Magnesium in PDB 8jjr: Cryo-Em Structure of Symbiodinium Photosystem I

The structure of Cryo-Em Structure of Symbiodinium Photosystem I also contains other interesting chemical elements:

Iron

(Fe)

12 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 - 216;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Symbiodinium Photosystem I (pdb code 8jjr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 216 binding sites of Magnesium where determined in the Cryo-Em Structure of Symbiodinium Photosystem I, PDB code: 8jjr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 216 in the Cryo-Em Structure of Symbiodinium Photosystem I


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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:27.6 occ:1.00 MG A:CLA601 0.0 27.6 1.0 NA A:CLA601 1.9 27.6 1.0 ND A:CLA601 1.9 27.6 1.0 NB A:CLA601 1.9 27.6 1.0 NC A:CLA601 2.0 27.6 1.0 O A:SER62 2.7 25.4 1.0 C4D A:CLA601 2.9 27.6 1.0 C4A A:CLA601 2.9 27.6 1.0 C1C A:CLA601 3.0 27.6 1.0 C1B A:CLA601 3.0 27.6 1.0 C1A A:CLA601 3.0 27.6 1.0 C4B A:CLA601 3.1 27.6 1.0 C4C A:CLA601 3.1 27.6 1.0 C1D A:CLA601 3.2 27.6 1.0 CHB A:CLA601 3.3 27.6 1.0 C8 A:SQD618 3.3 38.4 1.0 CHA A:CLA601 3.4 27.6 1.0 CHC A:CLA601 3.4 27.6 1.0 CHD A:CLA601 3.6 27.6 1.0 C A:SER62 3.9 25.4 1.0 C7 A:SQD618 4.0 38.4 1.0 O49 A:SQD618 4.1 38.4 1.0 C3D A:CLA601 4.2 27.6 1.0 C2B A:CLA601 4.2 27.6 1.0 C3B A:CLA601 4.2 27.6 1.0 C2C A:CLA601 4.3 27.6 1.0 C2D A:CLA601 4.3 27.6 1.0 C3A A:CLA601 4.3 27.6 1.0 C3C A:CLA601 4.3 27.6 1.0 C2A A:CLA601 4.3 27.6 1.0 CA A:SER62 4.4 25.4 1.0 CBA A:CLA601 4.6 27.6 1.0 C9 A:SQD618 4.7 38.4 1.0 C10 A:SQD618 4.9 38.4 1.0 CBD A:CLA601 4.9 27.6 1.0 O47 A:SQD618 5.0 38.4 1.0 N A:LEU63 5.0 25.2 1.0

Magnesium binding site 2 out of 216 in the Cryo-Em Structure of Symbiodinium Photosystem I


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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:25.4 occ:1.00 MG A:CLA602 0.0 25.4 1.0 NA A:CLA602 1.9 25.4 1.0 ND A:CLA602 1.9 25.4 1.0 NB A:CLA602 2.0 25.4 1.0 NC A:CLA602 2.0 25.4 1.0 C21 A:DD6614 2.9 25.9 1.0 C4D A:CLA602 2.9 25.4 1.0 OE2 A:GLU100 2.9 21.5 1.0 C4A A:CLA602 2.9 25.4 1.0 C1C A:CLA602 3.0 25.4 1.0 C1B A:CLA602 3.0 25.4 1.0 C1A A:CLA602 3.0 25.4 1.0 C4B A:CLA602 3.1 25.4 1.0 C4C A:CLA602 3.1 25.4 1.0 C1D A:CLA602 3.2 25.4 1.0 CHB A:CLA602 3.3 25.4 1.0 CHA A:CLA602 3.4 25.4 1.0 CHC A:CLA602 3.4 25.4 1.0 CHD A:CLA602 3.6 25.4 1.0 CD A:GLU100 3.7 21.5 1.0 C3D A:CLA602 4.2 25.4 1.0 C2B A:CLA602 4.2 25.4 1.0 C3B A:CLA602 4.2 25.4 1.0 C2D A:CLA602 4.3 25.4 1.0 C2C A:CLA602 4.3 25.4 1.0 C3A A:CLA602 4.3 25.4 1.0 C3C A:CLA602 4.3 25.4 1.0 C2A A:CLA602 4.3 25.4 1.0 C20 A:DD6614 4.4 25.9 1.0 CG A:GLU100 4.4 21.5 1.0 O2A A:CLA602 4.4 25.4 1.0 OE1 A:GLU100 4.4 21.5 1.0 CBA A:CLA602 4.6 25.4 1.0 NE A:ARG206 4.7 24.5 1.0 NH2 A:ARG206 4.8 24.5 1.0 CBD A:CLA602 4.9 25.4 1.0 CGA A:CLA602 5.0 25.4 1.0 CAA A:CLA602 5.0 25.4 1.0

Magnesium binding site 3 out of 216 in the Cryo-Em Structure of Symbiodinium Photosystem I


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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:26.0 occ:1.00 MG A:CLA603 0.0 26.0 1.0 NA A:CLA603 1.9 26.0 1.0 ND A:CLA603 1.9 26.0 1.0 NB A:CLA603 1.9 26.0 1.0 NC A:CLA603 2.0 26.0 1.0 NE2 A:HIS103 2.5 23.4 1.0 C4D A:CLA603 2.9 26.0 1.0 C4A A:CLA603 2.9 26.0 1.0 C1C A:CLA603 3.0 26.0 1.0 C1B A:CLA603 3.0 26.0 1.0 C1A A:CLA603 3.0 26.0 1.0 C4B A:CLA603 3.1 26.0 1.0 C4C A:CLA603 3.1 26.0 1.0 C1D A:CLA603 3.2 26.0 1.0 CHB A:CLA603 3.3 26.0 1.0 CHA A:CLA603 3.4 26.0 1.0 CHC A:CLA603 3.4 26.0 1.0 CD2 A:HIS103 3.5 23.4 1.0 CE1 A:HIS103 3.5 23.4 1.0 CHD A:CLA603 3.6 26.0 1.0 C8 A:CLA605 3.9 27.5 1.0 C3D A:CLA603 4.2 26.0 1.0 C2B A:CLA603 4.2 26.0 1.0 C3B A:CLA603 4.2 26.0 1.0 C2D A:CLA603 4.3 26.0 1.0 C2C A:CLA603 4.3 26.0 1.0 C3A A:CLA603 4.3 26.0 1.0 C3C A:CLA603 4.3 26.0 1.0 C9 A:CLA605 4.3 27.5 1.0 C2A A:CLA603 4.3 26.0 1.0 C10 A:CLA605 4.4 27.5 1.0 ND1 A:HIS103 4.6 23.4 1.0 CG A:HIS103 4.6 23.4 1.0 CBB A:CLA602 4.9 25.4 1.0 CBD A:CLA603 4.9 26.0 1.0 C7 A:CLA605 4.9 27.5 1.0

Magnesium binding site 4 out of 216 in the Cryo-Em Structure of Symbiodinium Photosystem I


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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:32.1 occ:1.00 MG A:CLA604 0.0 32.1 1.0 NA A:CLA604 1.9 32.1 1.0 ND A:CLA604 1.9 32.1 1.0 NB A:CLA604 2.0 32.1 1.0 NC A:CLA604 2.0 32.1 1.0 C4D A:CLA604 2.9 32.1 1.0 C4A A:CLA604 2.9 32.1 1.0 C1C A:CLA604 3.0 32.1 1.0 C1B A:CLA604 3.0 32.1 1.0 C1A A:CLA604 3.1 32.1 1.0 C4B A:CLA604 3.1 32.1 1.0 C4C A:CLA604 3.1 32.1 1.0 C1D A:CLA604 3.2 32.1 1.0 CHB A:CLA604 3.3 32.1 1.0 CHA A:CLA604 3.4 32.1 1.0 CHC A:CLA604 3.4 32.1 1.0 C29 A:UIX616 3.5 31.4 1.0 CHD A:CLA604 3.6 32.1 1.0 C3D A:CLA604 4.2 32.1 1.0 CGA A:CLA604 4.2 32.1 1.0 O1A A:CLA604 4.2 32.1 1.0 C2B A:CLA604 4.2 32.1 1.0 C3B A:CLA604 4.2 32.1 1.0 C2D A:CLA604 4.3 32.1 1.0 C2C A:CLA604 4.3 32.1 1.0 C3A A:CLA604 4.3 32.1 1.0 O2A A:CLA604 4.3 32.1 1.0 C3C A:CLA604 4.3 32.1 1.0 C2A A:CLA604 4.3 32.1 1.0 C26 A:UIX616 4.7 31.4 1.0 CBA A:CLA604 4.8 32.1 1.0 C34 A:UIX616 4.9 31.4 1.0 CBD A:CLA604 4.9 32.1 1.0

Magnesium binding site 5 out of 216 in the Cryo-Em Structure of Symbiodinium Photosystem I


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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:27.5 occ:1.00 MG A:CLA605 0.0 27.5 1.0 NA A:CLA605 1.9 27.5 1.0 ND A:CLA605 1.9 27.5 1.0 NB A:CLA605 2.0 27.5 1.0 NC A:CLA605 2.0 27.5 1.0 OE2 A:GLU154 2.7 30.3 1.0 C4D A:CLA605 2.9 27.5 1.0 C4A A:CLA605 2.9 27.5 1.0 C1C A:CLA605 3.0 27.5 1.0 C1B A:CLA605 3.0 27.5 1.0 C1A A:CLA605 3.0 27.5 1.0 C4B A:CLA605 3.1 27.5 1.0 C4C A:CLA605 3.1 27.5 1.0 C1D A:CLA605 3.2 27.5 1.0 CHB A:CLA605 3.3 27.5 1.0 CHA A:CLA605 3.4 27.5 1.0 CHC A:CLA605 3.4 27.5 1.0 CHD A:CLA605 3.6 27.5 1.0 CD A:GLU154 3.8 30.3 1.0 CMD A:CLA603 4.2 26.0 1.0 C3D A:CLA605 4.2 27.5 1.0 C2B A:CLA605 4.2 27.5 1.0 C3B A:CLA605 4.2 27.5 1.0 C2C A:CLA605 4.3 27.5 1.0 C2D A:CLA605 4.3 27.5 1.0 C3A A:CLA605 4.3 27.5 1.0 C3C A:CLA605 4.3 27.5 1.0 C2A A:CLA605 4.3 27.5 1.0 CG A:GLU154 4.3 30.3 1.0 CBA A:CLA605 4.6 27.5 1.0 NZ A:LYS102 4.7 25.4 1.0 OE1 A:GLU154 4.8 30.3 1.0 CBD A:CLA605 4.9 27.5 1.0

Magnesium binding site 6 out of 216 in the Cryo-Em Structure of Symbiodinium Photosystem I


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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:28.1 occ:1.00 MG A:CLA606 0.0 28.1 1.0 NA A:CLA606 1.9 28.1 1.0 ND A:CLA606 1.9 28.1 1.0 NB A:CLA606 1.9 28.1 1.0 NC A:CLA606 2.0 28.1 1.0 OE1 A:GLU201 2.8 24.5 1.0 C4D A:CLA606 2.9 28.1 1.0 C4A A:CLA606 2.9 28.1 1.0 C1C A:CLA606 3.0 28.1 1.0 C1B A:CLA606 3.0 28.1 1.0 C1A A:CLA606 3.0 28.1 1.0 C4B A:CLA606 3.1 28.1 1.0 C4C A:CLA606 3.1 28.1 1.0 C1D A:CLA606 3.2 28.1 1.0 C24 A:UIX613 3.2 28.1 1.0 CHB A:CLA606 3.3 28.1 1.0 CHA A:CLA606 3.4 28.1 1.0 CHC A:CLA606 3.4 28.1 1.0 O1A A:CLA606 3.5 28.1 1.0 CHD A:CLA606 3.5 28.1 1.0 CD A:GLU201 3.9 24.5 1.0 NH1 A:ARG105 4.0 24.4 1.0 C3D A:CLA606 4.2 28.1 1.0 C2B A:CLA606 4.2 28.1 1.0 C3B A:CLA606 4.2 28.1 1.0 C2D A:CLA606 4.3 28.1 1.0 C2C A:CLA606 4.3 28.1 1.0 C3A A:CLA606 4.3 28.1 1.0 C3C A:CLA606 4.3 28.1 1.0 C2A A:CLA606 4.3 28.1 1.0 C28 A:UIX613 4.4 28.1 1.0 CGA A:CLA606 4.5 28.1 1.0 OE2 A:GLU201 4.6 24.5 1.0 C16 A:UIX613 4.6 28.1 1.0 C25 A:UIX613 4.6 28.1 1.0 O3 A:UIX613 4.9 28.1 1.0 CBD A:CLA606 4.9 28.1 1.0 CG A:GLU201 5.0 24.5 1.0

Magnesium binding site 7 out of 216 in the Cryo-Em Structure of Symbiodinium Photosystem I


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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:31.4 occ:1.00 MG A:CLA607 0.0 31.4 1.0 NA A:CLA607 1.9 31.4 1.0 ND A:CLA607 1.9 31.4 1.0 NB A:CLA607 2.0 31.4 1.0 NC A:CLA607 2.0 31.4 1.0 C4D A:CLA607 2.9 31.4 1.0 C4A A:CLA607 2.9 31.4 1.0 C1C A:CLA607 3.0 31.4 1.0 C1B A:CLA607 3.0 31.4 1.0 C1A A:CLA607 3.0 31.4 1.0 C4B A:CLA607 3.1 31.4 1.0 C4C A:CLA607 3.1 31.4 1.0 C1D A:CLA607 3.2 31.4 1.0 CHB A:CLA607 3.3 31.4 1.0 CHA A:CLA607 3.4 31.4 1.0 CHC A:CLA607 3.4 31.4 1.0 CHD A:CLA607 3.6 31.4 1.0 O3 A:SQD618 4.0 38.4 1.0 C3D A:CLA607 4.2 31.4 1.0 C2B A:CLA607 4.2 31.4 1.0 C3B A:CLA607 4.2 31.4 1.0 C2C A:CLA607 4.3 31.4 1.0 C2D A:CLA607 4.3 31.4 1.0 C3A A:CLA607 4.3 31.4 1.0 C3C A:CLA607 4.3 31.4 1.0 CMD A:KC2608 4.3 29.4 1.0 C2A A:CLA607 4.3 31.4 1.0 CBA A:CLA607 4.7 31.4 1.0 CBD A:CLA607 4.9 31.4 1.0 O2 A:SQD618 5.0 38.4 1.0

Magnesium binding site 8 out of 216 in the Cryo-Em Structure of Symbiodinium Photosystem I


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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg608 b:29.4 occ:1.00 MG A:KC2608 0.0 29.4 1.0 ND A:KC2608 1.9 29.4 1.0 NC A:KC2608 2.1 29.4 1.0 NA A:KC2608 2.1 29.4 1.0 NB A:KC2608 2.1 29.4 1.0 C4D A:KC2608 2.7 29.4 1.0 OD1 A:ASN204 3.0 23.9 1.0 C1D A:KC2608 3.0 29.4 1.0 C1A A:KC2608 3.1 29.4 1.0 C4C A:KC2608 3.1 29.4 1.0 C4A A:KC2608 3.1 29.4 1.0 C1C A:KC2608 3.1 29.4 1.0 C1B A:KC2608 3.1 29.4 1.0 C4B A:KC2608 3.2 29.4 1.0 CHA A:KC2608 3.3 29.4 1.0 CHD A:KC2608 3.5 29.4 1.0 CHB A:KC2608 3.5 29.4 1.0 CHC A:KC2608 3.6 29.4 1.0 C3D A:KC2608 4.0 29.4 1.0 C2D A:KC2608 4.1 29.4 1.0 CG A:ASN204 4.1 23.9 1.0 C3C A:KC2608 4.3 29.4 1.0 C2A A:KC2608 4.3 29.4 1.0 C3A A:KC2608 4.3 29.4 1.0 C2C A:KC2608 4.3 29.4 1.0 C2B A:KC2608 4.4 29.4 1.0 C3B A:KC2608 4.4 29.4 1.0 ND2 A:ASN204 4.6 23.9 1.0 CBD A:KC2608 4.8 29.4 1.0

Magnesium binding site 9 out of 216 in the Cryo-Em Structure of Symbiodinium Photosystem I


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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg609 b:29.9 occ:1.00 MG A:CLA609 0.0 29.9 1.0 NA A:CLA609 1.9 29.9 1.0 ND A:CLA609 1.9 29.9 1.0 NB A:CLA609 1.9 29.9 1.0 NC A:CLA609 2.0 29.9 1.0 C4D A:CLA609 2.9 29.9 1.0 C4A A:CLA609 2.9 29.9 1.0 C1C A:CLA609 3.0 29.9 1.0 C1B A:CLA609 3.0 29.9 1.0 C1A A:CLA609 3.0 29.9 1.0 C4B A:CLA609 3.1 29.9 1.0 C4C A:CLA609 3.1 29.9 1.0 C1D A:CLA609 3.2 29.9 1.0 CMB D:CLA605 3.2 31.7 1.0 CHB A:CLA609 3.3 29.9 1.0 CHA A:CLA609 3.4 29.9 1.0 CHC A:CLA609 3.4 29.9 1.0 CHD A:CLA609 3.6 29.9 1.0 C3D A:CLA609 4.2 29.9 1.0 C2B A:CLA609 4.2 29.9 1.0 C3B A:CLA609 4.2 29.9 1.0 C2D A:CLA609 4.3 29.9 1.0 C2C A:CLA609 4.3 29.9 1.0 C3A A:CLA609 4.3 29.9 1.0 C3C A:CLA609 4.3 29.9 1.0 C2A A:CLA609 4.3 29.9 1.0 CA A:GLY214 4.5 25.1 1.0 C2B D:CLA605 4.6 31.7 1.0 CBA A:CLA609 4.7 29.9 1.0 CBD A:CLA609 4.9 29.9 1.0 O A:GLY214 5.0 25.1 1.0

Magnesium binding site 10 out of 216 in the Cryo-Em Structure of Symbiodinium Photosystem I


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 Symbiodinium Photosystem I within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg610 b:37.5 occ:1.00 MG A:CLA610 0.0 37.5 1.0 NA A:CLA610 1.9 37.5 1.0 ND A:CLA610 1.9 37.5 1.0 NB A:CLA610 2.0 37.5 1.0 NC A:CLA610 2.0 37.5 1.0 C4D A:CLA610 2.9 37.5 1.0 C4A A:CLA610 2.9 37.5 1.0 NE2 A:HIS217 3.0 27.6 1.0 C1C A:CLA610 3.0 37.5 1.0 C1B A:CLA610 3.0 37.5 1.0 C1A A:CLA610 3.0 37.5 1.0 C4B A:CLA610 3.1 37.5 1.0 C4C A:CLA610 3.1 37.5 1.0 C1D A:CLA610 3.2 37.5 1.0 CHB A:CLA610 3.3 37.5 1.0 CHA A:CLA610 3.4 37.5 1.0 CHC A:CLA610 3.4 37.5 1.0 CHD A:CLA610 3.6 37.5 1.0 O1A A:CLA610 3.6 37.5 1.0 C1 A:CLA610 3.7 37.5 1.0 CD2 A:HIS217 3.8 27.6 1.0 CE1 A:HIS217 4.0 27.6 1.0 CGA A:CLA610 4.0 37.5 1.0 O2A A:CLA610 4.0 37.5 1.0 C3D A:CLA610 4.2 37.5 1.0 C2B A:CLA610 4.2 37.5 1.0 C3B A:CLA610 4.2 37.5 1.0 C2D A:CLA610 4.3 37.5 1.0 C2C A:CLA610 4.3 37.5 1.0 C3A A:CLA610 4.3 37.5 1.0 C3C A:CLA610 4.3 37.5 1.0 C2A A:CLA610 4.3 37.5 1.0 C4 A:CLA610 4.8 37.5 1.0 C2 A:CLA610 4.9 37.5 1.0 CBD A:CLA610 4.9 37.5 1.0 CBA A:CLA610 5.0 37.5 1.0

L.S.Zhao, N.Wang, K.Li, C.Y.Li, J.P.Guo, F.Y.He, G.M.Liu, X.L.Chen, J.Gao, L.N.Liu, Y.Z.Zhang. Architecture of Symbiotic Dinoflagellate Photosystem I-Light-Harvesting Supercomplex in Symbiodinium. Nat Commun V. 15 2392 2024.
ISSN: ESSN 2041-1723
PubMed: 38493166
DOI: 10.1038/S41467-024-46791-X