Magnesium in PDB 3wu2: Crystal Structure Analysis of Photosystem II Complex

The structure of Crystal Structure Analysis of Photosystem II Complex, PDB code: 3wu2 was solved by Y.Umena, K.Kawakami, J.R.Shen, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	122.190, 228.510, 286.400, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 19.4

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

Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Chlorine	(Cl)	4 atoms
Calcium	(Ca)	9 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 3wu2). 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: 3wu2:
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:20.9 occ:1.00 MG A:CLA405 0.0 20.9 1.0 ND A:CLA405 2.0 18.7 1.0 NC A:CLA405 2.1 19.4 1.0 NB A:CLA405 2.1 18.7 1.0 NE2 A:HIS198 2.1 20.5 1.0 NA A:CLA405 2.2 18.9 1.0 C4D A:CLA405 2.9 18.5 1.0 C1C A:CLA405 3.1 17.5 1.0 CE1 A:HIS198 3.1 17.9 1.0 C1D A:CLA405 3.1 17.7 1.0 C4B A:CLA405 3.1 19.3 1.0 C4C A:CLA405 3.1 16.7 1.0 C1B A:CLA405 3.1 18.6 1.0 C4A A:CLA405 3.2 18.6 1.0 C1A A:CLA405 3.2 19.2 1.0 CD2 A:HIS198 3.2 19.3 1.0 CHC A:CLA405 3.5 17.3 1.0 CHA A:CLA405 3.5 18.6 1.0 CHB A:CLA405 3.5 17.0 1.0 CHD A:CLA405 3.6 18.9 1.0 CE A:MET183 4.1 17.7 1.0 C3D A:CLA405 4.2 17.6 1.0 ND1 A:HIS198 4.3 18.5 1.0 CG A:HIS198 4.3 18.7 1.0 C2D A:CLA405 4.3 18.7 1.0 C2C A:CLA405 4.4 15.8 1.0 C3B A:CLA405 4.4 17.3 1.0 C3C A:CLA405 4.4 17.0 1.0 CAB D:CLA402 4.4 18.1 1.0 C2B A:CLA405 4.4 19.6 1.0 C3A A:CLA405 4.5 19.3 1.0 C2A A:CLA405 4.5 17.8 1.0 CBD A:CLA405 5.0 19.4 1.0 CMA A:CLA405 5.0 19.7 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:18.1 occ:1.00 MG A:CLA406 0.0 18.1 1.0 O A:HOH552 2.0 16.0 1.0 NB A:CLA406 2.0 18.3 1.0 ND A:CLA406 2.1 16.1 1.0 NC A:CLA406 2.1 20.0 1.0 NA A:CLA406 2.1 16.9 1.0 C4D A:CLA406 2.9 16.8 1.0 C4B A:CLA406 3.0 19.9 1.0 C1B A:CLA406 3.0 18.7 1.0 C1C A:CLA406 3.1 17.4 1.0 C4C A:CLA406 3.1 18.1 1.0 C4A A:CLA406 3.1 18.5 1.0 C1D A:CLA406 3.1 17.1 1.0 C1A A:CLA406 3.1 16.8 1.0 CHB A:CLA406 3.4 16.9 1.0 CHC A:CLA406 3.4 19.2 1.0 CHA A:CLA406 3.5 16.6 1.0 CHD A:CLA406 3.6 17.2 1.0 CBB A:PHO408 4.0 21.5 1.0 O A:HOH563 4.0 17.2 1.0 C3D A:CLA406 4.2 13.9 1.0 C3B A:CLA406 4.3 18.5 1.0 C2B A:CLA406 4.3 17.8 1.0 C2D A:CLA406 4.4 15.9 1.0 CG2 A:THR179 4.4 18.7 1.0 C3C A:CLA406 4.4 19.9 1.0 C2C A:CLA406 4.4 20.2 1.0 C3A A:CLA406 4.4 16.6 1.0 C2A A:CLA406 4.5 17.6 1.0 OG1 A:THR179 4.5 20.4 1.0 C19 A:PHO408 4.7 19.4 1.0 CBA A:CLA406 4.8 18.6 1.0 CBD A:CLA406 4.9 16.6 1.0 CB A:THR179 4.9 18.5 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:Mg407 b:21.8 occ:1.00 MG A:CLA407 0.0 21.8 1.0 NB A:CLA407 2.0 21.9 1.0 ND A:CLA407 2.0 20.3 1.0 NC A:CLA407 2.0 19.5 1.0 O A:HOH565 2.1 18.3 1.0 NA A:CLA407 2.3 21.7 1.0 C4D A:CLA407 2.9 20.4 1.0 C4B A:CLA407 2.9 20.0 1.0 C1C A:CLA407 3.0 20.0 1.0 C1B A:CLA407 3.0 20.9 1.0 C4C A:CLA407 3.1 18.7 1.0 C1D A:CLA407 3.1 18.8 1.0 C4A A:CLA407 3.2 20.4 1.0 C1A A:CLA407 3.2 19.6 1.0 CHC A:CLA407 3.4 18.8 1.0 CHB A:CLA407 3.4 19.9 1.0 CHD A:CLA407 3.5 20.5 1.0 CHA A:CLA407 3.6 20.2 1.0 CBB A:PHO409 3.9 24.9 1.0 O A:HOH513 4.1 18.9 1.0 C3D A:CLA407 4.2 18.0 1.0 C3B A:CLA407 4.3 21.3 1.0 C2C A:CLA407 4.3 20.2 1.0 C3C A:CLA407 4.3 19.8 1.0 C2D A:CLA407 4.3 19.6 1.0 C2B A:CLA407 4.3 20.7 1.0 CG2 D:ILE178 4.4 19.3 1.0 C3A A:CLA407 4.5 20.9 1.0 C2A A:CLA407 4.6 20.2 1.0 C20 A:PHO409 4.8 19.9 1.0 CE1 A:PHE206 4.8 21.7 1.0 CG1 D:ILE178 4.9 18.6 1.0 CBA A:CLA407 4.9 20.4 1.0 CBD A:CLA407 5.0 21.2 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 A:Mg410 b:24.2 occ:1.00 MG A:CLA410 0.0 24.2 1.0 NB A:CLA410 1.9 24.2 1.0 ND A:CLA410 2.0 24.5 1.0 NC A:CLA410 2.1 25.2 1.0 NA A:CLA410 2.2 23.1 1.0 NE2 A:HIS118 2.2 22.9 1.0 C1B A:CLA410 3.0 23.5 1.0 C4B A:CLA410 3.0 23.9 1.0 C4D A:CLA410 3.0 22.2 1.0 C4A A:CLA410 3.0 22.2 1.0 C4C A:CLA410 3.1 21.8 1.0 C1A A:CLA410 3.1 22.2 1.0 CE1 A:HIS118 3.2 25.3 1.0 C1D A:CLA410 3.2 20.8 1.0 C1C A:CLA410 3.2 22.1 1.0 CD2 A:HIS118 3.2 23.6 1.0 CHB A:CLA410 3.4 20.8 1.0 CHC A:CLA410 3.5 24.7 1.0 CHD A:CLA410 3.6 20.5 1.0 CHA A:CLA410 3.6 20.0 1.0 C3D A:CLA410 4.2 20.5 1.0 C3B A:CLA410 4.3 24.6 1.0 C2B A:CLA410 4.3 23.7 1.0 ND1 A:HIS118 4.3 23.2 1.0 CG1 I:VAL8 4.3 26.0 1.0 C3A A:CLA410 4.3 24.1 1.0 CG A:HIS118 4.4 24.7 1.0 C2D A:CLA410 4.4 21.6 1.0 C3C A:CLA410 4.4 23.1 1.0 C2A A:CLA410 4.4 22.8 1.0 C2C A:CLA410 4.5 23.2 1.0 CG2 I:VAL12 4.5 29.0 1.0 CMA A:CLA410 4.9 22.5 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:Mg602 b:33.5 occ:1.00 MG B:CLA602 0.0 33.5 1.0 ND B:CLA602 2.0 37.2 1.0 O B:HOH979 2.1 35.7 1.0 NB B:CLA602 2.1 33.9 1.0 NC B:CLA602 2.1 33.0 1.0 NA B:CLA602 2.3 38.2 1.0 C4D B:CLA602 2.9 40.7 1.0 C4B B:CLA602 3.1 34.4 1.0 C4C B:CLA602 3.1 31.8 1.0 C1A B:CLA602 3.1 44.4 1.0 C1D B:CLA602 3.2 38.4 1.0 C1C B:CLA602 3.2 35.6 1.0 C1B B:CLA602 3.2 32.5 1.0 C4A B:CLA602 3.2 38.6 1.0 CHA B:CLA602 3.5 41.2 1.0 CHC B:CLA602 3.5 34.2 1.0 CHB B:CLA602 3.6 32.9 1.0 CHD B:CLA602 3.6 35.7 1.0 O B:TRP185 4.0 35.6 1.0 C10 B:CLA602 4.0 61.0 1.0 C3D B:CLA602 4.1 40.5 1.0 C12 B:CLA602 4.2 54.0 1.0 CE2 B:PHE190 4.2 32.3 1.0 C2D B:CLA602 4.4 38.9 1.0 C3B B:CLA602 4.4 31.6 1.0 C8 B:CLA602 4.4 63.0 1.0 C3C B:CLA602 4.4 32.5 1.0 C2A B:CLA602 4.5 44.0 1.0 C2B B:CLA602 4.5 30.8 1.0 C2C B:CLA602 4.5 31.7 1.0 C11 B:CLA602 4.5 55.5 1.0 C3A B:CLA602 4.5 41.2 1.0 CZ B:PHE190 4.5 32.6 1.0 CBB B:CLA603 4.6 29.5 1.0 O B:HOH936 4.7 34.3 1.0 CBD B:CLA602 4.9 45.4 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:Mg603 b:29.7 occ:1.00 MG B:CLA603 0.0 29.7 1.0 ND B:CLA603 2.1 24.7 1.0 ND1 B:HIS201 2.1 26.4 1.0 NB B:CLA603 2.1 28.6 1.0 NC B:CLA603 2.1 29.5 1.0 NA B:CLA603 2.3 26.4 1.0 CE1 B:HIS201 2.9 26.8 1.0 C4D B:CLA603 3.0 23.9 1.0 C4B B:CLA603 3.1 29.6 1.0 C4C B:CLA603 3.1 26.8 1.0 C1C B:CLA603 3.1 27.6 1.0 C1B B:CLA603 3.2 29.0 1.0 C1D B:CLA603 3.2 26.1 1.0 C4A B:CLA603 3.2 29.0 1.0 C1A B:CLA603 3.2 27.3 1.0 CG B:HIS201 3.3 24.9 1.0 CHC B:CLA603 3.5 27.4 1.0 CHB B:CLA603 3.5 26.2 1.0 CHA B:CLA603 3.5 23.9 1.0 CHD B:CLA603 3.6 25.5 1.0 CB B:HIS201 3.8 26.4 1.0 CZ H:PHE41 3.9 32.9 1.0 NE2 B:HIS201 4.1 27.9 1.0 C3D B:CLA603 4.2 25.7 1.0 CE2 H:PHE41 4.3 27.1 1.0 CD2 B:HIS201 4.3 24.5 1.0 CA B:HIS201 4.3 25.1 1.0 C2D B:CLA603 4.4 25.3 1.0 C3B B:CLA603 4.4 28.6 1.0 C2C B:CLA603 4.4 28.6 1.0 C3C B:CLA603 4.5 26.9 1.0 C2B B:CLA603 4.5 29.9 1.0 C3A B:CLA603 4.5 26.2 1.0 C2A B:CLA603 4.6 26.4 1.0 O B:HIS201 4.9 27.0 1.0 CMA B:CLA603 5.0 25.9 1.0 CBD B:CLA603 5.0 24.7 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:Mg604 b:24.4 occ:1.00 MG B:CLA604 0.0 24.4 1.0 NB B:CLA604 2.0 22.7 1.0 ND B:CLA604 2.0 23.8 1.0 NC B:CLA604 2.1 22.8 1.0 NE2 B:HIS202 2.1 23.9 1.0 NA B:CLA604 2.2 22.2 1.0 C4D B:CLA604 3.0 20.6 1.0 C4B B:CLA604 3.0 21.8 1.0 C4C B:CLA604 3.0 21.0 1.0 CD2 B:HIS202 3.1 27.2 1.0 C1B B:CLA604 3.1 21.4 1.0 C1C B:CLA604 3.1 21.0 1.0 C1D B:CLA604 3.1 23.3 1.0 C1A B:CLA604 3.2 21.5 1.0 C4A B:CLA604 3.2 22.3 1.0 CE1 B:HIS202 3.2 27.5 1.0 CHC B:CLA604 3.4 21.5 1.0 CHB B:CLA604 3.5 22.2 1.0 CHD B:CLA604 3.5 22.5 1.0 CHA B:CLA604 3.6 21.0 1.0 C3D B:CLA604 4.3 21.2 1.0 CG B:HIS202 4.3 24.0 1.0 ND1 B:HIS202 4.3 25.7 1.0 C3B B:CLA604 4.3 21.2 1.0 C3C B:CLA604 4.3 21.3 1.0 C2B B:CLA604 4.4 20.6 1.0 C2D B:CLA604 4.4 23.0 1.0 C2C B:CLA604 4.4 20.8 1.0 C2A B:CLA604 4.5 22.6 1.0 C3A B:CLA604 4.5 22.7 1.0 C6 B:CLA606 4.5 30.0 1.0 C4 B:CLA606 4.6 32.2 1.0 NE2 B:HIS201 4.7 27.9 1.0 CD2 B:HIS201 4.7 24.5 1.0 C7 B:CLA606 4.9 32.5 1.0 CBA B:CLA604 4.9 22.4 1.0 C5 B:CLA606 4.9 30.0 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:Mg605 b:21.8 occ:1.00 MG B:CLA605 0.0 21.8 1.0 NB B:CLA605 2.0 22.7 1.0 NC B:CLA605 2.1 21.8 1.0 NE2 B:HIS455 2.1 18.7 1.0 ND B:CLA605 2.1 21.4 1.0 NA B:CLA605 2.3 21.9 1.0 C4B B:CLA605 2.9 20.4 1.0 CD2 B:HIS455 3.0 18.4 1.0 C4D B:CLA605 3.1 22.3 1.0 C1C B:CLA605 3.1 21.3 1.0 C1B B:CLA605 3.1 20.0 1.0 C4C B:CLA605 3.1 21.9 1.0 C1D B:CLA605 3.2 20.7 1.0 C4A B:CLA605 3.2 21.0 1.0 CE1 B:HIS455 3.2 18.6 1.0 C1A B:CLA605 3.3 22.1 1.0 CHC B:CLA605 3.4 21.5 1.0 CHB B:CLA605 3.5 20.2 1.0 CHD B:CLA605 3.6 19.6 1.0 CHA B:CLA605 3.7 21.9 1.0 CG B:HIS455 4.2 17.6 1.0 C3B B:CLA605 4.3 22.6 1.0 ND1 B:HIS455 4.3 19.3 1.0 C3D B:CLA605 4.3 19.8 1.0 C2B B:CLA605 4.3 23.0 1.0 C14 B:CLA613 4.4 29.1 1.0 C3C B:CLA605 4.4 20.4 1.0 C2C B:CLA605 4.4 22.3 1.0 C2D B:CLA605 4.4 23.3 1.0 C3A B:CLA605 4.6 22.3 1.0 C2A B:CLA605 4.6 22.5 1.0 C13 B:CLA613 4.9 32.0 1.0 C15 B:CLA613 5.0 28.4 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:Mg606 b:23.9 occ:1.00 MG B:CLA606 0.0 23.9 1.0 NB B:CLA606 2.0 24.5 1.0 ND B:CLA606 2.0 24.2 1.0 NE2 B:HIS100 2.1 20.9 1.0 NC B:CLA606 2.2 25.4 1.0 NA B:CLA606 2.2 21.9 1.0 C4D B:CLA606 2.9 22.2 1.0 C4B B:CLA606 3.0 25.4 1.0 C1B B:CLA606 3.0 23.6 1.0 CD2 B:HIS100 3.1 19.7 1.0 CE1 B:HIS100 3.1 22.2 1.0 C1D B:CLA606 3.2 22.0 1.0 C4A B:CLA606 3.2 25.9 1.0 C1C B:CLA606 3.2 24.0 1.0 C1A B:CLA606 3.2 21.9 1.0 C4C B:CLA606 3.2 25.8 1.0 CHB B:CLA606 3.4 23.2 1.0 CHC B:CLA606 3.5 21.4 1.0 CHA B:CLA606 3.5 21.0 1.0 CHD B:CLA606 3.6 22.7 1.0 C1 B:CLA605 4.0 34.1 1.0 C2 B:CLA605 4.2 41.0 1.0 C3D B:CLA606 4.2 21.1 1.0 CG B:HIS100 4.2 20.3 1.0 ND1 B:HIS100 4.3 22.4 1.0 C3B B:CLA606 4.3 24.5 1.0 C2B B:CLA606 4.3 24.4 1.0 C2D B:CLA606 4.4 22.8 1.0 C2C B:CLA606 4.5 22.3 1.0 C3A B:CLA606 4.5 21.8 1.0 C3C B:CLA606 4.5 23.8 1.0 C2A B:CLA606 4.5 23.7 1.0 C4 B:CLA607 4.9 25.3 1.0 CBD B:CLA606 5.0 22.4 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:Mg607 b:26.8 occ:1.00 MG B:CLA607 0.0 26.8 1.0 ND B:CLA607 2.1 29.2 1.0 NC B:CLA607 2.1 27.0 1.0 NB B:CLA607 2.1 25.1 1.0 ND1 B:HIS157 2.2 24.9 1.0 NA B:CLA607 2.3 25.3 1.0 C4C B:CLA607 3.0 28.0 1.0 C4D B:CLA607 3.0 30.4 1.0 CE1 B:HIS157 3.1 29.9 1.0 C4B B:CLA607 3.1 24.0 1.0 C1B B:CLA607 3.1 23.9 1.0 C1D B:CLA607 3.1 29.1 1.0 C1C B:CLA607 3.2 27.6 1.0 C4A B:CLA607 3.2 25.8 1.0 CG B:HIS157 3.2 26.7 1.0 C1A B:CLA607 3.2 25.5 1.0 CHD B:CLA607 3.4 28.5 1.0 CHB B:CLA607 3.4 23.1 1.0 CHC B:CLA607 3.6 26.4 1.0 CHA B:CLA607 3.6 26.5 1.0 CB B:HIS157 3.7 27.2 1.0 C10 B:UNL627 4.0 43.9 1.0 NE2 B:HIS157 4.3 31.8 1.0 C9 B:UNL627 4.3 45.2 1.0 C3D B:CLA607 4.3 30.4 1.0 C11 B:UNL627 4.4 44.0 1.0 CD2 B:HIS157 4.4 26.3 1.0 C3C B:CLA607 4.4 29.0 1.0 C2B B:CLA607 4.4 24.0 1.0 C3B B:CLA607 4.4 22.8 1.0 C2D B:CLA607 4.4 32.0 1.0 C2C B:CLA607 4.4 27.9 1.0 C3A B:CLA607 4.6 22.1 1.0 C2A B:CLA607 4.6 23.3 1.0 CD B:PRO164 4.9 29.4 1.0 CA B:HIS157 4.9 24.7 1.0 C12 B:UNL627 5.0 44.3 1.0

Y.Umena, K.Kawakami, J.-R.Shen, N.Kamiya. Crystal Structure of Oxygen-Evolving Photosystem II at A Resolution of 1.9 A Nature V. 473 55 2011.
ISSN: ISSN 0028-0836
PubMed: 21499260
DOI: 10.1038/NATURE09913