.2 1.0 C1B A:CLA408 3.1 20.7 1.0 C1A A:CLA408 3.1 19.6 1.0 C4C A:CLA408 3.1 21.6 1.0 C1C A:CLA408 3.2 19.3 1.0 CD2 A:HIS118 3.2 23.9 1.0 CHB A:CLA408 3.4 20.6 1.0 CHA A:CLA408 3.5 19.2 1.0 CHC A:CLA408 3.5 19.3 1.0 CHD A:CLA408 3.6 18.7 1.0 C3D A:CLA408 4.1 19.5 1.0 C2D A:CLA408 4.3 19.3 1.0 ND1 A:HIS118 4.3 19.9 1.0 CG1 I:VAL8 4.3 23.6 1.0 C3B A:CLA408 4.4 19.6 1.0 CG A:HIS118 4.4 19.9 1.0 C2B A:CLA408 4.4 20.1 1.0 C3A A:CLA408 4.4 21.3 1.0 C3C A:CLA408 4.4 20.8 1.0 C2C A:CLA408 4.5 19.8 1.0 C2A A:CLA408 4.5 20.4 1.0 CG2 I:VAL12 4.5 27.5 1.0 CBD A:CLA408 4.9 23.1 1.0 CMA A:CLA408 5.0 20.8 1.0

Magnesium binding site 4 out of 72 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:35.5 occ:1.00 MG B:CLA602 0.0 35.5 1.0 NC B:CLA602 2.0 33.2 1.0 NB B:CLA602 2.1 33.7 1.0 ND B:CLA602 2.1 36.4 1.0 O B:HOH712 2.2 33.0 1.0 NA B:CLA602 2.3 35.2 1.0 C4B B:CLA602 3.0 31.5 1.0 C1C B:CLA602 3.0 31.6 1.0 C4C B:CLA602 3.0 31.9 1.0 C4D B:CLA602 3.1 40.5 1.0 C1B B:CLA602 3.1 31.1 1.0 C1A B:CLA602 3.2 40.3 1.0 C4A B:CLA602 3.2 37.3 1.0 C1D B:CLA602 3.2 38.1 1.0 CHC B:CLA602 3.4 30.4 1.0 CHB B:CLA602 3.6 36.2 1.0 CHD B:CLA602 3.6 32.7 1.0 CHA B:CLA602 3.7 38.6 1.0 C10 B:CLA602 4.0 52.9 1.0 C8 B:CLA602 4.0 54.5 1.0 CE2 B:PHE190 4.1 30.6 1.0 O B:TRP185 4.2 35.8 1.0 C3B B:CLA602 4.3 31.5 1.0 C3C B:CLA602 4.3 31.1 1.0 C2C B:CLA602 4.3 30.2 1.0 C3D B:CLA602 4.3 39.5 1.0 C2B B:CLA602 4.4 30.1 1.0 CZ B:PHE190 4.5 30.2 1.0 C2D B:CLA602 4.5 40.0 1.0 C3A B:CLA602 4.5 38.2 1.0 C11 B:CLA602 4.6 49.5 1.0 CBB B:CLA603 4.6 28.4 1.0 C12 B:CLA602 4.6 51.6 1.0 C2A B:CLA602 4.6 40.6 1.0 O B:HOH747 4.7 32.7 1.0 C9 B:CLA602 4.9 55.5 1.0

Magnesium binding site 5 out of 72 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:29.3 occ:1.00 MG B:CLA603 0.0 29.3 1.0 NB B:CLA603 2.1 29.1 1.0 ND B:CLA603 2.1 25.5 1.0 NC B:CLA603 2.1 27.4 1.0 ND1 B:HIS201 2.2 23.3 1.0 NA B:CLA603 2.2 26.2 1.0 CE1 B:HIS201 2.9 23.6 1.0 C4B B:CLA603 3.0 28.6 1.0 C4D B:CLA603 3.0 26.6 1.0 C1B B:CLA603 3.1 27.4 1.0 C1C B:CLA603 3.1 28.4 1.0 C4C B:CLA603 3.1 28.2 1.0 C4A B:CLA603 3.2 26.6 1.0 C1D B:CLA603 3.2 25.6 1.0 C1A B:CLA603 3.2 27.5 1.0 CG B:HIS201 3.3 23.2 1.0 CHC B:CLA603 3.4 26.0 1.0 CHB B:CLA603 3.5 25.6 1.0 CHD B:CLA603 3.6 26.7 1.0 CHA B:CLA603 3.6 24.2 1.0 CB B:HIS201 3.8 25.8 1.0 CZ H:PHE41 3.8 29.1 1.0 NE2 B:HIS201 4.2 24.9 1.0 CE1 H:PHE41 4.3 27.4 1.0 C3D B:CLA603 4.3 24.1 1.0 CA B:HIS201 4.3 25.0 1.0 C3B B:CLA603 4.3 30.1 1.0 CD2 B:HIS201 4.4 21.4 1.0 C2B B:CLA603 4.4 28.9 1.0 C2D B:CLA603 4.4 26.4 1.0 C3C B:CLA603 4.4 26.3 1.0 C2C B:CLA603 4.4 28.6 1.0 C3A B:CLA603 4.5 25.6 1.0 C2A B:CLA603 4.5 24.0 1.0 O B:HIS201 5.0 24.2 1.0 CE2 H:PHE41 5.0 29.6 1.0 CMA B:CLA603 5.0 26.8 1.0

Magnesium binding site 6 out of 72 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:21.8 occ:1.00 MG B:CLA604 0.0 21.8 1.0 NB B:CLA604 2.0 21.2 1.0 ND B:CLA604 2.1 21.2 1.0 NC B:CLA604 2.1 21.0 1.0 NA B:CLA604 2.2 20.8 1.0 NE2 B:HIS202 2.2 23.9 1.0 C4B B:CLA604 3.0 20.1 1.0 C4D B:CLA604 3.0 19.9 1.0 C1B B:CLA604 3.0 20.4 1.0 CD2 B:HIS202 3.1 25.9 1.0 C1A B:CLA604 3.1 20.2 1.0 C4C B:CLA604 3.1 20.3 1.0 C4A B:CLA604 3.1 20.5 1.0 C1C B:CLA604 3.2 20.7 1.0 C1D B:CLA604 3.2 20.1 1.0 CE1 B:HIS202 3.3 25.5 1.0 CHB B:CLA604 3.5 21.6 1.0 CHC B:CLA604 3.5 20.1 1.0 CHA B:CLA604 3.5 19.4 1.0 CHD B:CLA604 3.6 20.6 1.0 C3D B:CLA604 4.3 20.4 1.0 CG B:HIS202 4.3 26.1 1.0 C3B B:CLA604 4.3 20.6 1.0 C2B B:CLA604 4.3 21.2 1.0 ND1 B:HIS202 4.4 28.0 1.0 C3C B:CLA604 4.4 20.8 1.0 C2D B:CLA604 4.4 22.4 1.0 C2A B:CLA604 4.4 22.7 1.0 C3A B:CLA604 4.5 22.0 1.0 C2C B:CLA604 4.5 19.9 1.0 NE2 B:HIS201 4.6 24.9 1.0 C4 B:CLA606 4.6 27.2 1.0 CD2 B:HIS201 4.6 21.4 1.0 C7 B:CLA606 4.7 31.4 1.0 C6 B:CLA606 4.8 30.0 1.0 C5 B:CLA606 4.9 28.3 1.0 CBD B:CLA604 5.0 22.1 1.0

Magnesium binding site 7 out of 72 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:20.9 occ:1.00 MG B:CLA605 0.0 20.9 1.0 NB B:CLA605 2.0 20.6 1.0 NC B:CLA605 2.1 19.8 1.0 ND B:CLA605 2.1 20.1 1.0 NE2 B:HIS455 2.1 18.6 1.0 NA B:CLA605 2.3 19.2 1.0 C4B B:CLA605 2.9 18.9 1.0 C1B B:CLA605 3.0 18.5 1.0 CD2 B:HIS455 3.0 19.1 1.0 C4D B:CLA605 3.1 19.7 1.0 C1C B:CLA605 3.1 19.3 1.0 C4A B:CLA605 3.2 20.8 1.0 C4C B:CLA605 3.2 19.6 1.0 CE1 B:HIS455 3.2 18.0 1.0 C1D B:CLA605 3.2 20.4 1.0 C1A B:CLA605 3.3 21.1 1.0 CHB B:CLA605 3.4 18.2 1.0 CHC B:CLA605 3.4 18.6 1.0 CHD B:CLA605 3.6 20.1 1.0 CHA B:CLA605 3.7 19.4 1.0 CG B:HIS455 4.2 17.3 1.0 C3B B:CLA605 4.3 18.2 1.0 C2B B:CLA605 4.3 19.3 1.0 ND1 B:HIS455 4.3 18.9 1.0 C14 B:CLA613 4.3 30.5 1.0 C3D B:CLA605 4.3 19.7 1.0 C2C B:CLA605 4.4 19.3 1.0 C3C B:CLA605 4.5 19.4 1.0 C2D B:CLA605 4.5 21.7 1.0 C3A B:CLA605 4.5 19.7 1.0 C2A B:CLA605 4.6 20.6 1.0 C15 B:CLA613 4.9 29.3 1.0 CE2 B:PHE451 4.9 19.9 1.0 C13 B:CLA613 4.9 28.9 1.0

Magnesium binding site 8 out of 72 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:23.7 occ:1.00 MG B:CLA606 0.0 23.7 1.0 ND B:CLA606 2.0 22.8 1.0 NC B:CLA606 2.1 23.6 1.0 NB B:CLA606 2.1 22.1 1.0 NE2 B:HIS100 2.1 18.1 1.0 NA B:CLA606 2.2 22.6 1.0 C4D B:CLA606 3.0 22.0 1.0 CD2 B:HIS100 3.0 19.8 1.0 C4C B:CLA606 3.1 23.2 1.0 C4B B:CLA606 3.1 21.8 1.0 C1B B:CLA606 3.1 22.9 1.0 C1D B:CLA606 3.1 20.5 1.0 CE1 B:HIS100 3.1 19.1 1.0 C1C B:CLA606 3.1 21.8 1.0 C4A B:CLA606 3.2 23.7 1.0 C1A B:CLA606 3.2 20.5 1.0 CHB B:CLA606 3.5 24.1 1.0 CHC B:CLA606 3.5 20.7 1.0 CHD B:CLA606 3.5 22.5 1.0 CHA B:CLA606 3.6 18.8 1.0 C1 B:CLA605 4.2 27.6 1.0 CG B:HIS100 4.2 19.9 1.0 C3D B:CLA606 4.2 20.0 1.0 ND1 B:HIS100 4.2 21.3 1.0 C2 B:CLA605 4.3 32.8 1.0 C2D B:CLA606 4.3 20.1 1.0 C3C B:CLA606 4.4 22.0 1.0 C3B B:CLA606 4.4 21.7 1.0 C2B B:CLA606 4.4 21.2 1.0 C2C B:CLA606 4.4 22.3 1.0 C3A B:CLA606 4.5 21.4 1.0 C2A B:CLA606 4.6 20.5 1.0 C4 B:CLA607 4.9 23.0 1.0

Magnesium binding site 9 out of 72 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:25.8 occ:1.00 MG B:CLA607 0.0 25.8 1.0 NB B:CLA607 2.0 23.0 1.0 ND B:CLA607 2.0 26.7 1.0 NC B:CLA607 2.1 25.0 1.0 ND1 B:HIS157 2.2 23.2 1.0 NA B:CLA607 2.3 23.1 1.0 C4D B:CLA607 3.0 29.5 1.0 CE1 B:HIS157 3.0 26.9 1.0 C4B B:CLA607 3.0 23.9 1.0 C4C B:CLA607 3.1 27.0 1.0 C1B B:CLA607 3.1 24.9 1.0 C1D B:CLA607 3.1 30.1 1.0 C4A B:CLA607 3.2 23.7 1.0 C1C B:CLA607 3.2 24.9 1.0 C1A B:CLA607 3.2 25.0 1.0 CG B:HIS157 3.3 25.9 1.0 CHB B:CLA607 3.4 22.9 1.0 CHD B:CLA607 3.4 28.2 1.0 CHA B:CLA607 3.6 26.5 1.0 CHC B:CLA607 3.6 22.6 1.0 CB B:HIS157 3.7 25.9 1.0 C10 B:UNL627 4.1 38.8 1.0 C9 B:UNL627 4.1 40.9 1.0 C3D B:CLA607 4.3 29.5 1.0 NE2 B:HIS157 4.3 24.6 1.0 C3B B:CLA607 4.3 20.8 1.0 C2D B:CLA607 4.4 33.4 1.0 C2B B:CLA607 4.4 22.1 1.0 CD2 B:HIS157 4.4 26.1 1.0 C3C B:CLA607 4.4 27.7 1.0 C2C B:CLA607 4.5 27.0 1.0 C3A B:CLA607 4.5 21.3 1.0 C8 B:UNL627 4.6 43.2 1.0 C2A B:CLA607 4.6 22.1 1.0 CD B:PRO164 4.8 31.8 1.0 CA B:HIS157 4.9 24.6 1.0

Magnesium binding site 10 out of 72 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg608 b:19.2 occ:1.00 MG B:CLA608 0.0 19.2 1.0 O B:HOH986 2.0 18.7 1.0 NB B:CLA608 2.0 17.7 1.0 NC B:CLA608 2.1 20.5 1.0 ND B:CLA608 2.1 19.5 1.0 NA B:CLA608 2.3 19.3 1.0 C4B B:CLA608 3.0 18.7 1.0 C4D B:CLA608 3.1 18.2 1.0 C1B B:CLA608 3.1 18.1 1.0 C4C B:CLA608 3.1 18.9 1.0 C1C B:CLA608 3.1 19.1 1.0 C1D B:CLA608 3.2 19.4 1.0 C4A B:CLA608 3.2 19.6 1.0 C1A B:CLA608 3.2 17.2 1.0 CHC B:CLA608 3.4 18.2 1.0 CHB B:CLA608 3.5 19.4 1.0 CHD B:CLA608 3.6 18.8 1.0 CHA B:CLA608 3.6 18.0 1.0 C14 B:LMG622 4.0 34.0 1.0 O B:HOH819 4.1 14.7 1.0 SD B:MET37 4.3 19.1 1.0 C3D B:CLA608 4.3 17.7 1.0 C3B B:CLA608 4.4 18.9 1.0 C11 B:LMG622 4.4 36.3 1.0 C2B B:CLA608 4.4 18.1 1.0 C3C B:CLA608 4.4 16.6 1.0 C2C B:CLA608 4.4 18.0 1.0 C2D B:CLA608 4.5 17.9 1.0 CD1 B:PHE61 4.6 18.0 1.0 C3A B:CLA608 4.6 18.7 1.0 C2A B:CLA608 4.6 17.6 1.0 C13 B:LMG622 4.6 31.3 1.0 C12 B:LMG622 4.6 34.3 1.0 CE B:MET37 4.7 15.9 1.0 CB B:PHE61 4.7 18.9 1.0 C15 B:LMG622 4.8 33.5 1.0 CG B:PHE61 4.8 19.5 1.0 O9 B:LMG622 5.0 47.5 1.0

A.Tanaka, Y.Fukushima, N.Kamiya. Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II J. Am. Chem. Soc. V. 139 1718 2017.
ISSN: ESSN 1520-5126
PubMed: 28102667
DOI: 10.1021/JACS.6B09666