Magnesium in PDB 5h2f: Crystal Structure of the Psbm-Deletion Mutant of Photosystem II

All present enzymatic activity of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II:
1.10.3.9;

The structure of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II, PDB code: 5h2f was solved by S.Uto, K.Kawakami, Y.Umena, M.Iwai, M.Ikeuchi, J.R.Shen, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	121.954, 226.993, 285.886, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 22.6

The structure of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II 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 - 74;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II (pdb code 5h2f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 74 binding sites of Magnesium where determined in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II, PDB code: 5h2f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 74 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:23.8 occ:1.00 MG A:CLA405 0.0 23.8 1.0 ND A:CLA405 2.0 22.4 1.0 NA A:CLA405 2.0 23.6 1.0 NB A:CLA405 2.1 23.4 1.0 NE2 A:HIS198 2.2 22.5 1.0 NC A:CLA405 2.3 22.5 1.0 C4D A:CLA405 2.8 23.9 1.0 C1A A:CLA405 3.0 24.2 1.0 C4A A:CLA405 3.0 23.5 1.0 C4B A:CLA405 3.1 20.9 1.0 C1B A:CLA405 3.1 22.0 1.0 CE1 A:HIS198 3.1 20.2 1.0 C1D A:CLA405 3.1 22.1 1.0 CD2 A:HIS198 3.2 21.4 1.0 C4C A:CLA405 3.3 20.3 1.0 C1C A:CLA405 3.3 20.9 1.0 CHA A:CLA405 3.3 22.5 1.0 CHB A:CLA405 3.5 20.8 1.0 CHC A:CLA405 3.6 21.2 1.0 CHD A:CLA405 3.6 21.7 1.0 CE A:MET183 4.1 21.4 1.0 C3D A:CLA405 4.1 22.3 1.0 ND1 A:HIS198 4.3 23.0 1.0 C2D A:CLA405 4.3 23.5 1.0 C3A A:CLA405 4.3 23.3 1.0 C2A A:CLA405 4.3 24.8 1.0 CG A:HIS198 4.4 21.2 1.0 C3B A:CLA405 4.4 19.9 1.0 C2B A:CLA405 4.4 20.8 1.0 CAB D:CLA403 4.5 23.0 1.0 C3C A:CLA405 4.6 19.8 1.0 C2C A:CLA405 4.7 19.9 1.0 CBD A:CLA405 4.8 24.6 1.0 CMA A:CLA405 4.9 25.0 1.0

Magnesium binding site 2 out of 74 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:27.9 occ:1.00 MG A:CLA406 0.0 27.9 1.0 NB A:CLA406 2.0 26.4 1.0 NC A:CLA406 2.0 25.6 1.0 O A:HOH614 2.1 23.9 1.0 ND A:CLA406 2.1 28.2 1.0 NA A:CLA406 2.2 28.3 1.0 C4B A:CLA406 2.8 27.4 1.0 C1C A:CLA406 3.0 25.5 1.0 C4D A:CLA406 3.0 25.0 1.0 C1B A:CLA406 3.0 25.1 1.0 C4C A:CLA406 3.1 24.0 1.0 C4A A:CLA406 3.2 27.3 1.0 C1A A:CLA406 3.2 27.6 1.0 C1D A:CLA406 3.2 24.7 1.0 CHC A:CLA406 3.3 22.4 1.0 CHB A:CLA406 3.5 25.7 1.0 CHA A:CLA406 3.6 27.2 1.0 CHD A:CLA406 3.6 24.2 1.0 CBB D:PHO402 3.8 25.8 1.0 O D:HOH596 4.1 26.2 1.0 C3B A:CLA406 4.2 27.7 1.0 C3D A:CLA406 4.3 23.8 1.0 C2B A:CLA406 4.3 26.8 1.0 C2C A:CLA406 4.3 24.2 1.0 C3C A:CLA406 4.3 23.6 1.0 C2D A:CLA406 4.4 24.2 1.0 CG2 D:ILE178 4.5 24.8 1.0 C3A A:CLA406 4.5 27.6 1.0 C2A A:CLA406 4.5 27.4 1.0 C20 D:PHO402 4.5 27.4 1.0 CE2 A:PHE206 4.9 24.1 1.0 CBA A:CLA406 4.9 27.4 1.0

Magnesium binding site 3 out of 74 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:29.1 occ:1.00 MG A:CLA408 0.0 29.1 1.0 NB A:CLA408 2.0 26.2 1.0 ND A:CLA408 2.0 28.1 1.0 NC A:CLA408 2.2 29.8 1.0 NA A:CLA408 2.2 28.5 1.0 NE2 A:HIS118 2.2 24.2 1.0 C4D A:CLA408 2.9 27.3 1.0 C4B A:CLA408 3.0 24.0 1.0 C1B A:CLA408 3.0 24.6 1.0 C4A A:CLA408 3.1 26.9 1.0 CD2 A:HIS118 3.1 26.8 1.0 C1A A:CLA408 3.1 27.4 1.0 C1D A:CLA408 3.2 29.1 1.0 C4C A:CLA408 3.2 28.9 1.0 C1C A:CLA408 3.2 28.8 1.0 CE1 A:HIS118 3.3 27.9 1.0 CHB A:CLA408 3.4 25.4 1.0 CHC A:CLA408 3.5 25.2 1.0 CHA A:CLA408 3.5 25.9 1.0 CHD A:CLA408 3.6 27.6 1.0 C3D A:CLA408 4.2 24.2 1.0 C3B A:CLA408 4.3 23.4 1.0 C2B A:CLA408 4.3 24.1 1.0 CG A:HIS118 4.3 26.9 1.0 CG1 I:VAL8 4.3 32.6 1.0 ND1 A:HIS118 4.4 27.6 1.0 C2D A:CLA408 4.4 27.4 1.0 CG2 I:VAL12 4.4 40.6 1.0 C3A A:CLA408 4.4 30.1 1.0 C2A A:CLA408 4.5 29.4 1.0 C3C A:CLA408 4.5 27.8 1.0 C2C A:CLA408 4.5 27.1 1.0 CMA A:CLA408 4.9 29.4 1.0 CBD A:CLA408 4.9 26.7 1.0

Magnesium binding site 4 out of 74 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:49.7 occ:1.00 MG B:CLA602 0.0 49.7 1.0 O B:HOH705 2.0 41.0 1.0 ND B:CLA602 2.1 53.1 1.0 NC B:CLA602 2.1 47.5 1.0 NB B:CLA602 2.1 47.5 1.0 NA B:CLA602 2.4 48.1 1.0 C4B B:CLA602 3.0 44.2 1.0 C4D B:CLA602 3.0 54.7 1.0 C1C B:CLA602 3.1 44.1 1.0 C4C B:CLA602 3.1 49.9 1.0 C1D B:CLA602 3.2 53.3 1.0 C1B B:CLA602 3.2 43.4 1.0 C1A B:CLA602 3.3 53.1 1.0 CHC B:CLA602 3.3 45.0 1.0 C4A B:CLA602 3.4 48.8 1.0 CHD B:CLA602 3.5 47.7 1.0 CHA B:CLA602 3.6 55.3 1.0 CHB B:CLA602 3.6 44.9 1.0 C10 B:CLA602 3.8 78.3 1.0 C12 B:CLA602 4.1 70.6 1.0 CE2 B:PHE190 4.1 45.8 1.0 O B:TRP185 4.2 42.5 1.0 C3D B:CLA602 4.3 57.7 1.0 C11 B:CLA602 4.3 72.4 1.0 C3B B:CLA602 4.3 42.7 1.0 CZ B:PHE190 4.3 44.5 1.0 C2C B:CLA602 4.4 45.2 1.0 C2D B:CLA602 4.4 56.7 1.0 C3C B:CLA602 4.4 47.6 1.0 C2B B:CLA602 4.5 43.6 1.0 C8 B:CLA602 4.6 82.3 1.0 C2A B:CLA602 4.6 56.1 1.0 CBB B:CLA603 4.7 38.8 1.0 C3A B:CLA602 4.7 49.3 1.0 O B:HOH820 4.7 44.1 1.0

Magnesium binding site 5 out of 74 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:39.4 occ:1.00 MG B:CLA603 0.0 39.4 1.0 ND B:CLA603 1.9 34.6 1.0 NB B:CLA603 2.1 40.0 1.0 NC B:CLA603 2.2 36.8 1.0 NA B:CLA603 2.2 35.9 1.0 ND1 B:HIS201 2.3 29.9 1.0 C4D B:CLA603 2.8 33.9 1.0 C1D B:CLA603 3.0 34.3 1.0 C1A B:CLA603 3.1 38.9 1.0 C4C B:CLA603 3.1 37.1 1.0 CE1 B:HIS201 3.1 31.6 1.0 C4B B:CLA603 3.1 40.9 1.0 C1B B:CLA603 3.2 38.7 1.0 C4A B:CLA603 3.2 39.0 1.0 C1C B:CLA603 3.3 38.6 1.0 CG B:HIS201 3.4 29.8 1.0 CHA B:CLA603 3.5 35.0 1.0 CHD B:CLA603 3.5 34.8 1.0 CHB B:CLA603 3.6 36.5 1.0 CHC B:CLA603 3.6 36.7 1.0 CZ H:PHE41 3.8 41.5 1.0 CB B:HIS201 3.9 31.8 1.0 C3D B:CLA603 4.0 34.3 1.0 CE1 H:PHE41 4.2 40.2 1.0 C2D B:CLA603 4.2 32.9 1.0 NE2 B:HIS201 4.4 31.9 1.0 C2A B:CLA603 4.5 36.1 1.0 C3C B:CLA603 4.5 36.2 1.0 C3B B:CLA603 4.5 39.8 1.0 C3A B:CLA603 4.5 37.3 1.0 CA B:HIS201 4.5 33.5 1.0 C2B B:CLA603 4.5 38.4 1.0 CD2 B:HIS201 4.5 28.1 1.0 C2C B:CLA603 4.5 36.5 1.0 CBD B:CLA603 4.9 35.6 1.0

Magnesium binding site 6 out of 74 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:29.6 occ:1.00 MG B:CLA604 0.0 29.6 1.0 NB B:CLA604 2.0 30.7 1.0 ND B:CLA604 2.0 29.5 1.0 NE2 B:HIS202 2.2 34.9 1.0 NC B:CLA604 2.2 29.3 1.0 NA B:CLA604 2.3 26.8 1.0 C4D B:CLA604 2.9 29.3 1.0 C4B B:CLA604 2.9 29.1 1.0 CD2 B:HIS202 3.0 36.7 1.0 C1B B:CLA604 3.1 30.5 1.0 C1A B:CLA604 3.2 28.4 1.0 C1D B:CLA604 3.2 31.6 1.0 C1C B:CLA604 3.2 29.4 1.0 C4C B:CLA604 3.2 29.3 1.0 C4A B:CLA604 3.2 28.4 1.0 CE1 B:HIS202 3.3 38.0 1.0 CHC B:CLA604 3.4 27.8 1.0 CHA B:CLA604 3.5 28.3 1.0 CHB B:CLA604 3.5 31.0 1.0 CHD B:CLA604 3.6 30.5 1.0 C3D B:CLA604 4.2 30.3 1.0 C3B B:CLA604 4.3 26.7 1.0 CG B:HIS202 4.3 38.7 1.0 ND1 B:HIS202 4.3 36.6 1.0 C2B B:CLA604 4.3 28.4 1.0 C2D B:CLA604 4.4 29.6 1.0 C3C B:CLA604 4.5 28.8 1.0 C2C B:CLA604 4.5 28.8 1.0 C2A B:CLA604 4.5 30.5 1.0 C3A B:CLA604 4.6 28.7 1.0 NE2 B:HIS201 4.6 31.9 1.0 C4 B:CLA606 4.6 45.5 1.0 C6 B:CLA606 4.7 42.2 1.0 CD2 B:HIS201 4.7 28.1 1.0 C7 B:CLA606 4.7 45.0 1.0 C5 B:CLA606 4.8 39.9 1.0 CBA B:CLA604 4.9 28.5 1.0 CBD B:CLA604 5.0 31.9 1.0 C3 B:CLA606 5.0 43.7 1.0

Magnesium binding site 7 out of 74 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:27.1 occ:1.00 MG B:CLA605 0.0 27.1 1.0 NB B:CLA605 2.0 27.9 1.0 ND B:CLA605 2.1 24.9 1.0 NC B:CLA605 2.1 25.6 1.0 NE2 B:HIS455 2.2 27.4 1.0 NA B:CLA605 2.2 26.6 1.0 C4B B:CLA605 3.0 25.5 1.0 CD2 B:HIS455 3.0 26.7 1.0 C4D B:CLA605 3.0 26.4 1.0 C1B B:CLA605 3.1 26.7 1.0 C4A B:CLA605 3.1 28.4 1.0 C4C B:CLA605 3.1 24.9 1.0 C1C B:CLA605 3.1 27.0 1.0 CE1 B:HIS455 3.2 29.5 1.0 C1A B:CLA605 3.2 25.4 1.0 C1D B:CLA605 3.2 25.2 1.0 CHB B:CLA605 3.4 27.3 1.0 CHC B:CLA605 3.5 25.4 1.0 CHD B:CLA605 3.6 24.5 1.0 CHA B:CLA605 3.6 27.8 1.0 C14 B:CLA613 4.0 32.9 1.0 CG B:HIS455 4.3 26.7 1.0 C3D B:CLA605 4.3 26.2 1.0 ND1 B:HIS455 4.3 28.3 1.0 C3B B:CLA605 4.3 27.1 1.0 C2B B:CLA605 4.4 26.5 1.0 C3C B:CLA605 4.4 25.6 1.0 C2C B:CLA605 4.5 26.7 1.0 C2D B:CLA605 4.5 25.2 1.0 C3A B:CLA605 4.5 26.0 1.0 C2A B:CLA605 4.5 26.8 1.0 C13 B:CLA613 4.7 34.8 1.0 C15 B:CLA613 4.8 32.0 1.0 CE2 B:PHE451 4.9 25.1 1.0

Magnesium binding site 8 out of 74 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:28.7 occ:1.00 MG B:CLA606 0.0 28.7 1.0 ND B:CLA606 2.0 30.3 1.0 NC B:CLA606 2.1 31.3 1.0 NE2 B:HIS100 2.1 21.9 1.0 NB B:CLA606 2.2 30.1 1.0 NA B:CLA606 2.4 29.9 1.0 C4D B:CLA606 3.0 27.5 1.0 CD2 B:HIS100 3.0 22.4 1.0 C1D B:CLA606 3.0 27.9 1.0 C4C B:CLA606 3.0 30.0 1.0 C4B B:CLA606 3.1 30.7 1.0 C1C B:CLA606 3.1 30.4 1.0 C1B B:CLA606 3.2 30.0 1.0 CE1 B:HIS100 3.2 23.1 1.0 C1A B:CLA606 3.3 28.3 1.0 C4A B:CLA606 3.4 32.1 1.0 CHD B:CLA606 3.4 27.4 1.0 CHC B:CLA606 3.4 27.7 1.0 CHB B:CLA606 3.6 33.5 1.0 CHA B:CLA606 3.7 27.6 1.0 C3D B:CLA606 4.2 28.4 1.0 C1 B:CLA605 4.2 40.2 1.0 CG B:HIS100 4.2 23.2 1.0 C2D B:CLA606 4.3 27.1 1.0 ND1 B:HIS100 4.3 24.0 1.0 C3C B:CLA606 4.3 28.4 1.0 C2 B:CLA605 4.4 45.1 1.0 C3B B:CLA606 4.4 29.6 1.0 C2C B:CLA606 4.4 29.2 1.0 C2B B:CLA606 4.5 30.4 1.0 C2A B:CLA606 4.7 25.9 1.0 C3A B:CLA606 4.7 29.7 1.0

Magnesium binding site 9 out of 74 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:33.5 occ:1.00 MG B:CLA607 0.0 33.5 1.0 ND B:CLA607 2.0 37.8 1.0 NB B:CLA607 2.1 32.7 1.0 ND1 B:HIS157 2.2 27.2 1.0 NC B:CLA607 2.2 33.9 1.0 NA B:CLA607 2.2 31.1 1.0 CE1 B:HIS157 2.9 30.7 1.0 C4D B:CLA607 2.9 35.8 1.0 C1B B:CLA607 3.0 31.0 1.0 C1D B:CLA607 3.1 38.8 1.0 C4B B:CLA607 3.1 32.8 1.0 C4C B:CLA607 3.2 35.3 1.0 C4A B:CLA607 3.2 31.4 1.0 C1A B:CLA607 3.2 31.6 1.0 C1C B:CLA607 3.3 33.3 1.0 CG B:HIS157 3.4 32.7 1.0 CHB B:CLA607 3.4 28.8 1.0 CHD B:CLA607 3.5 34.8 1.0 CHA B:CLA607 3.6 36.3 1.0 CHC B:CLA607 3.6 30.5 1.0 CB B:HIS157 3.9 35.0 1.0 C8 B:UNL625 4.1 46.8 1.0 C3D B:CLA607 4.1 39.1 1.0 NE2 B:HIS157 4.2 32.4 1.0 C2D B:CLA607 4.3 40.6 1.0 C6 B:UNL625 4.3 44.0 1.0 C3B B:CLA607 4.3 28.7 1.0 C2B B:CLA607 4.4 32.5 1.0 CD2 B:HIS157 4.4 29.2 1.0 C7 B:UNL625 4.5 46.4 1.0 C3C B:CLA607 4.5 36.6 1.0 C3A B:CLA607 4.5 31.2 1.0 C2A B:CLA607 4.6 29.1 1.0 C2C B:CLA607 4.6 33.0 1.0 C9 B:UNL625 4.9 51.8 1.0 CBD B:CLA607 5.0 36.3 1.0 CD B:PRO164 5.0 36.7 1.0

Magnesium binding site 10 out of 74 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg608 b:28.2 occ:1.00 MG B:CLA608 0.0 28.2 1.0 O B:HOH855 1.9 22.1 1.0 NB B:CLA608 2.0 27.3 1.0 ND B:CLA608 2.1 28.9 1.0 NC B:CLA608 2.1 28.4 1.0 NA B:CLA608 2.3 27.3 1.0 C4B B:CLA608 3.0 28.4 1.0 C1B B:CLA608 3.1 26.7 1.0 C4D B:CLA608 3.1 26.5 1.0 C4C B:CLA608 3.1 28.8 1.0 C1C B:CLA608 3.1 27.9 1.0 C1D B:CLA608 3.2 29.4 1.0 C4A B:CLA608 3.2 27.6 1.0 C1A B:CLA608 3.3 27.2 1.0 CHC B:CLA608 3.4 27.9 1.0 CHB B:CLA608 3.4 27.4 1.0 CHD B:CLA608 3.5 30.2 1.0 CHA B:CLA608 3.7 28.0 1.0 C12 B:LMG621 3.9 75.2 1.0 O B:HOH831 4.2 28.4 1.0 C14 B:LMG621 4.3 62.0 1.0 C3B B:CLA608 4.3 27.0 1.0 C3D B:CLA608 4.3 26.9 1.0 C2B B:CLA608 4.3 26.4 1.0 C3C B:CLA608 4.4 27.3 1.0 C2C B:CLA608 4.4 27.4 1.0 C2D B:CLA608 4.4 25.4 1.0 C13 B:LMG621 4.4 70.7 1.0 C15 B:LMG621 4.5 54.1 1.0 SD B:MET37 4.5 30.0 1.0 C3A B:CLA608 4.5 25.7 1.0 CD1 B:PHE61 4.6 29.8 1.0 C2A B:CLA608 4.6 25.8 1.0 CB B:PHE61 4.8 28.8 1.0 CG B:PHE61 4.9 28.7 1.0 CE B:MET37 5.0 26.7 1.0

S.Uto, K.Kawakami, Y.Umena, M.Iwai, M.Ikeuchi, J.R.Shen, N.Kamiya. Mutual Relationships Between Structural and Functional Changes in A Psbm-Deletion Mutant of Photosystem II. Faraday Discuss. V. 198 107 2017.
ISSN: ISSN 1359-6640
PubMed: 28272640
DOI: 10.1039/C6FD00213G