Magnesium in PDB 8gn1: Crystal Structure of Dbbq-Bound Photosystem II Complex

All present enzymatic activity of Crystal Structure of Dbbq-Bound Photosystem II Complex:
1.10.3.9;

The structure of Crystal Structure of Dbbq-Bound Photosystem II Complex, PDB code: 8gn1 was solved by S.Kamada, Y.Nakajima, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.02 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	122.185, 228.462, 286.626, 90, 90, 90
R / Rfree (%)	15.7 / 19.1

The structure of Crystal Structure of Dbbq-Bound Photosystem II Complex also contains other interesting chemical elements:

Calcium	(Ca)	7 atoms
Bromine	(Br)	12 atoms
Manganese	(Mn)	8 atoms
Chlorine	(Cl)	4 atoms
Iron	(Fe)	6 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 of Dbbq-Bound Photosystem II Complex (pdb code 8gn1). 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 of Dbbq-Bound Photosystem II Complex, PDB code: 8gn1:
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 of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:39.0 occ:1.00 MG A:CLA405 0.0 39.0 1.0 ND A:CLA405 1.9 40.4 1.0 NB A:CLA405 2.1 38.3 1.0 NC A:CLA405 2.2 37.7 1.0 NA A:CLA405 2.2 37.6 1.0 NE2 A:HIS198 2.3 36.6 1.0 C4D A:CLA405 2.9 34.9 1.0 C1B A:CLA405 3.1 33.7 1.0 C4B A:CLA405 3.1 34.6 1.0 C1C A:CLA405 3.1 34.1 1.0 C4A A:CLA405 3.1 40.0 1.0 C1D A:CLA405 3.1 31.1 1.0 CE1 A:HIS198 3.1 34.4 1.0 C1A A:CLA405 3.2 38.8 1.0 C4C A:CLA405 3.2 33.0 1.0 CD2 A:HIS198 3.3 37.7 1.0 CHB A:CLA405 3.4 36.1 1.0 CHC A:CLA405 3.5 31.4 1.0 CHA A:CLA405 3.5 34.0 1.0 CHD A:CLA405 3.6 34.1 1.0 CE A:MET183 4.0 34.9 1.0 C3D A:CLA405 4.2 35.2 1.0 ND1 A:HIS198 4.3 38.9 1.0 C2B A:CLA405 4.4 36.1 1.0 C2D A:CLA405 4.4 38.1 1.0 C3B A:CLA405 4.4 30.5 1.0 CAB D:CLA404 4.4 37.3 1.0 CG A:HIS198 4.4 40.0 1.0 C2C A:CLA405 4.5 34.5 1.0 C3A A:CLA405 4.5 35.9 1.0 C2A A:CLA405 4.5 39.9 1.0 C3C A:CLA405 4.5 36.3 1.0 CBD A:CLA405 4.9 38.1 1.0

Magnesium binding site 2 out of 72 in the Crystal Structure of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:40.8 occ:1.00 MG A:CLA406 0.0 40.8 1.0 ND A:CLA406 2.0 39.9 1.0 NB A:CLA406 2.0 39.4 1.0 O A:HOH616 2.1 43.2 1.0 NA A:CLA406 2.2 38.6 1.0 NC A:CLA406 2.2 37.0 1.0 C4D A:CLA406 2.9 38.7 1.0 C1B A:CLA406 3.0 38.9 1.0 C4B A:CLA406 3.0 40.3 1.0 C4A A:CLA406 3.1 41.6 1.0 C1C A:CLA406 3.1 37.0 1.0 C1A A:CLA406 3.1 35.9 1.0 C1D A:CLA406 3.2 37.1 1.0 C4C A:CLA406 3.2 35.7 1.0 CHB A:CLA406 3.4 44.9 1.0 CHC A:CLA406 3.4 35.0 1.0 CHA A:CLA406 3.4 36.2 1.0 CHD A:CLA406 3.7 38.5 1.0 CBB A:PHO408 3.8 41.3 1.0 O A:HOH610 4.2 38.0 1.0 C3D A:CLA406 4.2 39.4 1.0 C2B A:CLA406 4.3 41.1 1.0 C3B A:CLA406 4.3 41.0 1.0 C2D A:CLA406 4.4 38.1 1.0 C2C A:CLA406 4.4 35.8 1.0 C2A A:CLA406 4.5 41.1 1.0 C3A A:CLA406 4.5 43.0 1.0 C3C A:CLA406 4.5 37.3 1.0 CG2 D:ILE178 4.7 36.1 1.0 C20 A:PHO408 4.8 37.8 1.0 CBA A:CLA406 4.8 43.4 1.0 CE2 A:PHE206 4.9 43.3 1.0 CBD A:CLA406 4.9 40.7 1.0

Magnesium binding site 3 out of 72 in the Crystal Structure of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:44.2 occ:1.00 MG A:CLA409 0.0 44.2 1.0 ND A:CLA409 2.0 44.2 1.0 NB A:CLA409 2.1 43.7 1.0 NA A:CLA409 2.1 46.7 1.0 NC A:CLA409 2.2 48.6 1.0 NE2 A:HIS118 2.2 42.8 1.0 C4D A:CLA409 2.9 43.5 1.0 CE1 A:HIS118 3.0 45.2 1.0 C4A A:CLA409 3.1 44.2 1.0 C1A A:CLA409 3.1 44.6 1.0 C4B A:CLA409 3.1 43.5 1.0 C1B A:CLA409 3.1 45.4 1.0 C1C A:CLA409 3.1 45.8 1.0 C1D A:CLA409 3.2 43.8 1.0 C4C A:CLA409 3.2 47.6 1.0 CD2 A:HIS118 3.3 42.6 1.0 CHB A:CLA409 3.4 41.6 1.0 CHA A:CLA409 3.4 35.9 1.0 CHC A:CLA409 3.5 43.8 1.0 CHD A:CLA409 3.7 38.5 1.0 C3D A:CLA409 4.2 40.9 1.0 ND1 A:HIS118 4.2 41.0 1.0 CG1 I:VAL8 4.3 44.3 1.0 CG A:HIS118 4.4 40.4 1.0 C3A A:CLA409 4.4 46.6 1.0 C3B A:CLA409 4.4 40.7 1.0 C2D A:CLA409 4.4 45.0 1.0 C2A A:CLA409 4.4 45.6 1.0 C2B A:CLA409 4.4 39.3 1.0 CG2 I:VAL12 4.5 47.9 1.0 C2C A:CLA409 4.5 42.5 1.0 C3C A:CLA409 4.5 42.3 1.0 CBD A:CLA409 4.9 44.1 1.0 CMA A:CLA409 4.9 39.3 1.0

Magnesium binding site 4 out of 72 in the Crystal Structure of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:59.7 occ:1.00 MG B:CLA602 0.0 59.7 1.0 ND B:CLA602 2.0 62.5 1.0 NB B:CLA602 2.1 59.9 1.0 O B:HOH768 2.1 60.7 1.0 NC B:CLA602 2.2 55.0 1.0 NA B:CLA602 2.2 64.3 1.0 C4D B:CLA602 2.9 64.6 1.0 C4B B:CLA602 3.1 58.0 1.0 C1C B:CLA602 3.1 56.3 1.0 C1B B:CLA602 3.1 56.9 1.0 C1A B:CLA602 3.2 68.3 1.0 C4A B:CLA602 3.2 65.7 1.0 C4C B:CLA602 3.2 58.5 1.0 C1D B:CLA602 3.2 60.8 1.0 CHC B:CLA602 3.4 57.5 1.0 CHA B:CLA602 3.5 63.9 1.0 CHB B:CLA602 3.5 58.9 1.0 CHD B:CLA602 3.7 56.8 1.0 C10 B:CLA602 3.9 80.0 1.0 C8 B:CLA602 4.1 83.0 1.0 C12 B:CLA602 4.1 76.4 1.0 C3D B:CLA602 4.2 66.1 1.0 CE2 B:PHE190 4.2 51.2 1.0 O B:TRP185 4.3 57.5 1.0 C11 B:CLA602 4.4 78.0 1.0 C3B B:CLA602 4.4 55.6 1.0 C2C B:CLA602 4.4 57.5 1.0 C2B B:CLA602 4.4 55.2 1.0 C2D B:CLA602 4.4 63.6 1.0 CZ B:PHE190 4.5 53.2 1.0 C3C B:CLA602 4.5 61.2 1.0 C2A B:CLA602 4.5 71.7 1.0 C3A B:CLA602 4.5 67.9 1.0 CBB B:CLA603 4.6 57.9 1.0 O B:HOH783 4.9 54.4 1.0 CBD B:CLA602 4.9 71.1 1.0

Magnesium binding site 5 out of 72 in the Crystal Structure of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:49.7 occ:1.00 MG B:CLA603 0.0 49.7 1.0 ND B:CLA603 1.9 47.3 1.0 NB B:CLA603 2.1 51.5 1.0 NC B:CLA603 2.2 49.0 1.0 NA B:CLA603 2.2 45.6 1.0 ND1 B:HIS201 2.3 48.0 1.0 C4D B:CLA603 2.9 43.3 1.0 CE1 B:HIS201 3.0 48.4 1.0 C4B B:CLA603 3.1 51.5 1.0 C1B B:CLA603 3.1 48.1 1.0 C1C B:CLA603 3.1 51.0 1.0 C1D B:CLA603 3.2 45.3 1.0 C1A B:CLA603 3.2 47.9 1.0 C4A B:CLA603 3.2 48.2 1.0 C4C B:CLA603 3.2 51.5 1.0 CG B:HIS201 3.4 48.6 1.0 CHC B:CLA603 3.4 46.6 1.0 CHA B:CLA603 3.5 42.1 1.0 CHB B:CLA603 3.5 42.5 1.0 CHD B:CLA603 3.7 47.0 1.0 CB B:HIS201 3.9 47.4 1.0 CZ H:PHE41 3.9 53.1 1.0 C3D B:CLA603 4.2 44.4 1.0 NE2 B:HIS201 4.2 49.4 1.0 CE2 H:PHE41 4.3 54.7 1.0 C3B B:CLA603 4.4 49.9 1.0 C2D B:CLA603 4.4 44.7 1.0 C2B B:CLA603 4.4 50.2 1.0 CD2 B:HIS201 4.4 49.3 1.0 C2C B:CLA603 4.5 48.2 1.0 CA B:HIS201 4.5 48.8 1.0 C3A B:CLA603 4.5 49.3 1.0 C3C B:CLA603 4.5 48.3 1.0 C2A B:CLA603 4.5 47.7 1.0 CBD B:CLA603 4.9 45.1 1.0 CE1 H:PHE41 5.0 54.7 1.0

Magnesium binding site 6 out of 72 in the Crystal Structure of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:45.1 occ:1.00 MG B:CLA604 0.0 45.1 1.0 ND B:CLA604 2.0 44.1 1.0 NB B:CLA604 2.0 46.0 1.0 NE2 B:HIS202 2.1 47.8 1.0 NC B:CLA604 2.2 41.0 1.0 NA B:CLA604 2.2 45.2 1.0 C4D B:CLA604 2.9 40.5 1.0 C4B B:CLA604 3.0 47.1 1.0 C1B B:CLA604 3.0 46.3 1.0 CD2 B:HIS202 3.1 46.3 1.0 CE1 B:HIS202 3.1 48.9 1.0 C1C B:CLA604 3.1 45.2 1.0 C4A B:CLA604 3.2 44.4 1.0 C1A B:CLA604 3.2 44.0 1.0 C1D B:CLA604 3.2 43.2 1.0 C4C B:CLA604 3.2 43.5 1.0 CHC B:CLA604 3.4 45.4 1.0 CHB B:CLA604 3.4 43.0 1.0 CHA B:CLA604 3.5 44.7 1.0 CHD B:CLA604 3.7 40.2 1.0 C3D B:CLA604 4.2 43.1 1.0 ND1 B:HIS202 4.2 44.9 1.0 CG B:HIS202 4.2 47.5 1.0 C3B B:CLA604 4.3 42.9 1.0 C2B B:CLA604 4.4 43.4 1.0 C2D B:CLA604 4.4 40.6 1.0 C2C B:CLA604 4.5 51.0 1.0 C2A B:CLA604 4.5 44.6 1.0 C3A B:CLA604 4.5 41.9 1.0 C3C B:CLA604 4.5 51.3 1.0 C6 B:CLA606 4.7 55.5 1.0 C4 B:CLA606 4.7 54.4 1.0 NE2 B:HIS201 4.7 49.4 1.0 C7 B:CLA606 4.8 59.0 1.0 CD2 B:HIS201 4.8 49.3 1.0 CBD B:CLA604 5.0 45.6 1.0 C5 B:CLA606 5.0 46.7 1.0 CBA B:CLA604 5.0 41.6 1.0

Magnesium binding site 7 out of 72 in the Crystal Structure of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:40.8 occ:1.00 MG B:CLA605 0.0 40.8 1.0 ND B:CLA605 1.9 38.6 1.0 NB B:CLA605 2.1 40.8 1.0 NE2 B:HIS455 2.2 44.8 1.0 NA B:CLA605 2.2 40.7 1.0 NC B:CLA605 2.3 35.7 1.0 C4D B:CLA605 2.9 38.1 1.0 CD2 B:HIS455 3.1 38.7 1.0 C4B B:CLA605 3.1 37.7 1.0 C1B B:CLA605 3.1 41.5 1.0 C4A B:CLA605 3.1 40.2 1.0 C1D B:CLA605 3.1 36.4 1.0 C1A B:CLA605 3.2 34.6 1.0 C1C B:CLA605 3.2 34.0 1.0 CE1 B:HIS455 3.2 42.7 1.0 C4C B:CLA605 3.3 34.5 1.0 CHB B:CLA605 3.4 37.9 1.0 CHA B:CLA605 3.5 35.1 1.0 CHC B:CLA605 3.5 31.3 1.0 CHD B:CLA605 3.7 36.3 1.0 C14 B:CLA613 4.1 44.5 1.0 C3D B:CLA605 4.2 33.5 1.0 CG B:HIS455 4.2 43.1 1.0 ND1 B:HIS455 4.3 44.2 1.0 C2D B:CLA605 4.4 39.2 1.0 C3B B:CLA605 4.4 36.1 1.0 C2B B:CLA605 4.4 38.2 1.0 C3A B:CLA605 4.5 42.2 1.0 C2A B:CLA605 4.5 40.5 1.0 C2C B:CLA605 4.5 38.6 1.0 C3C B:CLA605 4.6 40.2 1.0 C13 B:CLA613 4.7 47.9 1.0 C15 B:CLA613 4.9 42.9 1.0 CBD B:CLA605 4.9 43.0 1.0 CE2 B:PHE451 5.0 38.6 1.0

Magnesium binding site 8 out of 72 in the Crystal Structure of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:43.6 occ:1.00 MG B:CLA606 0.0 43.6 1.0 ND B:CLA606 2.0 43.3 1.0 NB B:CLA606 2.1 38.6 1.0 NC B:CLA606 2.2 43.0 1.0 NA B:CLA606 2.2 44.5 1.0 NE2 B:HIS100 2.2 43.3 1.0 C4D B:CLA606 2.9 38.7 1.0 C4B B:CLA606 3.1 40.5 1.0 C1B B:CLA606 3.1 40.9 1.0 C1C B:CLA606 3.1 38.9 1.0 C4A B:CLA606 3.1 45.5 1.0 CE1 B:HIS100 3.2 42.4 1.0 C1A B:CLA606 3.2 40.3 1.0 C1D B:CLA606 3.2 44.5 1.0 C4C B:CLA606 3.2 45.2 1.0 CD2 B:HIS100 3.3 42.3 1.0 CHB B:CLA606 3.4 37.8 1.0 CHC B:CLA606 3.4 37.1 1.0 CHA B:CLA606 3.5 35.7 1.0 CHD B:CLA606 3.7 44.5 1.0 C1 B:CLA605 4.1 56.5 1.0 C2 B:CLA605 4.2 59.0 1.0 C3D B:CLA606 4.2 40.0 1.0 ND1 B:HIS100 4.3 38.9 1.0 C3B B:CLA606 4.4 40.5 1.0 CG B:HIS100 4.4 41.1 1.0 C2B B:CLA606 4.4 38.4 1.0 C2D B:CLA606 4.4 39.7 1.0 C2C B:CLA606 4.4 39.8 1.0 C3C B:CLA606 4.5 41.2 1.0 C3A B:CLA606 4.5 43.3 1.0 C2A B:CLA606 4.5 41.9 1.0 CBD B:CLA606 5.0 40.0 1.0

Magnesium binding site 9 out of 72 in the Crystal Structure of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:49.0 occ:1.00 MG B:CLA607 0.0 49.0 1.0 ND B:CLA607 2.0 52.5 1.0 NB B:CLA607 2.0 47.3 1.0 NC B:CLA607 2.2 43.9 1.0 ND1 B:HIS157 2.2 48.0 1.0 NA B:CLA607 2.3 43.6 1.0 C4D B:CLA607 2.9 49.3 1.0 CE1 B:HIS157 3.0 44.9 1.0 C4B B:CLA607 3.0 41.9 1.0 C1B B:CLA607 3.0 39.7 1.0 C1C B:CLA607 3.1 46.7 1.0 C4A B:CLA607 3.2 45.0 1.0 C1D B:CLA607 3.2 53.2 1.0 C4C B:CLA607 3.2 47.7 1.0 C1A B:CLA607 3.2 41.9 1.0 CHB B:CLA607 3.4 42.1 1.0 CG B:HIS157 3.4 46.2 1.0 CHC B:CLA607 3.4 43.4 1.0 CHA B:CLA607 3.5 42.5 1.0 CHD B:CLA607 3.7 52.5 1.0 C27 B:UNL633 3.7 61.3 1.0 C26 B:UNL633 3.8 68.8 1.0 CB B:HIS157 3.9 52.2 1.0 C29 B:UNL633 4.1 73.6 1.0 NE2 B:HIS157 4.2 47.0 1.0 C3D B:CLA607 4.2 53.5 1.0 C3B B:CLA607 4.3 38.5 1.0 C2B B:CLA607 4.3 41.0 1.0 C2D B:CLA607 4.4 54.1 1.0 CD2 B:HIS157 4.4 42.9 1.0 C28 B:UNL633 4.5 65.8 1.0 C2C B:CLA607 4.5 42.2 1.0 C3C B:CLA607 4.5 45.3 1.0 C3A B:CLA607 4.6 37.5 1.0 C2A B:CLA607 4.6 41.4 1.0 CD B:PRO164 5.0 52.7 1.0 CBD B:CLA607 5.0 46.6 1.0

Magnesium binding site 10 out of 72 in the Crystal Structure of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg608 b:42.4 occ:1.00 MG B:CLA608 0.0 42.4 1.0 ND B:CLA608 2.0 44.3 1.0 O B:HOH901 2.0 35.3 1.0 NB B:CLA608 2.1 40.1 1.0 NC B:CLA608 2.2 42.5 1.0 NA B:CLA608 2.3 43.8 1.0 C4D B:CLA608 2.9 40.7 1.0 C4B B:CLA608 3.0 42.1 1.0 C1B B:CLA608 3.1 43.2 1.0 C1C B:CLA608 3.1 41.4 1.0 C1D B:CLA608 3.2 43.1 1.0 C4A B:CLA608 3.2 43.9 1.0 C1A B:CLA608 3.2 42.1 1.0 C4C B:CLA608 3.2 39.6 1.0 CHB B:CLA608 3.5 43.3 1.0 CHC B:CLA608 3.5 39.3 1.0 CHA B:CLA608 3.5 40.3 1.0 C12 B:LMG622 3.6 63.7 1.0 CHD B:CLA608 3.6 39.4 1.0 C14 B:LMG622 3.8 60.8 1.0 O B:HOH814 4.2 40.2 1.0 C3D B:CLA608 4.2 38.6 1.0 C3B B:CLA608 4.4 41.5 1.0 C13 B:LMG622 4.4 59.7 1.0 C2B B:CLA608 4.4 42.3 1.0 C2D B:CLA608 4.4 43.8 1.0 SD B:MET37 4.4 42.5 1.0 C2C B:CLA608 4.5 41.6 1.0 C3C B:CLA608 4.5 41.5 1.0 C3A B:CLA608 4.5 37.4 1.0 C2A B:CLA608 4.5 40.3 1.0 O9 B:LMG622 4.6 83.5 1.0 CD2 B:PHE61 4.6 39.4 1.0 CE B:MET37 4.8 36.6 1.0 C11 B:LMG622 4.8 64.9 1.0 CBA B:CLA608 4.9 36.8 1.0 CB B:PHE61 4.9 37.3 1.0 CBD B:CLA608 5.0 38.6 1.0 CG B:PHE61 5.0 44.8 1.0

S.Kamada, Y.Nakajima, J.R.Shen. Structural Insights Into the Action Mechanisms of Artificial Electron Acceptors in Photosystem II. J.Biol.Chem. V. 299 04839 2023.
ISSN: ESSN 1083-351X
PubMed: 37209822
DOI: 10.1016/J.JBC.2023.104839