Magnesium in PDB 5mdx: Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana

All present enzymatic activity of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana:
1.10.3.9;

The structure of Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana also contains other interesting chemical elements:

Iron

(Fe)

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 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 280; Page 29, Binding sites: 281 - 290; Page 30, Binding sites: 291 - 300; Page 31, Binding sites: 301 - 308;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana (pdb code 5mdx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 308 binding sites of Magnesium where determined in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana, PDB code: 5mdx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:0.1 occ:1.00 MG A:CLA402 0.0 0.1 1.0 NB A:CLA402 2.0 0.1 1.0 ND A:CLA402 2.0 0.1 1.0 NC A:CLA402 2.1 0.1 1.0 NA A:CLA402 2.1 0.1 1.0 NE2 A:HIS198 2.2 0.9 1.0 C4D A:CLA402 2.8 0.1 1.0 C4B A:CLA402 3.0 0.1 1.0 C1B A:CLA402 3.0 0.1 1.0 CE1 A:HIS198 3.1 0.9 1.0 C1C A:CLA402 3.1 0.1 1.0 C4A A:CLA402 3.1 0.1 1.0 C4C A:CLA402 3.1 0.1 1.0 C1A A:CLA402 3.1 0.1 1.0 C1D A:CLA402 3.1 0.1 1.0 CD2 A:HIS198 3.3 0.9 1.0 CHB A:CLA402 3.4 0.1 1.0 CHA A:CLA402 3.4 0.1 1.0 CHC A:CLA402 3.4 0.1 1.0 CHD A:CLA402 3.6 0.1 1.0 CAB D:CLA403 4.1 0.1 1.0 C3D A:CLA402 4.1 0.1 1.0 ND1 A:HIS198 4.2 0.9 1.0 C3B A:CLA402 4.3 0.1 1.0 C2B A:CLA402 4.3 0.1 1.0 C2D A:CLA402 4.4 0.1 1.0 CG A:HIS198 4.4 0.9 1.0 CE A:MET183 4.4 0.5 1.0 C2C A:CLA402 4.4 0.1 1.0 C3C A:CLA402 4.4 0.1 1.0 C3A A:CLA402 4.4 0.1 1.0 C2A A:CLA402 4.4 0.1 1.0 CBB D:CLA403 4.5 0.1 1.0 CBD A:CLA402 4.9 0.1 1.0 CHC D:CLA403 4.9 0.1 1.0 O1D A:CLA402 5.0 0.1 1.0

Magnesium binding site 2 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:0.1 occ:1.00 MG A:CLA403 0.0 0.1 1.0 NB A:CLA403 2.0 0.1 1.0 ND A:CLA403 2.0 0.1 1.0 NC A:CLA403 2.1 0.1 1.0 NA A:CLA403 2.1 0.1 1.0 C4D A:CLA403 2.8 0.1 1.0 C4B A:CLA403 3.0 0.1 1.0 C1B A:CLA403 3.0 0.1 1.0 C1C A:CLA403 3.1 0.1 1.0 C4A A:CLA403 3.1 0.1 1.0 C4C A:CLA403 3.1 0.1 1.0 C1A A:CLA403 3.1 0.1 1.0 C1D A:CLA403 3.1 0.1 1.0 O2A A:CLA403 3.3 0.1 1.0 CHB A:CLA403 3.4 0.1 1.0 CHC A:CLA403 3.4 0.1 1.0 CHA A:CLA403 3.4 0.1 1.0 CHD A:CLA403 3.6 0.1 1.0 CBB D:PHO402 3.8 0.1 1.0 C3D A:CLA403 4.1 0.1 1.0 C3B A:CLA403 4.3 0.1 1.0 C2B A:CLA403 4.3 0.1 1.0 CGA A:CLA403 4.3 0.1 1.0 C2D A:CLA403 4.3 0.1 1.0 C2C A:CLA403 4.4 0.1 1.0 C3C A:CLA403 4.4 0.1 1.0 C3A A:CLA403 4.4 0.1 1.0 C2A A:CLA403 4.4 0.1 1.0 CAB D:PHO402 4.7 0.1 1.0 O2A D:CLA403 4.8 0.1 1.0 CBD A:CLA403 4.9 0.1 1.0 O1A A:CLA403 5.0 0.1 1.0

Magnesium binding site 3 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:0.1 occ:1.00 MG A:CLA405 0.0 0.1 1.0 NB A:CLA405 2.0 0.1 1.0 ND A:CLA405 2.0 0.1 1.0 NC A:CLA405 2.1 0.1 1.0 NA A:CLA405 2.1 0.1 1.0 NE2 A:HIS118 2.3 1.0 1.0 C4D A:CLA405 2.8 0.1 1.0 C4B A:CLA405 2.9 0.1 1.0 C1B A:CLA405 3.0 0.1 1.0 C1C A:CLA405 3.1 0.1 1.0 C4A A:CLA405 3.1 0.1 1.0 C1D A:CLA405 3.1 0.1 1.0 C4C A:CLA405 3.1 0.1 1.0 C1A A:CLA405 3.1 0.1 1.0 CE1 A:HIS118 3.2 1.0 1.0 CD2 A:HIS118 3.3 1.0 1.0 CHB A:CLA405 3.4 0.1 1.0 CHC A:CLA405 3.4 0.1 1.0 CHA A:CLA405 3.4 0.1 1.0 CHD A:CLA405 3.6 0.1 1.0 C3D A:CLA405 4.1 0.1 1.0 C3B A:CLA405 4.3 0.1 1.0 C2B A:CLA405 4.3 0.1 1.0 C2D A:CLA405 4.3 0.1 1.0 ND1 A:HIS118 4.3 1.0 1.0 C3C A:CLA405 4.4 0.1 1.0 C2C A:CLA405 4.4 0.1 1.0 C3A A:CLA405 4.4 0.1 1.0 CG A:HIS118 4.5 1.0 1.0 C2A A:CLA405 4.5 0.1 1.0 CG1 I:VAL12 4.5 0.3 1.0 CBD A:CLA405 4.9 0.1 1.0 O1D A:CLA405 4.9 0.1 1.0

Magnesium binding site 4 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:0.1 occ:1.00 MG B:CLA601 0.0 0.1 1.0 NB B:CLA601 2.0 0.1 1.0 ND B:CLA601 2.1 0.1 1.0 NC B:CLA601 2.1 0.1 1.0 NA B:CLA601 2.1 0.1 1.0 C4D B:CLA601 2.9 0.1 1.0 C4B B:CLA601 3.0 0.1 1.0 O B:TRP185 3.0 0.7 1.0 C1B B:CLA601 3.0 0.1 1.0 C1C B:CLA601 3.1 0.1 1.0 C4C B:CLA601 3.1 0.1 1.0 C4A B:CLA601 3.1 0.1 1.0 C1D B:CLA601 3.1 0.1 1.0 C1A B:CLA601 3.1 0.1 1.0 CHB B:CLA601 3.4 0.1 1.0 CHC B:CLA601 3.4 0.1 1.0 CHA B:CLA601 3.5 0.1 1.0 CHD B:CLA601 3.6 0.1 1.0 O2A B:CLA601 3.7 0.1 1.0 C3D B:CLA601 4.1 0.1 1.0 C B:TRP185 4.2 0.7 1.0 C3B B:CLA601 4.3 0.1 1.0 C2B B:CLA601 4.3 0.1 1.0 C2D B:CLA601 4.4 0.1 1.0 C3C B:CLA601 4.4 0.1 1.0 C2C B:CLA601 4.4 0.1 1.0 C3A B:CLA601 4.5 0.1 1.0 C2A B:CLA601 4.5 0.1 1.0 CGA B:CLA601 4.8 0.1 1.0 CBD B:CLA601 4.9 0.1 1.0 CA B:GLY186 5.0 0.0 1.0

Magnesium binding site 5 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:0.1 occ:1.00 MG B:CLA602 0.0 0.1 1.0 NB B:CLA602 2.0 0.1 1.0 ND B:CLA602 2.1 0.1 1.0 NC B:CLA602 2.1 0.1 1.0 NA B:CLA602 2.1 0.1 1.0 ND1 B:HIS201 2.2 0.1 1.0 C4D B:CLA602 2.9 0.1 1.0 CE1 B:HIS201 2.9 0.1 1.0 C4B B:CLA602 3.0 0.1 1.0 C1B B:CLA602 3.0 0.1 1.0 C1C B:CLA602 3.1 0.1 1.0 C4A B:CLA602 3.1 0.1 1.0 C4C B:CLA602 3.1 0.1 1.0 C1D B:CLA602 3.1 0.1 1.0 C1A B:CLA602 3.2 0.1 1.0 CG B:HIS201 3.4 0.1 1.0 CHB B:CLA602 3.4 0.1 1.0 CHC B:CLA602 3.5 0.1 1.0 CHA B:CLA602 3.5 0.1 1.0 CHD B:CLA602 3.6 0.1 1.0 CB B:HIS201 3.9 0.1 1.0 CD1 H:ILE57 4.1 0.3 1.0 C3D B:CLA602 4.2 0.1 1.0 NE2 B:HIS201 4.2 0.1 1.0 C3B B:CLA602 4.3 0.1 1.0 C2B B:CLA602 4.3 0.1 1.0 C2D B:CLA602 4.4 0.1 1.0 CD2 B:HIS201 4.4 0.1 1.0 C3C B:CLA602 4.4 0.1 1.0 C2C B:CLA602 4.4 0.1 1.0 C3A B:CLA602 4.4 0.1 1.0 CA B:HIS201 4.5 0.0 1.0 C2A B:CLA602 4.5 0.1 1.0 CBD B:CLA602 4.9 0.1 1.0

Magnesium binding site 6 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:0.1 occ:1.00 MG B:CLA603 0.0 0.1 1.0 NB B:CLA603 2.0 0.1 1.0 ND B:CLA603 2.0 0.1 1.0 NC B:CLA603 2.1 0.1 1.0 NA B:CLA603 2.1 0.1 1.0 NE2 B:HIS202 2.2 0.1 1.0 C4D B:CLA603 2.8 0.1 1.0 C4B B:CLA603 3.0 0.1 1.0 C1B B:CLA603 3.0 0.1 1.0 CD2 B:HIS202 3.1 0.1 1.0 C4A B:CLA603 3.1 0.1 1.0 C1C B:CLA603 3.1 0.1 1.0 C4C B:CLA603 3.1 0.1 1.0 C1D B:CLA603 3.1 0.1 1.0 C1A B:CLA603 3.1 0.1 1.0 CE1 B:HIS202 3.3 0.1 1.0 CHB B:CLA603 3.3 0.1 1.0 CHC B:CLA603 3.5 0.1 1.0 CHA B:CLA603 3.5 0.1 1.0 CHD B:CLA603 3.6 0.1 1.0 C3D B:CLA603 4.1 0.1 1.0 CG B:HIS202 4.3 0.1 1.0 C2B B:CLA603 4.3 0.1 1.0 C3B B:CLA603 4.3 0.1 1.0 ND1 B:HIS202 4.3 0.1 1.0 C2D B:CLA603 4.4 0.1 1.0 C3A B:CLA603 4.4 0.1 1.0 C3C B:CLA603 4.4 0.1 1.0 C2C B:CLA603 4.4 0.1 1.0 C2A B:CLA603 4.4 0.1 1.0 CBD B:CLA603 4.9 0.1 1.0 CMA B:CLA603 5.0 0.1 1.0

Magnesium binding site 7 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:0.1 occ:1.00 MG B:CLA604 0.0 0.1 1.0 NB B:CLA604 2.0 0.1 1.0 ND B:CLA604 2.0 0.1 1.0 NC B:CLA604 2.1 0.1 1.0 NA B:CLA604 2.1 0.1 1.0 NE2 B:HIS455 2.2 0.8 1.0 C4D B:CLA604 2.8 0.1 1.0 C4B B:CLA604 3.0 0.1 1.0 C1B B:CLA604 3.0 0.1 1.0 C1C B:CLA604 3.0 0.1 1.0 C4A B:CLA604 3.1 0.1 1.0 C4C B:CLA604 3.1 0.1 1.0 C1D B:CLA604 3.1 0.1 1.0 C1A B:CLA604 3.1 0.1 1.0 CD2 B:HIS455 3.2 0.8 1.0 CE1 B:HIS455 3.2 0.8 1.0 CHB B:CLA604 3.4 0.1 1.0 CHA B:CLA604 3.4 0.1 1.0 CHC B:CLA604 3.4 0.1 1.0 CHD B:CLA604 3.6 0.1 1.0 C3D B:CLA604 4.1 0.1 1.0 C3B B:CLA604 4.3 0.1 1.0 ND1 B:HIS455 4.3 0.8 1.0 CG B:HIS455 4.3 0.8 1.0 C2D B:CLA604 4.3 0.1 1.0 C2B B:CLA604 4.3 0.1 1.0 C2C B:CLA604 4.4 0.1 1.0 C3C B:CLA604 4.4 0.1 1.0 C3A B:CLA604 4.4 0.1 1.0 C2A B:CLA604 4.5 0.1 1.0 CE1 B:PHE451 4.7 0.7 1.0 CBD B:CLA604 4.9 0.1 1.0 CBB B:CLA613 4.9 0.1 1.0 CAB B:CLA613 4.9 0.1 1.0

Magnesium binding site 8 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:0.1 occ:1.00 MG B:CLA605 0.0 0.1 1.0 NB B:CLA605 2.0 0.1 1.0 ND B:CLA605 2.0 0.1 1.0 NC B:CLA605 2.1 0.1 1.0 NA B:CLA605 2.1 0.1 1.0 NE2 B:HIS100 2.2 0.9 1.0 C4D B:CLA605 2.8 0.1 1.0 C4B B:CLA605 3.0 0.1 1.0 C1B B:CLA605 3.0 0.1 1.0 C1C B:CLA605 3.1 0.1 1.0 C4A B:CLA605 3.1 0.1 1.0 CD2 B:HIS100 3.1 0.9 1.0 C4C B:CLA605 3.1 0.1 1.0 C1A B:CLA605 3.1 0.1 1.0 C1D B:CLA605 3.1 0.1 1.0 CE1 B:HIS100 3.2 0.9 1.0 CHB B:CLA605 3.4 0.1 1.0 CHA B:CLA605 3.4 0.1 1.0 CHC B:CLA605 3.4 0.1 1.0 CHD B:CLA605 3.6 0.1 1.0 C3D B:CLA605 4.1 0.1 1.0 CG B:HIS100 4.3 0.9 1.0 C3B B:CLA605 4.3 0.1 1.0 ND1 B:HIS100 4.3 0.9 1.0 C2B B:CLA605 4.3 0.1 1.0 C2D B:CLA605 4.3 0.1 1.0 O2A B:CLA604 4.4 0.1 1.0 C2C B:CLA605 4.4 0.1 1.0 C3C B:CLA605 4.4 0.1 1.0 C3A B:CLA605 4.4 0.1 1.0 C2A B:CLA605 4.4 0.1 1.0 O1A B:CLA604 4.8 0.1 1.0 CBA B:CLA605 4.8 0.1 1.0 CBD B:CLA605 4.8 0.1 1.0 O2D B:CLA605 4.9 0.1 1.0 CGA B:CLA604 5.0 0.1 1.0

Magnesium binding site 9 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:0.1 occ:1.00 MG B:CLA606 0.0 0.1 1.0 NB B:CLA606 2.0 0.1 1.0 ND B:CLA606 2.1 0.1 1.0 NC B:CLA606 2.1 0.1 1.0 NA B:CLA606 2.1 0.1 1.0 ND1 B:HIS157 2.2 0.7 1.0 C4D B:CLA606 2.9 0.1 1.0 C4B B:CLA606 3.0 0.1 1.0 CE1 B:HIS157 3.0 0.7 1.0 C1B B:CLA606 3.1 0.1 1.0 C1C B:CLA606 3.1 0.1 1.0 C4A B:CLA606 3.1 0.1 1.0 C4C B:CLA606 3.1 0.1 1.0 C1D B:CLA606 3.1 0.1 1.0 C1A B:CLA606 3.2 0.1 1.0 CG B:HIS157 3.4 0.7 1.0 CHB B:CLA606 3.4 0.1 1.0 CHC B:CLA606 3.5 0.1 1.0 CHA B:CLA606 3.5 0.1 1.0 CHD B:CLA606 3.6 0.1 1.0 CB B:HIS157 3.9 0.7 1.0 C3D B:CLA606 4.1 0.1 1.0 NE2 B:HIS157 4.2 0.7 1.0 C3B B:CLA606 4.3 0.1 1.0 C2D B:CLA606 4.3 0.1 1.0 C2B B:CLA606 4.4 0.1 1.0 CD2 B:HIS157 4.4 0.7 1.0 C3C B:CLA606 4.4 0.1 1.0 C2C B:CLA606 4.4 0.1 1.0 C3A B:CLA606 4.4 0.1 1.0 CD B:PRO164 4.5 0.7 1.0 C2A B:CLA606 4.5 0.1 1.0 CA B:HIS157 4.8 0.7 1.0 CBD B:CLA606 4.9 0.1 1.0

Magnesium binding site 10 out of 308 in the Cryo-Em Structure of the Psii Supercomplex From Arabidopsis Thaliana


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 the Psii Supercomplex From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:0.1 occ:1.00 MG B:CLA607 0.0 0.1 1.0 NB B:CLA607 2.0 0.1 1.0 ND B:CLA607 2.0 0.1 1.0 NC B:CLA607 2.1 0.1 1.0 NA B:CLA607 2.1 0.1 1.0 C4D B:CLA607 2.8 0.1 1.0 C4B B:CLA607 3.0 0.1 1.0 C1B B:CLA607 3.0 0.1 1.0 C1C B:CLA607 3.1 0.1 1.0 C4A B:CLA607 3.1 0.1 1.0 C4C B:CLA607 3.1 0.1 1.0 C1D B:CLA607 3.1 0.1 1.0 C1A B:CLA607 3.1 0.1 1.0 CHB B:CLA607 3.4 0.1 1.0 CHA B:CLA607 3.4 0.1 1.0 CHC B:CLA607 3.4 0.1 1.0 CHD B:CLA607 3.6 0.1 1.0 C3D B:CLA607 4.1 0.1 1.0 C3B B:CLA607 4.3 0.1 1.0 C2B B:CLA607 4.3 0.1 1.0 C2D B:CLA607 4.3 0.1 1.0 C2C B:CLA607 4.4 0.1 1.0 C3C B:CLA607 4.4 0.1 1.0 C3A B:CLA607 4.4 0.1 1.0 C2A B:CLA607 4.5 0.1 1.0 CE B:MET37 4.7 0.7 1.0 CBD B:CLA607 4.9 0.1 1.0

L.S.Van Bezouwen, S.Caffarri, R.S.Kale, R.Kouril, A.W.H.Thunnissen, G.T.Oostergetel, E.J.Boekema. Subunit and Chlorophyll Organization of the Plant Photosystem II Supercomplex. Nat Plants V. 3 17080 2017.
ISSN: ESSN 2055-0278
PubMed: 28604725
DOI: 10.1038/NPLANTS.2017.80