Magnesium in PDB 8kde: Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair

All present enzymatic activity of Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair:
1.10.3.9;

The structure of Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair also contains other interesting chemical elements:

Iron

(Fe)

2 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 Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair (pdb code 8kde). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 35 binding sites of Magnesium where determined in the Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair, PDB code: 8kde:
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 Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair


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 An Intermediate-State Complex During the Process of Photosystem II Repair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:56.4 occ:1.00 MG B:CLA601 0.0 56.4 1.0 NB B:CLA601 2.0 56.4 1.0 ND B:CLA601 2.0 56.4 1.0 NC B:CLA601 2.1 56.4 1.0 NA B:CLA601 2.1 56.4 1.0 C4D B:CLA601 2.9 56.4 1.0 C1B B:CLA601 3.0 56.4 1.0 C4A B:CLA601 3.1 56.4 1.0 C4B B:CLA601 3.1 56.4 1.0 C1C B:CLA601 3.1 56.4 1.0 C1A B:CLA601 3.2 56.4 1.0 C4C B:CLA601 3.2 56.4 1.0 C1D B:CLA601 3.2 56.4 1.0 CHB B:CLA601 3.4 56.4 1.0 CHC B:CLA601 3.4 56.4 1.0 CHA B:CLA601 3.5 56.4 1.0 CHD B:CLA601 3.5 56.4 1.0 O B:TRP185 3.8 56.7 1.0 C3D B:CLA601 4.2 56.4 1.0 C15 B:CLA601 4.3 56.4 1.0 C2B B:CLA601 4.3 56.4 1.0 C3B B:CLA601 4.3 56.4 1.0 C2C B:CLA601 4.4 56.4 1.0 C2D B:CLA601 4.4 56.4 1.0 C3C B:CLA601 4.4 56.4 1.0 C3A B:CLA601 4.4 56.4 1.0 C2A B:CLA601 4.5 56.4 1.0 CE2 B:PHE190 4.8 51.7 1.0 C17 B:CLA601 4.9 56.4 1.0 C12 B:CLA601 4.9 56.4 1.0 CBD B:CLA601 4.9 56.4 1.0 C16 B:CLA601 5.0 56.4 1.0 C B:TRP185 5.0 56.7 1.0

Magnesium binding site 2 out of 35 in the Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair


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 An Intermediate-State Complex During the Process of Photosystem II Repair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:47.8 occ:1.00 MG B:CLA602 0.0 47.8 1.0 NB B:CLA602 2.0 47.8 1.0 ND B:CLA602 2.0 47.8 1.0 NC B:CLA602 2.1 47.8 1.0 NA B:CLA602 2.1 47.8 1.0 ND1 B:HIS201 2.3 46.0 1.0 C4D B:CLA602 2.9 47.8 1.0 CE1 B:HIS201 3.0 46.0 1.0 C1B B:CLA602 3.0 47.8 1.0 C4B B:CLA602 3.1 47.8 1.0 C4A B:CLA602 3.1 47.8 1.0 C1C B:CLA602 3.1 47.8 1.0 C1A B:CLA602 3.1 47.8 1.0 C4C B:CLA602 3.2 47.8 1.0 C1D B:CLA602 3.2 47.8 1.0 CHB B:CLA602 3.4 47.8 1.0 CHC B:CLA602 3.4 47.8 1.0 CG B:HIS201 3.4 46.0 1.0 CHA B:CLA602 3.5 47.8 1.0 CHD B:CLA602 3.6 47.8 1.0 CB B:HIS201 3.9 46.0 1.0 CZ H:PHE60 3.9 49.5 1.0 NE2 B:HIS201 4.2 46.0 1.0 C3D B:CLA602 4.2 47.8 1.0 C2B B:CLA602 4.3 47.8 1.0 C3B B:CLA602 4.3 47.8 1.0 C2C B:CLA602 4.3 47.8 1.0 C2D B:CLA602 4.4 47.8 1.0 C3C B:CLA602 4.4 47.8 1.0 C3A B:CLA602 4.4 47.8 1.0 CE2 H:PHE60 4.4 49.5 1.0 CD2 B:HIS201 4.5 46.0 1.0 C2A B:CLA602 4.5 47.8 1.0 CA B:HIS201 4.6 46.0 1.0 CBD B:CLA602 4.9 47.8 1.0

Magnesium binding site 3 out of 35 in the Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair


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 An Intermediate-State Complex During the Process of Photosystem II Repair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:45.7 occ:1.00 MG B:CLA603 0.0 45.7 1.0 NB B:CLA603 2.0 45.7 1.0 ND B:CLA603 2.0 45.7 1.0 NC B:CLA603 2.1 45.7 1.0 NA B:CLA603 2.1 45.7 1.0 NE2 B:HIS202 2.3 44.7 1.0 C4D B:CLA603 2.9 45.7 1.0 C1B B:CLA603 3.0 45.7 1.0 C4A B:CLA603 3.1 45.7 1.0 C4B B:CLA603 3.1 45.7 1.0 C1C B:CLA603 3.1 45.7 1.0 CE1 B:HIS202 3.1 44.7 1.0 C4C B:CLA603 3.2 45.7 1.0 C1D B:CLA603 3.2 45.7 1.0 C1A B:CLA603 3.2 45.7 1.0 CD2 B:HIS202 3.3 44.7 1.0 CHB B:CLA603 3.4 45.7 1.0 CHC B:CLA603 3.5 45.7 1.0 CHA B:CLA603 3.5 45.7 1.0 CHD B:CLA603 3.5 45.7 1.0 C9 B:CLA605 3.8 45.2 1.0 ND1 B:HIS202 4.2 44.7 1.0 C3D B:CLA603 4.3 45.7 1.0 C2B B:CLA603 4.3 45.7 1.0 C3B B:CLA603 4.3 45.7 1.0 C2C B:CLA603 4.4 45.7 1.0 C2D B:CLA603 4.4 45.7 1.0 CG B:HIS202 4.4 44.7 1.0 C3C B:CLA603 4.4 45.7 1.0 C3A B:CLA603 4.4 45.7 1.0 C2A B:CLA603 4.5 45.7 1.0 O1A B:CLA603 4.5 45.7 1.0 C6 B:CLA605 4.7 45.2 1.0 NE2 B:HIS201 4.8 46.0 1.0 CBD B:CLA603 4.9 45.7 1.0 C7 B:CLA605 5.0 45.2 1.0 C8 B:CLA605 5.0 45.2 1.0

Magnesium binding site 4 out of 35 in the Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair


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 An Intermediate-State Complex During the Process of Photosystem II Repair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:45.6 occ:1.00 MG B:CLA604 0.0 45.6 1.0 NB B:CLA604 2.0 45.6 1.0 ND B:CLA604 2.0 45.6 1.0 NA B:CLA604 2.1 45.6 1.0 NC B:CLA604 2.1 45.6 1.0 NE2 B:HIS455 2.2 43.3 1.0 C4D B:CLA604 2.9 45.6 1.0 CE1 B:HIS455 3.0 43.3 1.0 C1B B:CLA604 3.0 45.6 1.0 C4B B:CLA604 3.1 45.6 1.0 C4A B:CLA604 3.1 45.6 1.0 C1C B:CLA604 3.1 45.6 1.0 C1A B:CLA604 3.2 45.6 1.0 C4C B:CLA604 3.2 45.6 1.0 C1D B:CLA604 3.2 45.6 1.0 CD2 B:HIS455 3.3 43.3 1.0 CHB B:CLA604 3.4 45.6 1.0 CHC B:CLA604 3.4 45.6 1.0 CHA B:CLA604 3.5 45.6 1.0 CHD B:CLA604 3.6 45.6 1.0 ND1 B:HIS455 4.1 43.3 1.0 C3D B:CLA604 4.3 45.6 1.0 CG B:HIS455 4.3 43.3 1.0 C2B B:CLA604 4.3 45.6 1.0 C3B B:CLA604 4.3 45.6 1.0 C2C B:CLA604 4.4 45.6 1.0 C2D B:CLA604 4.4 45.6 1.0 C3C B:CLA604 4.4 45.6 1.0 C3A B:CLA604 4.4 45.6 1.0 C2A B:CLA604 4.5 45.6 1.0 C13 B:CLA612 4.6 44.7 1.0 CBD B:CLA604 4.9 45.6 1.0 C14 B:CLA612 4.9 44.7 1.0

Magnesium binding site 5 out of 35 in the Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair


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 An Intermediate-State Complex During the Process of Photosystem II Repair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:45.2 occ:1.00 MG B:CLA605 0.0 45.2 1.0 NB B:CLA605 2.0 45.2 1.0 ND B:CLA605 2.0 45.2 1.0 NC B:CLA605 2.1 45.2 1.0 NA B:CLA605 2.1 45.2 1.0 NE2 B:HIS100 2.3 45.1 1.0 C4D B:CLA605 2.9 45.2 1.0 C1B B:CLA605 3.0 45.2 1.0 C4B B:CLA605 3.1 45.2 1.0 C4A B:CLA605 3.1 45.2 1.0 C1C B:CLA605 3.1 45.2 1.0 C1A B:CLA605 3.2 45.2 1.0 C4C B:CLA605 3.2 45.2 1.0 C1D B:CLA605 3.2 45.2 1.0 CE1 B:HIS100 3.2 45.1 1.0 CD2 B:HIS100 3.4 45.1 1.0 CHB B:CLA605 3.4 45.2 1.0 CHC B:CLA605 3.5 45.2 1.0 CHA B:CLA605 3.5 45.2 1.0 CHD B:CLA605 3.5 45.2 1.0 O1A B:CLA605 4.0 45.2 1.0 C3D B:CLA605 4.2 45.2 1.0 C2B B:CLA605 4.3 45.2 1.0 C3B B:CLA605 4.3 45.2 1.0 C2D B:CLA605 4.3 45.2 1.0 C2C B:CLA605 4.4 45.2 1.0 ND1 B:HIS100 4.4 45.1 1.0 C3C B:CLA605 4.4 45.2 1.0 C3A B:CLA605 4.4 45.2 1.0 C2A B:CLA605 4.5 45.2 1.0 CG B:HIS100 4.5 45.1 1.0 C2 B:CLA604 4.5 45.6 1.0 O2A B:CLA604 4.9 45.6 1.0 CBD B:CLA605 4.9 45.2 1.0 C1 B:CLA604 4.9 45.6 1.0

Magnesium binding site 6 out of 35 in the Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair


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 An Intermediate-State Complex During the Process of Photosystem II Repair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:48.5 occ:1.00 MG B:CLA606 0.0 48.5 1.0 NB B:CLA606 2.0 48.5 1.0 ND B:CLA606 2.0 48.5 1.0 NC B:CLA606 2.1 48.5 1.0 NA B:CLA606 2.1 48.5 1.0 ND1 B:HIS157 2.2 48.5 1.0 CE1 B:HIS157 2.7 48.5 1.0 C4D B:CLA606 2.9 48.5 1.0 C1B B:CLA606 3.0 48.5 1.0 C4A B:CLA606 3.1 48.5 1.0 C4B B:CLA606 3.1 48.5 1.0 C1C B:CLA606 3.1 48.5 1.0 C4C B:CLA606 3.2 48.5 1.0 C1A B:CLA606 3.2 48.5 1.0 C1D B:CLA606 3.2 48.5 1.0 CHB B:CLA606 3.4 48.5 1.0 CHC B:CLA606 3.5 48.5 1.0 CHA B:CLA606 3.5 48.5 1.0 CG B:HIS157 3.5 48.5 1.0 CHD B:CLA606 3.6 48.5 1.0 NE2 B:HIS157 3.9 48.5 1.0 CB B:HIS157 4.3 48.5 1.0 C3D B:CLA606 4.3 48.5 1.0 C2B B:CLA606 4.3 48.5 1.0 C3B B:CLA606 4.3 48.5 1.0 CD2 B:HIS157 4.4 48.5 1.0 C2C B:CLA606 4.4 48.5 1.0 C2D B:CLA606 4.4 48.5 1.0 C3C B:CLA606 4.4 48.5 1.0 C3A B:CLA606 4.4 48.5 1.0 C2A B:CLA606 4.5 48.5 1.0 CBD B:CLA606 4.9 48.5 1.0

Magnesium binding site 7 out of 35 in the Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair


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 An Intermediate-State Complex During the Process of Photosystem II Repair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:52.5 occ:1.00 MG B:CLA607 0.0 52.5 1.0 NB B:CLA607 2.0 52.5 1.0 ND B:CLA607 2.0 52.5 1.0 NC B:CLA607 2.1 52.5 1.0 NA B:CLA607 2.1 52.5 1.0 C4D B:CLA607 2.9 52.5 1.0 C1B B:CLA607 3.0 52.5 1.0 C4A B:CLA607 3.1 52.5 1.0 C4B B:CLA607 3.1 52.5 1.0 C1C B:CLA607 3.1 52.5 1.0 C4C B:CLA607 3.2 52.5 1.0 C1A B:CLA607 3.2 52.5 1.0 C1D B:CLA607 3.2 52.5 1.0 CHB B:CLA607 3.4 52.5 1.0 CHC B:CLA607 3.4 52.5 1.0 CHA B:CLA607 3.5 52.5 1.0 CHD B:CLA607 3.6 52.5 1.0 CE B:MET37 4.0 49.8 1.0 O1A B:CLA607 4.0 52.5 1.0 C12 B:LMG620 4.1 56.5 1.0 C15 B:LMG620 4.1 56.5 1.0 C3D B:CLA607 4.3 52.5 1.0 C2B B:CLA607 4.3 52.5 1.0 C3B B:CLA607 4.3 52.5 1.0 C2C B:CLA607 4.4 52.5 1.0 C2D B:CLA607 4.4 52.5 1.0 C3C B:CLA607 4.4 52.5 1.0 C3A B:CLA607 4.4 52.5 1.0 C2A B:CLA607 4.5 52.5 1.0 C16 B:LMG620 4.7 56.5 1.0 CD2 B:PHE61 4.9 48.7 1.0 CBD B:CLA607 4.9 52.5 1.0 CB B:PHE61 4.9 48.7 1.0

Magnesium binding site 8 out of 35 in the Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair


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 An Intermediate-State Complex During the Process of Photosystem II Repair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg608 b:50.5 occ:1.00 MG B:CLA608 0.0 50.5 1.0 NB B:CLA608 2.0 50.5 1.0 ND B:CLA608 2.0 50.5 1.0 NA B:CLA608 2.1 50.5 1.0 NC B:CLA608 2.1 50.5 1.0 NE2 B:HIS466 2.2 43.9 1.0 C4D B:CLA608 2.9 50.5 1.0 C1B B:CLA608 3.0 50.5 1.0 C4B B:CLA608 3.1 50.5 1.0 C4A B:CLA608 3.1 50.5 1.0 C1C B:CLA608 3.1 50.5 1.0 CE1 B:HIS466 3.1 43.9 1.0 C1A B:CLA608 3.2 50.5 1.0 C1D B:CLA608 3.2 50.5 1.0 C4C B:CLA608 3.2 50.5 1.0 CD2 B:HIS466 3.3 43.9 1.0 CHB B:CLA608 3.4 50.5 1.0 CHC B:CLA608 3.4 50.5 1.0 CHA B:CLA608 3.5 50.5 1.0 CHD B:CLA608 3.6 50.5 1.0 O1A B:CLA608 4.0 50.5 1.0 C3D B:CLA608 4.2 50.5 1.0 ND1 B:HIS466 4.3 43.9 1.0 C2B B:CLA608 4.3 50.5 1.0 C3B B:CLA608 4.3 50.5 1.0 C2D B:CLA608 4.4 50.5 1.0 C2C B:CLA608 4.4 50.5 1.0 CG B:HIS466 4.4 43.9 1.0 C3C B:CLA608 4.4 50.5 1.0 C3A B:CLA608 4.4 50.5 1.0 C2A B:CLA608 4.5 50.5 1.0 C4 B:CLA608 4.5 50.5 1.0 C1 B:CLA608 4.5 50.5 1.0 CGA B:CLA608 4.6 50.5 1.0 C9 B:CLA609 4.8 51.1 1.0 CBD B:CLA608 4.9 50.5 1.0 O2A B:CLA608 5.0 50.5 1.0

Magnesium binding site 9 out of 35 in the Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair


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 An Intermediate-State Complex During the Process of Photosystem II Repair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg609 b:51.1 occ:1.00 MG B:CLA609 0.0 51.1 1.0 NB B:CLA609 2.0 51.1 1.0 ND B:CLA609 2.0 51.1 1.0 NA B:CLA609 2.1 51.1 1.0 NC B:CLA609 2.1 51.1 1.0 NE2 B:HIS216 2.2 48.3 1.0 C4D B:CLA609 2.9 51.1 1.0 CE1 B:HIS216 3.0 48.3 1.0 C1B B:CLA609 3.0 51.1 1.0 C4A B:CLA609 3.1 51.1 1.0 C4B B:CLA609 3.1 51.1 1.0 C1C B:CLA609 3.1 51.1 1.0 C1A B:CLA609 3.2 51.1 1.0 C4C B:CLA609 3.2 51.1 1.0 C1D B:CLA609 3.2 51.1 1.0 CD2 B:HIS216 3.4 48.3 1.0 CHB B:CLA609 3.4 51.1 1.0 CHC B:CLA609 3.5 51.1 1.0 CHA B:CLA609 3.5 51.1 1.0 CHD B:CLA609 3.6 51.1 1.0 C4 H:BCR101 3.8 52.9 1.0 ND1 B:HIS216 4.2 48.3 1.0 C3D B:CLA609 4.3 51.1 1.0 C2B B:CLA609 4.3 51.1 1.0 C3B B:CLA609 4.3 51.1 1.0 C2D B:CLA609 4.4 51.1 1.0 C2C B:CLA609 4.4 51.1 1.0 C3C B:CLA609 4.4 51.1 1.0 C3A B:CLA609 4.4 51.1 1.0 CG B:HIS216 4.4 48.3 1.0 C2A B:CLA609 4.4 51.1 1.0 C5 H:BCR101 4.6 52.9 1.0 CE2 B:PHE139 4.7 47.5 1.0 CBD B:CLA609 4.9 51.1 1.0 C3 H:BCR101 5.0 52.9 1.0

Magnesium binding site 10 out of 35 in the Cryo-Em Structure of An Intermediate-State Complex During the Process of Photosystem II Repair


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 An Intermediate-State Complex During the Process of Photosystem II Repair within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg610 b:45.5 occ:1.00 MG B:CLA610 0.0 45.5 1.0 NB B:CLA610 2.0 45.5 1.0 ND B:CLA610 2.0 45.5 1.0 NC B:CLA610 2.1 45.5 1.0 NA B:CLA610 2.1 45.5 1.0 C4D B:CLA610 2.9 45.5 1.0 C1B B:CLA610 3.0 45.5 1.0 C4B B:CLA610 3.1 45.5 1.0 C4A B:CLA610 3.1 45.5 1.0 C1C B:CLA610 3.1 45.5 1.0 C1A B:CLA610 3.1 45.5 1.0 C4C B:CLA610 3.2 45.5 1.0 C1D B:CLA610 3.2 45.5 1.0 CHB B:CLA610 3.4 45.5 1.0 CHC B:CLA610 3.4 45.5 1.0 CHA B:CLA610 3.5 45.5 1.0 CHD B:CLA610 3.5 45.5 1.0 CG2 B:VAL237 4.2 46.0 1.0 C3D B:CLA610 4.2 45.5 1.0 C2B B:CLA610 4.3 45.5 1.0 C3B B:CLA610 4.3 45.5 1.0 C2C B:CLA610 4.3 45.5 1.0 C2D B:CLA610 4.4 45.5 1.0 CB B:SER240 4.4 44.6 1.0 C3C B:CLA610 4.4 45.5 1.0 C3A B:CLA610 4.4 45.5 1.0 C2A B:CLA610 4.5 45.5 1.0 OG B:SER241 4.5 42.9 1.0 CD1 B:PHE139 4.6 47.5 1.0 CE1 B:PHE139 4.6 47.5 1.0 O B:VAL237 4.9 46.0 1.0 CBD B:CLA610 4.9 45.5 1.0 CMB B:CLA609 4.9 51.1 1.0

A.Li, T.You, X.Pang, Y.Wang, L.Tian, X.Li, Z.Liu. Structural Basis For An Early Stage of the Photosystem II Repair Cycle in Chlamydomonas Reinhardtii To Be Published.