Magnesium in PDB 7d1u: Cryo-Em Structure of Psii at 2.08 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution:
1.10.3.9;

The structure of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Calcium	(Ca)	2 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 Cryo-Em Structure of Psii at 2.08 Angstrom Resolution (pdb code 7d1u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 72 binding sites of Magnesium where determined in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution, PDB code: 7d1u:
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 Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:8.5 occ:1.00 MG A:CLA405 0.0 8.5 1.0 ND A:CLA405 2.0 8.5 1.0 NB A:CLA405 2.0 8.5 1.0 NC A:CLA405 2.1 8.5 1.0 NA A:CLA405 2.1 8.6 1.0 NE2 A:HIS198 2.3 8.4 1.0 C4D A:CLA405 2.9 8.5 1.0 C1C A:CLA405 3.0 8.5 1.0 C1B A:CLA405 3.0 8.5 1.0 C4B A:CLA405 3.0 8.5 1.0 C4A A:CLA405 3.0 8.6 1.0 C1A A:CLA405 3.1 8.6 1.0 C4C A:CLA405 3.2 8.5 1.0 CE1 A:HIS198 3.2 8.4 1.0 C1D A:CLA405 3.2 8.5 1.0 CD2 A:HIS198 3.4 8.4 1.0 CHB A:CLA405 3.4 8.5 1.0 CHC A:CLA405 3.4 8.5 1.0 CHA A:CLA405 3.4 8.6 1.0 CHD A:CLA405 3.7 8.5 1.0 CE A:MET183 3.9 7.9 1.0 C3D A:CLA405 4.2 8.5 1.0 ND1 A:HIS198 4.3 8.4 1.0 C3B A:CLA405 4.4 8.5 1.0 C2B A:CLA405 4.4 8.5 1.0 CAB D:CLA403 4.4 8.5 1.0 C2C A:CLA405 4.4 8.4 1.0 C3A A:CLA405 4.4 8.6 1.0 C2A A:CLA405 4.4 8.7 1.0 C2D A:CLA405 4.4 8.5 1.0 C3C A:CLA405 4.4 8.4 1.0 CG A:HIS198 4.5 8.4 1.0 CBD A:CLA405 4.8 8.5 1.0

Magnesium binding site 2 out of 72 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:11.3 occ:1.00 MG A:CLA406 0.0 11.3 1.0 NB A:CLA406 2.0 11.3 1.0 ND A:CLA406 2.0 11.3 1.0 NC A:CLA406 2.1 11.3 1.0 NA A:CLA406 2.1 11.5 1.0 O A:HOH607 2.2 9.5 1.0 C4D A:CLA406 3.0 11.3 1.0 C1C A:CLA406 3.0 11.2 1.0 C4B A:CLA406 3.0 11.3 1.0 C1B A:CLA406 3.0 11.4 1.0 C4A A:CLA406 3.0 11.6 1.0 C1A A:CLA406 3.1 11.6 1.0 C4C A:CLA406 3.1 11.2 1.0 C1D A:CLA406 3.3 11.3 1.0 CHC A:CLA406 3.4 11.3 1.0 CHB A:CLA406 3.4 11.5 1.0 CHA A:CLA406 3.4 11.4 1.0 CHD A:CLA406 3.7 11.2 1.0 CBB D:PHO402 3.9 10.3 1.0 O A:HOH600 4.1 8.7 1.0 C3D A:CLA406 4.2 11.3 1.0 C3B A:CLA406 4.3 11.3 1.0 C2B A:CLA406 4.4 11.4 1.0 C2C A:CLA406 4.4 11.2 1.0 C3A A:CLA406 4.4 11.7 1.0 C2A A:CLA406 4.4 11.8 1.0 C3C A:CLA406 4.4 11.2 1.0 C2D A:CLA406 4.5 11.3 1.0 CG2 D:ILE178 4.5 8.5 1.0 CE2 A:PHE206 4.8 8.2 1.0 C20 D:PHO402 4.8 11.2 1.0 CBA A:CLA406 4.9 12.9 1.0 CBD A:CLA406 4.9 11.3 1.0 CG1 D:ILE178 5.0 8.5 1.0

Magnesium binding site 3 out of 72 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:15.3 occ:1.00 MG A:CLA408 0.0 15.3 1.0 ND A:CLA408 2.0 15.2 1.0 NB A:CLA408 2.0 15.2 1.0 NC A:CLA408 2.1 15.2 1.0 NA A:CLA408 2.1 15.5 1.0 NE2 A:HIS118 2.3 9.5 1.0 C4D A:CLA408 3.0 15.2 1.0 C1C A:CLA408 3.0 15.2 1.0 C4A A:CLA408 3.0 15.6 1.0 C4B A:CLA408 3.0 15.2 1.0 C1B A:CLA408 3.0 15.3 1.0 C1A A:CLA408 3.1 15.6 1.0 C4C A:CLA408 3.1 15.2 1.0 CE1 A:HIS118 3.1 9.5 1.0 C1D A:CLA408 3.2 15.2 1.0 CD2 A:HIS118 3.3 9.4 1.0 CHB A:CLA408 3.4 15.4 1.0 CHC A:CLA408 3.4 15.2 1.0 CHA A:CLA408 3.5 15.3 1.0 CHD A:CLA408 3.7 15.2 1.0 CG1 I:VAL8 4.2 18.4 1.0 C3D A:CLA408 4.2 15.2 1.0 CG2 I:VAL12 4.3 17.2 1.0 ND1 A:HIS118 4.3 9.4 1.0 C3B A:CLA408 4.3 15.2 1.0 C2B A:CLA408 4.3 15.2 1.0 C2C A:CLA408 4.4 15.1 1.0 C3A A:CLA408 4.4 15.8 1.0 CG A:HIS118 4.4 9.4 1.0 C2A A:CLA408 4.4 16.0 1.0 C3C A:CLA408 4.4 15.1 1.0 C2D A:CLA408 4.5 15.2 1.0 CBD A:CLA408 4.9 15.2 1.0

Magnesium binding site 4 out of 72 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:29.2 occ:1.00 MG B:CLA601 0.0 29.2 1.0 ND B:CLA601 2.0 29.2 1.0 NB B:CLA601 2.0 29.0 1.0 NC B:CLA601 2.1 28.9 1.0 NA B:CLA601 2.1 29.6 1.0 O B:HOH807 2.3 21.9 1.0 C4D B:CLA601 3.0 29.4 1.0 C1C B:CLA601 3.0 28.8 1.0 C4A B:CLA601 3.0 29.6 1.0 C4B B:CLA601 3.0 28.9 1.0 C1B B:CLA601 3.0 29.0 1.0 C1A B:CLA601 3.1 29.9 1.0 C4C B:CLA601 3.1 28.9 1.0 C1D B:CLA601 3.2 29.2 1.0 CHB B:CLA601 3.4 29.4 1.0 CHC B:CLA601 3.4 28.9 1.0 CHA B:CLA601 3.5 29.6 1.0 CHD B:CLA601 3.7 29.0 1.0 C10 B:CLA601 3.8 40.9 1.0 C12 B:CLA601 4.0 41.9 1.0 C11 B:CLA601 4.1 41.4 1.0 C3D B:CLA601 4.3 29.4 1.0 O B:TRP185 4.3 15.8 1.0 C2C B:CLA601 4.3 28.8 1.0 C3B B:CLA601 4.3 28.9 1.0 C2B B:CLA601 4.4 29.0 1.0 C3A B:CLA601 4.4 30.0 1.0 C2A B:CLA601 4.4 30.4 1.0 C3C B:CLA601 4.4 28.8 1.0 CE2 B:PHE190 4.5 14.4 1.0 C2D B:CLA601 4.5 29.3 1.0 CBB B:CLA602 4.6 14.1 1.0 C7 B:CLA601 4.7 39.9 1.0 O B:HOH711 4.8 17.1 1.0 CZ B:PHE190 4.8 14.3 1.0 C8 B:CLA601 4.9 40.5 1.0 CBD B:CLA601 4.9 29.6 1.0

Magnesium binding site 5 out of 72 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:14.0 occ:1.00 MG B:CLA602 0.0 14.0 1.0 ND B:CLA602 2.0 14.0 1.0 NB B:CLA602 2.0 14.0 1.0 NC B:CLA602 2.1 14.0 1.0 NA B:CLA602 2.1 14.1 1.0 ND1 B:HIS201 2.2 12.0 1.0 CE1 B:HIS201 2.9 12.0 1.0 C4D B:CLA602 3.0 14.0 1.0 C1C B:CLA602 3.0 14.0 1.0 C4A B:CLA602 3.0 14.1 1.0 C1B B:CLA602 3.0 14.0 1.0 C4B B:CLA602 3.0 14.0 1.0 C1A B:CLA602 3.1 14.1 1.0 C4C B:CLA602 3.1 13.9 1.0 C1D B:CLA602 3.3 13.9 1.0 CHB B:CLA602 3.4 14.1 1.0 CG B:HIS201 3.4 12.1 1.0 CHC B:CLA602 3.4 14.0 1.0 CHA B:CLA602 3.5 14.0 1.0 CZ H:PHE41 3.7 14.5 1.0 CHD B:CLA602 3.7 13.9 1.0 CB B:HIS201 3.9 12.1 1.0 NE2 B:HIS201 4.1 12.0 1.0 C3D B:CLA602 4.3 13.9 1.0 CE2 H:PHE41 4.3 14.5 1.0 C2C B:CLA602 4.3 14.0 1.0 C3B B:CLA602 4.3 14.0 1.0 C2B B:CLA602 4.4 14.0 1.0 CD2 B:HIS201 4.4 12.0 1.0 C3A B:CLA602 4.4 14.2 1.0 C3C B:CLA602 4.4 13.9 1.0 C2A B:CLA602 4.4 14.3 1.0 CA B:HIS201 4.5 12.1 1.0 C2D B:CLA602 4.5 13.9 1.0 CE1 H:PHE41 4.6 14.5 1.0 CE1 B:PHE190 4.9 14.3 1.0 CBD B:CLA602 4.9 14.0 1.0 CMA B:CLA602 5.0 14.2 1.0

Magnesium binding site 6 out of 72 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:11.8 occ:1.00 MG B:CLA603 0.0 11.8 1.0 ND B:CLA603 2.0 11.8 1.0 NB B:CLA603 2.0 11.8 1.0 NC B:CLA603 2.1 11.7 1.0 NA B:CLA603 2.1 11.8 1.0 NE2 B:HIS202 2.2 12.1 1.0 C4D B:CLA603 3.0 11.8 1.0 C1B B:CLA603 3.0 11.8 1.0 C4A B:CLA603 3.0 11.8 1.0 C4B B:CLA603 3.0 11.7 1.0 C1C B:CLA603 3.0 11.7 1.0 C1A B:CLA603 3.1 11.8 1.0 C4C B:CLA603 3.1 11.7 1.0 CD2 B:HIS202 3.1 12.1 1.0 C1D B:CLA603 3.2 11.7 1.0 CE1 B:HIS202 3.2 12.1 1.0 CHB B:CLA603 3.4 11.8 1.0 CHC B:CLA603 3.4 11.7 1.0 CHA B:CLA603 3.5 11.8 1.0 CHD B:CLA603 3.6 11.7 1.0 C3D B:CLA603 4.3 11.7 1.0 CG B:HIS202 4.3 12.1 1.0 C2B B:CLA603 4.3 11.8 1.0 ND1 B:HIS202 4.3 12.1 1.0 C3B B:CLA603 4.3 11.8 1.0 C2C B:CLA603 4.4 11.7 1.0 C3A B:CLA603 4.4 11.8 1.0 C2A B:CLA603 4.4 11.9 1.0 C3C B:CLA603 4.4 11.7 1.0 C2D B:CLA603 4.4 11.7 1.0 C6 B:CLA605 4.5 13.7 1.0 C7 B:CLA605 4.6 13.9 1.0 C5 B:CLA605 4.7 13.4 1.0 C9 B:CLA605 4.7 14.1 1.0 C4 B:CLA605 4.8 13.2 1.0 CD2 B:HIS201 4.8 12.0 1.0 NE2 B:HIS201 4.9 12.0 1.0 CBD B:CLA603 5.0 11.8 1.0

Magnesium binding site 7 out of 72 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:11.7 occ:1.00 MG B:CLA604 0.0 11.7 1.0 ND B:CLA604 2.0 11.7 1.0 NB B:CLA604 2.0 11.7 1.0 NC B:CLA604 2.1 11.6 1.0 NA B:CLA604 2.1 11.9 1.0 NE2 B:HIS455 2.2 8.1 1.0 C4D B:CLA604 3.0 11.7 1.0 C4B B:CLA604 3.0 11.6 1.0 C1B B:CLA604 3.0 11.7 1.0 C1C B:CLA604 3.0 11.6 1.0 C4A B:CLA604 3.0 11.9 1.0 C1A B:CLA604 3.1 12.0 1.0 C4C B:CLA604 3.1 11.6 1.0 CE1 B:HIS455 3.1 8.0 1.0 CD2 B:HIS455 3.2 8.1 1.0 C1D B:CLA604 3.2 11.6 1.0 CHB B:CLA604 3.4 11.8 1.0 CHC B:CLA604 3.4 11.6 1.0 CHA B:CLA604 3.5 11.8 1.0 CHD B:CLA604 3.7 11.6 1.0 C14 B:CLA612 3.9 12.4 1.0 C3D B:CLA604 4.2 11.7 1.0 ND1 B:HIS455 4.2 8.0 1.0 CG B:HIS455 4.3 8.0 1.0 C3B B:CLA604 4.3 11.6 1.0 C2B B:CLA604 4.3 11.7 1.0 C2C B:CLA604 4.4 11.6 1.0 C3A B:CLA604 4.4 12.1 1.0 C3C B:CLA604 4.4 11.6 1.0 C2A B:CLA604 4.4 12.2 1.0 C2D B:CLA604 4.4 11.7 1.0 C13 B:CLA612 4.6 12.4 1.0 C15 B:CLA612 4.7 12.5 1.0 CBD B:CLA604 4.9 11.8 1.0 CE1 B:PHE451 5.0 8.3 1.0

Magnesium binding site 8 out of 72 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:11.4 occ:1.00 MG B:CLA605 0.0 11.4 1.0 ND B:CLA605 2.0 11.4 1.0 NB B:CLA605 2.0 11.4 1.0 NC B:CLA605 2.1 11.4 1.0 NA B:CLA605 2.1 11.5 1.0 NE2 B:HIS100 2.2 11.6 1.0 C4D B:CLA605 3.0 11.4 1.0 C4A B:CLA605 3.0 11.5 1.0 C1B B:CLA605 3.0 11.4 1.0 C1C B:CLA605 3.0 11.4 1.0 C4B B:CLA605 3.1 11.4 1.0 C1A B:CLA605 3.1 11.5 1.0 C4C B:CLA605 3.1 11.4 1.0 CD2 B:HIS100 3.2 11.6 1.0 CE1 B:HIS100 3.2 11.6 1.0 C1D B:CLA605 3.2 11.4 1.0 CHB B:CLA605 3.4 11.5 1.0 CHC B:CLA605 3.4 11.4 1.0 CHA B:CLA605 3.5 11.4 1.0 CHD B:CLA605 3.7 11.4 1.0 C1 B:CLA604 4.0 15.2 1.0 C3D B:CLA605 4.3 11.4 1.0 ND1 B:HIS100 4.3 11.6 1.0 C2B B:CLA605 4.4 11.4 1.0 CG B:HIS100 4.4 11.6 1.0 C3B B:CLA605 4.4 11.4 1.0 C2C B:CLA605 4.4 11.4 1.0 C3A B:CLA605 4.4 11.6 1.0 C2A B:CLA605 4.4 11.6 1.0 C3C B:CLA605 4.4 11.3 1.0 C2D B:CLA605 4.5 11.4 1.0 C4 B:CLA604 4.6 16.6 1.0 C2 B:CLA604 4.8 15.9 1.0 CBD B:CLA605 4.9 11.4 1.0 O1A B:CLA604 4.9 13.8 1.0

Magnesium binding site 9 out of 72 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:15.5 occ:1.00 MG B:CLA606 0.0 15.5 1.0 ND B:CLA606 2.0 15.6 1.0 NB B:CLA606 2.0 15.5 1.0 NC B:CLA606 2.1 15.5 1.0 NA B:CLA606 2.1 15.6 1.0 ND1 B:HIS157 2.2 13.8 1.0 CE1 B:HIS157 2.9 13.8 1.0 C4D B:CLA606 3.0 15.6 1.0 C1B B:CLA606 3.0 15.5 1.0 C4A B:CLA606 3.0 15.6 1.0 C1C B:CLA606 3.0 15.5 1.0 C4B B:CLA606 3.0 15.5 1.0 C1A B:CLA606 3.1 15.7 1.0 C4C B:CLA606 3.1 15.5 1.0 C1D B:CLA606 3.2 15.5 1.0 CHB B:CLA606 3.3 15.6 1.0 CHC B:CLA606 3.4 15.5 1.0 CG B:HIS157 3.4 13.8 1.0 CHA B:CLA606 3.5 15.6 1.0 CHD B:CLA606 3.6 15.5 1.0 C15 B:UNL622 3.7 23.0 1.0 C13 B:UNL622 3.9 23.0 1.0 CB B:HIS157 4.0 13.8 1.0 NE2 B:HIS157 4.1 13.8 1.0 C3D B:CLA606 4.3 15.6 1.0 C2B B:CLA606 4.3 15.5 1.0 C3B B:CLA606 4.3 15.5 1.0 C2C B:CLA606 4.4 15.5 1.0 CD2 B:HIS157 4.4 13.8 1.0 C14 B:UNL622 4.4 23.1 1.0 C3A B:CLA606 4.4 15.7 1.0 C3C B:CLA606 4.4 15.5 1.0 C2A B:CLA606 4.4 15.8 1.0 C2D B:CLA606 4.5 15.6 1.0 C16 B:UNL622 4.9 23.0 1.0 CD B:PRO164 4.9 14.6 1.0 CBD B:CLA606 5.0 15.6 1.0

Magnesium binding site 10 out of 72 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:12.4 occ:1.00 MG B:CLA607 0.0 12.4 1.0 NB B:CLA607 2.0 12.3 1.0 ND B:CLA607 2.0 12.4 1.0 NC B:CLA607 2.1 12.3 1.0 NA B:CLA607 2.1 12.5 1.0 O B:HOH894 2.2 10.6 1.0 C4D B:CLA607 3.0 12.4 1.0 C1B B:CLA607 3.0 12.3 1.0 C4B B:CLA607 3.0 12.3 1.0 C1C B:CLA607 3.0 12.3 1.0 C4A B:CLA607 3.0 12.5 1.0 C1A B:CLA607 3.1 12.6 1.0 C4C B:CLA607 3.1 12.3 1.0 C1D B:CLA607 3.2 12.3 1.0 CHB B:CLA607 3.4 12.4 1.0 CHC B:CLA607 3.4 12.3 1.0 C12 B:LMG620 3.5 26.7 1.0 CHA B:CLA607 3.5 12.4 1.0 CHD B:CLA607 3.7 12.3 1.0 C14 B:LMG620 4.3 27.1 1.0 O B:HOH748 4.3 11.0 1.0 C3D B:CLA607 4.3 12.4 1.0 SD B:MET37 4.3 10.0 1.0 C2B B:CLA607 4.3 12.3 1.0 C3B B:CLA607 4.3 12.3 1.0 C2C B:CLA607 4.4 12.3 1.0 C3A B:CLA607 4.4 12.6 1.0 C2A B:CLA607 4.4 12.8 1.0 C3C B:CLA607 4.4 12.3 1.0 C11 B:LMG620 4.4 26.5 1.0 C2D B:CLA607 4.5 12.3 1.0 C13 B:LMG620 4.5 26.9 1.0 CD2 B:PHE61 4.6 11.2 1.0 CE B:MET37 4.6 10.0 1.0 CB B:PHE61 4.8 11.2 1.0 CG B:PHE61 4.9 11.2 1.0 CBD B:CLA607 4.9 12.4 1.0

K.Kato, N.Miyazaki, T.Hamaguchi, Y.Nakajima, F.Akita, K.Yonekura, J.R.Shen. High-Resolution Cryo-Em Structure of Photosystem II Reveals Damage From High-Dose Electron Beams Commun Biol 2021.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-021-01919-3