Magnesium in PDB 7eda: Structure of Monomeric Photosystem II

All present enzymatic activity of Structure of Monomeric Photosystem II:
1.10.3.9;

The structure of Structure of Monomeric Photosystem II also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Manganese	(Mn)	4 atoms
Iron	(Fe)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Magnesium atom in the Structure of Monomeric Photosystem II (pdb code 7eda). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 35 binding sites of Magnesium where determined in the Structure of Monomeric Photosystem II, PDB code: 7eda:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 35 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Monomeric Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:22.2 occ:1.00 MG A:CLA405 0.0 22.2 1.0 ND A:CLA405 2.0 22.2 1.0 NB A:CLA405 2.0 22.2 1.0 NC A:CLA405 2.1 22.2 1.0 NA A:CLA405 2.1 22.2 1.0 NE2 A:HIS198 2.2 22.2 1.0 CE1 A:HIS198 2.9 22.2 1.0 C4D A:CLA405 3.0 22.2 1.0 C1C A:CLA405 3.0 22.2 1.0 C4B A:CLA405 3.0 22.2 1.0 C4A A:CLA405 3.0 22.2 1.0 C1B A:CLA405 3.0 22.2 1.0 C1A A:CLA405 3.0 22.2 1.0 C4C A:CLA405 3.1 22.2 1.0 C1D A:CLA405 3.2 22.2 1.0 CD2 A:HIS198 3.4 22.2 1.0 CHC A:CLA405 3.4 22.2 1.0 CHB A:CLA405 3.4 22.2 1.0 CHA A:CLA405 3.5 22.2 1.0 CBB D:CLA402 3.5 13.2 1.0 CHD A:CLA405 3.7 22.2 1.0 CE A:MET183 4.1 14.3 1.0 ND1 A:HIS198 4.2 22.2 1.0 C3D A:CLA405 4.2 22.2 1.0 C2C A:CLA405 4.3 22.2 1.0 C3B A:CLA405 4.3 22.2 1.0 C2B A:CLA405 4.3 22.2 1.0 C2A A:CLA405 4.4 22.2 1.0 C3A A:CLA405 4.4 22.2 1.0 CG A:HIS198 4.4 22.2 1.0 C3C A:CLA405 4.4 22.2 1.0 C2D A:CLA405 4.5 22.2 1.0 CAB D:CLA402 4.7 13.2 1.0 CBD A:CLA405 4.9 22.2 1.0 CG2 A:VAL202 4.9 10.8 1.0

Magnesium binding site 2 out of 35 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Monomeric Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:9.6 occ:1.00 MG A:CLA406 0.0 9.6 1.0 ND A:CLA406 2.0 9.6 1.0 NC A:CLA406 2.0 9.6 1.0 NB A:CLA406 2.0 9.6 1.0 NA A:CLA406 2.1 9.6 1.0 O A:HOH552 2.2 11.9 1.0 C4D A:CLA406 3.0 9.6 1.0 C1C A:CLA406 3.0 9.6 1.0 C4A A:CLA406 3.0 9.6 1.0 C1B A:CLA406 3.0 9.6 1.0 C4B A:CLA406 3.0 9.6 1.0 C1A A:CLA406 3.0 9.6 1.0 C4C A:CLA406 3.1 9.6 1.0 C1D A:CLA406 3.3 9.6 1.0 CHB A:CLA406 3.3 9.6 1.0 CHC A:CLA406 3.4 9.6 1.0 CHA A:CLA406 3.4 9.6 1.0 CBB A:PHO408 3.6 22.2 1.0 CHD A:CLA406 3.7 9.6 1.0 C3D A:CLA406 4.2 9.6 1.0 C2C A:CLA406 4.3 9.6 1.0 C2B A:CLA406 4.3 9.6 1.0 C3C A:CLA406 4.3 9.6 1.0 C3B A:CLA406 4.3 9.6 1.0 C3A A:CLA406 4.4 9.6 1.0 C2A A:CLA406 4.4 9.6 1.0 C2D A:CLA406 4.5 9.6 1.0 CG2 A:THR179 4.5 9.9 1.0 OG1 A:THR179 4.6 9.9 1.0 CAB A:PHO408 4.8 22.2 1.0 CBA A:CLA406 4.8 9.6 1.0 CBD A:CLA406 4.9 9.6 1.0

Magnesium binding site 3 out of 35 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Monomeric Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:12.5 occ:1.00 MG A:CLA407 0.0 12.5 1.0 ND A:CLA407 2.0 12.5 1.0 NB A:CLA407 2.0 12.5 1.0 NC A:CLA407 2.0 12.5 1.0 NA A:CLA407 2.1 12.5 1.0 O A:HOH565 2.2 7.0 1.0 C4D A:CLA407 3.0 12.5 1.0 C1C A:CLA407 3.0 12.5 1.0 C4B A:CLA407 3.0 12.5 1.0 C1B A:CLA407 3.0 12.5 1.0 C4A A:CLA407 3.0 12.5 1.0 C1A A:CLA407 3.1 12.5 1.0 C4C A:CLA407 3.1 12.5 1.0 C1D A:CLA407 3.2 12.5 1.0 CHC A:CLA407 3.3 12.5 1.0 CHB A:CLA407 3.4 12.5 1.0 CHA A:CLA407 3.4 12.5 1.0 CBB A:PHO409 3.6 22.2 1.0 CHD A:CLA407 3.7 12.5 1.0 O A:HOH513 4.0 6.6 1.0 C3D A:CLA407 4.2 12.5 1.0 C2C A:CLA407 4.3 12.5 1.0 C2B A:CLA407 4.3 12.5 1.0 C3B A:CLA407 4.3 12.5 1.0 C3A A:CLA407 4.4 12.5 1.0 C3C A:CLA407 4.4 12.5 1.0 C2A A:CLA407 4.4 12.5 1.0 C2D A:CLA407 4.5 12.5 1.0 CG2 D:ILE178 4.6 8.7 1.0 C20 A:PHO409 4.6 22.2 1.0 CE2 A:PHE206 4.7 12.5 1.0 CG1 D:ILE178 4.7 8.7 1.0 CAB A:PHO409 4.8 22.2 1.0 CBA A:CLA407 4.9 12.5 1.0 C19 A:PHO409 4.9 22.2 1.0 CBD A:CLA407 4.9 12.5 1.0

Magnesium binding site 4 out of 35 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Monomeric Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg410 b:16.9 occ:1.00 MG A:CLA410 0.0 16.9 1.0 ND A:CLA410 2.0 16.9 1.0 NB A:CLA410 2.0 16.9 1.0 NC A:CLA410 2.1 16.9 1.0 NA A:CLA410 2.1 16.9 1.0 NE2 A:HIS118 2.2 13.7 1.0 C4D A:CLA410 3.0 16.9 1.0 C1C A:CLA410 3.0 16.9 1.0 C4B A:CLA410 3.0 16.9 1.0 C4A A:CLA410 3.0 16.9 1.0 C1B A:CLA410 3.0 16.9 1.0 C1A A:CLA410 3.1 16.9 1.0 C4C A:CLA410 3.1 16.9 1.0 CD2 A:HIS118 3.2 13.7 1.0 CE1 A:HIS118 3.2 13.7 1.0 C1D A:CLA410 3.2 16.9 1.0 CHB A:CLA410 3.4 16.9 1.0 CHC A:CLA410 3.4 16.9 1.0 CHA A:CLA410 3.4 16.9 1.0 CHD A:CLA410 3.7 16.9 1.0 CG2 I:VAL12 4.1 25.9 1.0 CG1 I:VAL8 4.2 26.0 1.0 C3D A:CLA410 4.2 16.9 1.0 ND1 A:HIS118 4.3 13.7 1.0 CG A:HIS118 4.3 13.7 1.0 C3B A:CLA410 4.3 16.9 1.0 C2B A:CLA410 4.3 16.9 1.0 C2C A:CLA410 4.4 16.9 1.0 C2A A:CLA410 4.4 16.9 1.0 C3A A:CLA410 4.4 16.9 1.0 C3C A:CLA410 4.4 16.9 1.0 C2D A:CLA410 4.5 16.9 1.0 CBD A:CLA410 4.9 16.9 1.0

Magnesium binding site 5 out of 35 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Monomeric Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:32.4 occ:1.00 MG B:CLA602 0.0 32.4 1.0 ND B:CLA602 2.0 32.4 1.0 NB B:CLA602 2.0 32.4 1.0 NC B:CLA602 2.1 32.4 1.0 NA B:CLA602 2.1 32.4 1.0 O B:HOH979 2.2 30.4 1.0 C4D B:CLA602 3.0 32.4 1.0 C1C B:CLA602 3.0 32.4 1.0 C4B B:CLA602 3.0 32.4 1.0 C1B B:CLA602 3.0 32.4 1.0 C4A B:CLA602 3.0 32.4 1.0 C1A B:CLA602 3.1 32.4 1.0 C4C B:CLA602 3.1 32.4 1.0 C1D B:CLA602 3.3 32.4 1.0 CHC B:CLA602 3.4 32.4 1.0 CHB B:CLA602 3.4 32.4 1.0 CHA B:CLA602 3.5 32.4 1.0 C12 B:CLA602 3.5 32.4 1.0 C10 B:CLA602 3.5 32.4 1.0 CHD B:CLA602 3.7 32.4 1.0 C11 B:CLA602 4.1 32.4 1.0 C3D B:CLA602 4.2 32.4 1.0 C3B B:CLA602 4.3 32.4 1.0 C2B B:CLA602 4.3 32.4 1.0 C2C B:CLA602 4.3 32.4 1.0 C3A B:CLA602 4.4 32.4 1.0 C2A B:CLA602 4.4 32.4 1.0 C3C B:CLA602 4.4 32.4 1.0 O B:TRP185 4.4 26.4 1.0 C8 B:CLA602 4.4 32.4 1.0 C2D B:CLA602 4.5 32.4 1.0 C13 B:CLA602 4.8 32.4 1.0 C15 B:CLA602 4.9 32.4 1.0 CBA B:CLA602 4.9 32.4 1.0 CBD B:CLA602 4.9 32.4 1.0 CE2 B:PHE190 4.9 23.7 1.0

Magnesium binding site 6 out of 35 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Monomeric Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:16.6 occ:1.00 MG B:CLA603 0.0 16.6 1.0 ND B:CLA603 2.0 16.6 1.0 NB B:CLA603 2.0 16.6 1.0 NC B:CLA603 2.1 16.6 1.0 NA B:CLA603 2.1 16.6 1.0 ND1 B:HIS201 2.2 16.4 1.0 C4D B:CLA603 3.0 16.6 1.0 CE1 B:HIS201 3.0 16.4 1.0 C1C B:CLA603 3.0 16.6 1.0 C4A B:CLA603 3.0 16.6 1.0 C1B B:CLA603 3.0 16.6 1.0 C4B B:CLA603 3.0 16.6 1.0 C1A B:CLA603 3.1 16.6 1.0 C4C B:CLA603 3.1 16.6 1.0 C1D B:CLA603 3.3 16.6 1.0 CG B:HIS201 3.3 16.4 1.0 CHC B:CLA603 3.4 16.6 1.0 CHB B:CLA603 3.4 16.6 1.0 CHA B:CLA603 3.4 16.6 1.0 CZ H:PHE41 3.6 22.7 1.0 CHD B:CLA603 3.7 16.6 1.0 CB B:HIS201 3.8 16.4 1.0 NE2 B:HIS201 4.2 16.4 1.0 C3D B:CLA603 4.2 16.6 1.0 C2C B:CLA603 4.3 16.6 1.0 C3B B:CLA603 4.3 16.6 1.0 C2B B:CLA603 4.4 16.6 1.0 CD2 B:HIS201 4.4 16.4 1.0 C3A B:CLA603 4.4 16.6 1.0 C2A B:CLA603 4.4 16.6 1.0 CA B:HIS201 4.4 16.4 1.0 C3C B:CLA603 4.4 16.6 1.0 CE2 H:PHE41 4.4 22.7 1.0 C2D B:CLA603 4.5 16.6 1.0 CE1 B:PHE190 4.5 23.7 1.0 CE1 H:PHE41 4.5 22.7 1.0 CBD B:CLA603 4.9 16.6 1.0

Magnesium binding site 7 out of 35 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Monomeric Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:18.0 occ:1.00 MG B:CLA604 0.0 18.0 1.0 ND B:CLA604 2.0 18.0 1.0 NB B:CLA604 2.0 18.0 1.0 NC B:CLA604 2.1 18.0 1.0 NA B:CLA604 2.1 18.0 1.0 NE2 B:HIS202 2.2 14.7 1.0 C4D B:CLA604 3.0 18.0 1.0 C1B B:CLA604 3.0 18.0 1.0 CD2 B:HIS202 3.0 14.7 1.0 C1C B:CLA604 3.0 18.0 1.0 C4A B:CLA604 3.0 18.0 1.0 C4B B:CLA604 3.0 18.0 1.0 C1A B:CLA604 3.1 18.0 1.0 C4C B:CLA604 3.1 18.0 1.0 C1D B:CLA604 3.2 18.0 1.0 CE1 B:HIS202 3.3 14.7 1.0 CHB B:CLA604 3.3 18.0 1.0 CHC B:CLA604 3.4 18.0 1.0 CHA B:CLA604 3.5 18.0 1.0 CHD B:CLA604 3.7 18.0 1.0 C9 B:CLA606 3.7 18.7 1.0 CG B:HIS202 4.2 14.7 1.0 C3D B:CLA604 4.2 18.0 1.0 ND1 B:HIS202 4.3 14.7 1.0 C2B B:CLA604 4.3 18.0 1.0 C3B B:CLA604 4.3 18.0 1.0 C2C B:CLA604 4.3 18.0 1.0 C3A B:CLA604 4.4 18.0 1.0 C2A B:CLA604 4.4 18.0 1.0 C3C B:CLA604 4.4 18.0 1.0 C2D B:CLA604 4.4 18.0 1.0 C4 B:CLA606 4.5 18.7 1.0 C7 B:CLA606 4.6 18.7 1.0 C8 B:CLA606 4.7 18.7 1.0 CD2 B:HIS201 4.8 16.4 1.0 CE2 B:PHE153 4.8 16.8 1.0 CBD B:CLA604 4.9 18.0 1.0 NE2 B:HIS201 4.9 16.4 1.0

Magnesium binding site 8 out of 35 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Monomeric Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:11.3 occ:1.00 MG B:CLA605 0.0 11.3 1.0 ND B:CLA605 2.0 11.3 1.0 NB B:CLA605 2.0 11.3 1.0 NC B:CLA605 2.1 11.3 1.0 NA B:CLA605 2.1 11.3 1.0 NE2 B:HIS455 2.2 13.8 1.0 C4D B:CLA605 3.0 11.3 1.0 C1C B:CLA605 3.0 11.3 1.0 C4B B:CLA605 3.0 11.3 1.0 C4A B:CLA605 3.0 11.3 1.0 C1B B:CLA605 3.0 11.3 1.0 CD2 B:HIS455 3.0 13.8 1.0 C1A B:CLA605 3.1 11.3 1.0 C4C B:CLA605 3.1 11.3 1.0 CE1 B:HIS455 3.2 13.8 1.0 C1D B:CLA605 3.2 11.3 1.0 CHB B:CLA605 3.3 11.3 1.0 CHC B:CLA605 3.4 11.3 1.0 CHA B:CLA605 3.5 11.3 1.0 CHD B:CLA605 3.7 11.3 1.0 C14 B:CLA613 4.0 8.8 1.0 CG B:HIS455 4.2 13.8 1.0 C3D B:CLA605 4.2 11.3 1.0 ND1 B:HIS455 4.2 13.8 1.0 C3B B:CLA605 4.3 11.3 1.0 C2C B:CLA605 4.3 11.3 1.0 C2B B:CLA605 4.3 11.3 1.0 C3A B:CLA605 4.4 11.3 1.0 C2A B:CLA605 4.4 11.3 1.0 C3C B:CLA605 4.4 11.3 1.0 C2D B:CLA605 4.4 11.3 1.0 C13 B:CLA613 4.6 8.8 1.0 C15 B:CLA613 4.6 8.8 1.0 CAB B:CLA614 4.7 22.2 1.0 CE2 B:PHE451 4.8 12.1 1.0 CZ B:PHE451 4.9 12.1 1.0 CBD B:CLA605 4.9 11.3 1.0 CBB B:CLA614 4.9 22.2 1.0

Magnesium binding site 9 out of 35 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Monomeric Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:18.7 occ:1.00 MG B:CLA606 0.0 18.7 1.0 ND B:CLA606 2.0 18.7 1.0 NB B:CLA606 2.0 18.7 1.0 NC B:CLA606 2.1 18.7 1.0 NA B:CLA606 2.1 18.7 1.0 NE2 B:HIS100 2.2 16.2 1.0 C4D B:CLA606 3.0 18.7 1.0 C1C B:CLA606 3.0 18.7 1.0 C4B B:CLA606 3.0 18.7 1.0 C4A B:CLA606 3.0 18.7 1.0 C1B B:CLA606 3.0 18.7 1.0 CE1 B:HIS100 3.1 16.2 1.0 C1A B:CLA606 3.1 18.7 1.0 C4C B:CLA606 3.1 18.7 1.0 C1D B:CLA606 3.3 18.7 1.0 CD2 B:HIS100 3.3 16.2 1.0 CHC B:CLA606 3.4 18.7 1.0 CHB B:CLA606 3.4 18.7 1.0 CHA B:CLA606 3.5 18.7 1.0 CHD B:CLA606 3.7 18.7 1.0 C1 B:CLA605 3.8 11.3 1.0 C2 B:CLA605 4.0 11.3 1.0 ND1 B:HIS100 4.2 16.2 1.0 C3D B:CLA606 4.2 18.7 1.0 C3B B:CLA606 4.3 18.7 1.0 CG B:HIS100 4.4 16.2 1.0 C2C B:CLA606 4.4 18.7 1.0 C2B B:CLA606 4.4 18.7 1.0 C3A B:CLA606 4.4 18.7 1.0 C2A B:CLA606 4.4 18.7 1.0 C3C B:CLA606 4.4 18.7 1.0 C2D B:CLA606 4.5 18.7 1.0 C3 B:CLA605 4.7 11.3 1.0 O1A B:CLA605 4.7 11.3 1.0 CBD B:CLA606 4.9 18.7 1.0 O2A B:CLA605 5.0 11.3 1.0

Magnesium binding site 10 out of 35 in the Structure of Monomeric Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Monomeric Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:19.9 occ:1.00 MG B:CLA607 0.0 19.9 1.0 ND B:CLA607 2.0 19.9 1.0 NB B:CLA607 2.0 19.9 1.0 NC B:CLA607 2.1 19.9 1.0 NA B:CLA607 2.1 19.9 1.0 ND1 B:HIS157 2.2 18.0 1.0 CE1 B:HIS157 2.9 18.0 1.0 C4D B:CLA607 3.0 19.9 1.0 C4A B:CLA607 3.0 19.9 1.0 C1C B:CLA607 3.0 19.9 1.0 C4B B:CLA607 3.0 19.9 1.0 C1B B:CLA607 3.0 19.9 1.0 C1A B:CLA607 3.1 19.9 1.0 C4C B:CLA607 3.1 19.9 1.0 C1D B:CLA607 3.2 19.9 1.0 CG B:HIS157 3.3 18.0 1.0 CHB B:CLA607 3.4 19.9 1.0 CHC B:CLA607 3.4 19.9 1.0 CHA B:CLA607 3.5 19.9 1.0 CHD B:CLA607 3.6 19.9 1.0 CB B:HIS157 3.8 18.0 1.0 NE2 B:HIS157 4.1 18.0 1.0 C3D B:CLA607 4.3 19.9 1.0 CD2 B:HIS157 4.3 18.0 1.0 C3B B:CLA607 4.3 19.9 1.0 C2C B:CLA607 4.3 19.9 1.0 C2B B:CLA607 4.3 19.9 1.0 C3A B:CLA607 4.4 19.9 1.0 C3C B:CLA607 4.4 19.9 1.0 C2A B:CLA607 4.4 19.9 1.0 C2D B:CLA607 4.5 19.9 1.0 CBD B:CLA607 5.0 19.9 1.0 CA B:HIS157 5.0 18.0 1.0

H.Yu, T.Hamaguchi, Y.Nakajima, K.Kato, K.Kawakami, F.Akita, K.Yonekura, J.R.Shen. Structure of Monomeric Photosystem II To Be Published.