Magnesium in PDB 8r2i: Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii

All present enzymatic activity of Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii:
1.10.3.9;

The structure of Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii 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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii (pdb code 8r2i). 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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii, PDB code: 8r2i:
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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii


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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:25.6 occ:1.00 MG A:CLA402 0.0 25.6 1.0 NE2 A:HIS198 1.9 27.2 1.0 ND A:CLA402 2.0 25.6 1.0 NB A:CLA402 2.0 25.6 1.0 NC A:CLA402 2.1 25.6 1.0 NA A:CLA402 2.2 25.6 1.0 CE1 A:HIS198 2.6 27.2 1.0 C4D A:CLA402 2.9 25.6 1.0 C4B A:CLA402 3.0 25.6 1.0 C1C A:CLA402 3.0 25.6 1.0 C1B A:CLA402 3.1 25.6 1.0 C1D A:CLA402 3.1 25.6 1.0 CD2 A:HIS198 3.1 27.2 1.0 C4A A:CLA402 3.2 25.6 1.0 C1A A:CLA402 3.2 25.6 1.0 C4C A:CLA402 3.2 25.6 1.0 CHC A:CLA402 3.3 25.6 1.0 CHB A:CLA402 3.4 25.6 1.0 CHA A:CLA402 3.5 25.6 1.0 CHD A:CLA402 3.5 25.6 1.0 CBB D:CLA404 3.6 31.1 1.0 ND1 A:HIS198 3.8 27.2 1.0 CE A:MET183 4.1 26.6 1.0 CG A:HIS198 4.1 27.2 1.0 C3D A:CLA402 4.2 25.6 1.0 C3B A:CLA402 4.2 25.6 1.0 C2B A:CLA402 4.3 25.6 1.0 C2D A:CLA402 4.3 25.6 1.0 C2C A:CLA402 4.4 25.6 1.0 C3C A:CLA402 4.4 25.6 1.0 C3A A:CLA402 4.5 25.6 1.0 C2A A:CLA402 4.5 25.6 1.0 CBD A:CLA402 4.9 25.6 1.0 CAB D:CLA404 5.0 31.1 1.0

Magnesium binding site 2 out of 35 in the Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii


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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:34.8 occ:1.00 MG A:CLA403 0.0 34.8 1.0 ND A:CLA403 2.0 34.8 1.0 NB A:CLA403 2.0 34.8 1.0 O A:HOH501 2.1 30.0 1.0 NC A:CLA403 2.1 34.8 1.0 NA A:CLA403 2.2 34.8 1.0 C4D A:CLA403 2.9 34.8 1.0 C4B A:CLA403 3.0 34.8 1.0 C1C A:CLA403 3.0 34.8 1.0 C1B A:CLA403 3.1 34.8 1.0 C1D A:CLA403 3.1 34.8 1.0 C4A A:CLA403 3.2 34.8 1.0 C4C A:CLA403 3.2 34.8 1.0 C1A A:CLA403 3.2 34.8 1.0 CHC A:CLA403 3.3 34.8 1.0 CHB A:CLA403 3.4 34.8 1.0 CHA A:CLA403 3.5 34.8 1.0 CHD A:CLA403 3.5 34.8 1.0 CBB D:PHO402 3.9 39.0 1.0 C3D A:CLA403 4.1 34.8 1.0 C3B A:CLA403 4.2 34.8 1.0 C2B A:CLA403 4.3 34.8 1.0 C2D A:CLA403 4.3 34.8 1.0 C2C A:CLA403 4.4 34.8 1.0 C3C A:CLA403 4.4 34.8 1.0 C3A A:CLA403 4.5 34.8 1.0 C2A A:CLA403 4.5 34.8 1.0 O1A D:CLA404 4.7 31.1 1.0 CE2 A:PHE206 4.9 28.1 1.0 CBD A:CLA403 4.9 34.8 1.0 O1A A:CLA403 5.0 34.8 1.0

Magnesium binding site 3 out of 35 in the Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii


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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:25.2 occ:1.00 MG A:CLA405 0.0 25.2 1.0 NE2 A:HIS118 1.9 20.4 1.0 ND A:CLA405 2.0 25.2 1.0 NB A:CLA405 2.0 25.2 1.0 NC A:CLA405 2.1 25.2 1.0 NA A:CLA405 2.2 25.2 1.0 CE1 A:HIS118 2.5 20.4 1.0 C4D A:CLA405 2.9 25.2 1.0 C4B A:CLA405 3.0 25.2 1.0 C1C A:CLA405 3.0 25.2 1.0 C1B A:CLA405 3.1 25.2 1.0 C1D A:CLA405 3.1 25.2 1.0 CD2 A:HIS118 3.2 20.4 1.0 C4A A:CLA405 3.2 25.2 1.0 C1A A:CLA405 3.2 25.2 1.0 C4C A:CLA405 3.2 25.2 1.0 CHC A:CLA405 3.3 25.2 1.0 CHB A:CLA405 3.4 25.2 1.0 CHA A:CLA405 3.5 25.2 1.0 CHD A:CLA405 3.5 25.2 1.0 ND1 A:HIS118 3.8 20.4 1.0 CG A:HIS118 4.1 20.4 1.0 C3D A:CLA405 4.2 25.2 1.0 CG2 I:VAL12 4.2 47.9 1.0 C3B A:CLA405 4.2 25.2 1.0 C2B A:CLA405 4.3 25.2 1.0 C2D A:CLA405 4.3 25.2 1.0 O1A A:CLA405 4.4 25.2 1.0 C2C A:CLA405 4.4 25.2 1.0 C3C A:CLA405 4.4 25.2 1.0 C3A A:CLA405 4.5 25.2 1.0 C2A A:CLA405 4.5 25.2 1.0 CG1 I:VAL8 4.6 53.0 1.0 CBD A:CLA405 4.9 25.2 1.0

Magnesium binding site 4 out of 35 in the Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii


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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:67.0 occ:1.00 MG B:CLA501 0.0 67.0 1.0 ND B:CLA501 2.0 67.0 1.0 NB B:CLA501 2.0 67.0 1.0 O B:HOH602 2.1 30.0 1.0 NC B:CLA501 2.1 67.0 1.0 NA B:CLA501 2.2 67.0 1.0 C4D B:CLA501 2.9 67.0 1.0 C4B B:CLA501 3.0 67.0 1.0 C1C B:CLA501 3.0 67.0 1.0 C1B B:CLA501 3.1 67.0 1.0 C1D B:CLA501 3.1 67.0 1.0 C4A B:CLA501 3.2 67.0 1.0 C1A B:CLA501 3.2 67.0 1.0 C4C B:CLA501 3.2 67.0 1.0 CHC B:CLA501 3.3 67.0 1.0 CHB B:CLA501 3.5 67.0 1.0 CHA B:CLA501 3.5 67.0 1.0 CHD B:CLA501 3.5 67.0 1.0 C3D B:CLA501 4.2 67.0 1.0 O B:TRP185 4.2 66.0 1.0 C3B B:CLA501 4.3 67.0 1.0 C2B B:CLA501 4.3 67.0 1.0 C2D B:CLA501 4.3 67.0 1.0 C2C B:CLA501 4.4 67.0 1.0 C3C B:CLA501 4.4 67.0 1.0 C3A B:CLA501 4.5 67.0 1.0 C2A B:CLA501 4.5 67.0 1.0 CBB B:CLA502 4.8 54.7 1.0 CE2 B:PHE190 4.8 60.8 1.0 CBD B:CLA501 4.9 67.0 1.0

Magnesium binding site 5 out of 35 in the Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii


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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:54.7 occ:1.00 MG B:CLA502 0.0 54.7 1.0 ND1 B:HIS201 1.9 55.4 1.0 ND B:CLA502 2.0 54.7 1.0 NB B:CLA502 2.0 54.7 1.0 NC B:CLA502 2.1 54.7 1.0 NA B:CLA502 2.2 54.7 1.0 CE1 B:HIS201 2.3 55.4 1.0 C4D B:CLA502 2.9 54.7 1.0 C4B B:CLA502 3.0 54.7 1.0 C1C B:CLA502 3.0 54.7 1.0 C1B B:CLA502 3.1 54.7 1.0 C1D B:CLA502 3.1 54.7 1.0 C4A B:CLA502 3.2 54.7 1.0 C1A B:CLA502 3.2 54.7 1.0 C4C B:CLA502 3.2 54.7 1.0 CG B:HIS201 3.2 55.4 1.0 CHC B:CLA502 3.3 54.7 1.0 CZ H:PHE60 3.4 59.8 1.0 CHA B:CLA502 3.5 54.7 1.0 CHB B:CLA502 3.5 54.7 1.0 CHD B:CLA502 3.5 54.7 1.0 NE2 B:HIS201 3.6 55.4 1.0 CD2 B:HIS201 4.0 55.4 1.0 CB B:HIS201 4.0 55.4 1.0 CE2 H:PHE60 4.1 59.8 1.0 C3D B:CLA502 4.2 54.7 1.0 C3B B:CLA502 4.2 54.7 1.0 C2B B:CLA502 4.3 54.7 1.0 C2D B:CLA502 4.3 54.7 1.0 C2C B:CLA502 4.4 54.7 1.0 CE1 H:PHE60 4.4 59.8 1.0 C3C B:CLA502 4.4 54.7 1.0 CE1 B:PHE190 4.5 60.8 1.0 C3A B:CLA502 4.5 54.7 1.0 C2A B:CLA502 4.5 54.7 1.0 CA B:HIS201 4.8 55.4 1.0 CBD B:CLA502 4.9 54.7 1.0

Magnesium binding site 6 out of 35 in the Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii


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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:53.0 occ:1.00 MG B:CLA503 0.0 53.0 1.0 NE2 B:HIS202 1.9 56.2 1.0 ND B:CLA503 2.0 53.0 1.0 NB B:CLA503 2.0 53.0 1.0 NC B:CLA503 2.1 53.0 1.0 NA B:CLA503 2.2 53.0 1.0 CE1 B:HIS202 2.6 56.2 1.0 C4D B:CLA503 2.9 53.0 1.0 C4B B:CLA503 3.0 53.0 1.0 C1C B:CLA503 3.0 53.0 1.0 C1B B:CLA503 3.1 53.0 1.0 C1D B:CLA503 3.1 53.0 1.0 CD2 B:HIS202 3.1 56.2 1.0 C4A B:CLA503 3.2 53.0 1.0 C4C B:CLA503 3.2 53.0 1.0 C1A B:CLA503 3.2 53.0 1.0 CHC B:CLA503 3.3 53.0 1.0 CHB B:CLA503 3.4 53.0 1.0 CHA B:CLA503 3.5 53.0 1.0 CHD B:CLA503 3.5 53.0 1.0 ND1 B:HIS202 3.8 56.2 1.0 O1A B:CLA503 3.9 53.0 1.0 CG B:HIS202 4.1 56.2 1.0 C3D B:CLA503 4.2 53.0 1.0 C9 B:CLA505 4.2 43.5 1.0 C3B B:CLA503 4.2 53.0 1.0 C2B B:CLA503 4.3 53.0 1.0 C2D B:CLA503 4.3 53.0 1.0 C2C B:CLA503 4.4 53.0 1.0 C3C B:CLA503 4.4 53.0 1.0 C3A B:CLA503 4.5 53.0 1.0 C2A B:CLA503 4.5 53.0 1.0 C6 B:CLA505 4.6 43.5 1.0 C7 B:CLA505 4.7 43.5 1.0 CGA B:CLA503 4.8 53.0 1.0 CBD B:CLA503 4.9 53.0 1.0 C8 B:CLA505 5.0 43.5 1.0

Magnesium binding site 7 out of 35 in the Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii


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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:42.7 occ:1.00 MG B:CLA504 0.0 42.7 1.0 NE2 B:HIS455 1.9 38.5 1.0 ND B:CLA504 2.0 42.7 1.0 NB B:CLA504 2.0 42.7 1.0 NC B:CLA504 2.1 42.7 1.0 NA B:CLA504 2.2 42.7 1.0 CE1 B:HIS455 2.7 38.5 1.0 C4D B:CLA504 2.9 42.7 1.0 C4B B:CLA504 3.0 42.7 1.0 C1C B:CLA504 3.0 42.7 1.0 CD2 B:HIS455 3.1 38.5 1.0 C1B B:CLA504 3.1 42.7 1.0 C1D B:CLA504 3.1 42.7 1.0 C4A B:CLA504 3.2 42.7 1.0 C4C B:CLA504 3.2 42.7 1.0 C1A B:CLA504 3.2 42.7 1.0 CHC B:CLA504 3.3 42.7 1.0 CHB B:CLA504 3.4 42.7 1.0 CHA B:CLA504 3.5 42.7 1.0 CHD B:CLA504 3.5 42.7 1.0 C14 B:CLA512 3.7 43.3 1.0 ND1 B:HIS455 3.9 38.5 1.0 CG B:HIS455 4.1 38.5 1.0 C3D B:CLA504 4.2 42.7 1.0 C3B B:CLA504 4.2 42.7 1.0 C2B B:CLA504 4.3 42.7 1.0 C2D B:CLA504 4.3 42.7 1.0 C2C B:CLA504 4.4 42.7 1.0 C3C B:CLA504 4.4 42.7 1.0 C3A B:CLA504 4.5 42.7 1.0 C2A B:CLA504 4.5 42.7 1.0 C13 B:CLA512 4.9 43.3 1.0 CBD B:CLA504 4.9 42.7 1.0 CE2 B:PHE451 5.0 38.0 1.0

Magnesium binding site 8 out of 35 in the Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii


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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:43.5 occ:1.00 MG B:CLA505 0.0 43.5 1.0 NE2 B:HIS100 1.9 40.6 1.0 ND B:CLA505 2.0 43.5 1.0 NB B:CLA505 2.0 43.5 1.0 NC B:CLA505 2.1 43.5 1.0 NA B:CLA505 2.2 43.5 1.0 CE1 B:HIS100 2.8 40.6 1.0 C4D B:CLA505 2.9 43.5 1.0 C4B B:CLA505 3.0 43.5 1.0 CD2 B:HIS100 3.0 40.6 1.0 C1C B:CLA505 3.0 43.5 1.0 C1B B:CLA505 3.1 43.5 1.0 C1D B:CLA505 3.1 43.5 1.0 C4A B:CLA505 3.2 43.5 1.0 C4C B:CLA505 3.2 43.5 1.0 C1A B:CLA505 3.2 43.5 1.0 CHC B:CLA505 3.3 43.5 1.0 CHB B:CLA505 3.4 43.5 1.0 CHA B:CLA505 3.5 43.5 1.0 CHD B:CLA505 3.5 43.5 1.0 ND1 B:HIS100 3.9 40.6 1.0 CG B:HIS100 4.1 40.6 1.0 C3D B:CLA505 4.2 43.5 1.0 C1 B:CLA504 4.2 42.7 1.0 C3B B:CLA505 4.2 43.5 1.0 C2B B:CLA505 4.3 43.5 1.0 C2D B:CLA505 4.3 43.5 1.0 C2C B:CLA505 4.4 43.5 1.0 O1A B:CLA505 4.4 43.5 1.0 C3C B:CLA505 4.4 43.5 1.0 C4 B:CLA504 4.5 42.7 1.0 C3A B:CLA505 4.5 43.5 1.0 C2A B:CLA505 4.5 43.5 1.0 C2 B:CLA504 4.6 42.7 1.0 C3 B:CLA504 4.7 42.7 1.0 CBD B:CLA505 4.9 43.5 1.0

Magnesium binding site 9 out of 35 in the Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii


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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:51.5 occ:1.00 MG B:CLA506 0.0 51.5 1.0 ND B:CLA506 2.0 51.5 1.0 NB B:CLA506 2.0 51.5 1.0 NC B:CLA506 2.1 51.5 1.0 NA B:CLA506 2.2 51.5 1.0 C4D B:CLA506 2.9 51.5 1.0 ND1 B:HIS157 3.0 55.2 1.0 C4B B:CLA506 3.0 51.5 1.0 C1C B:CLA506 3.0 51.5 1.0 C1B B:CLA506 3.1 51.5 1.0 C1D B:CLA506 3.1 51.5 1.0 C4A B:CLA506 3.2 51.5 1.0 C4C B:CLA506 3.2 51.5 1.0 C1A B:CLA506 3.2 51.5 1.0 CHC B:CLA506 3.3 51.5 1.0 C7 B:LMT521 3.4 20.0 1.0 CHB B:CLA506 3.4 51.5 1.0 CHA B:CLA506 3.5 51.5 1.0 CE1 B:HIS157 3.5 55.2 1.0 CHD B:CLA506 3.5 51.5 1.0 C6 B:LMT521 4.0 20.0 1.0 C3D B:CLA506 4.2 51.5 1.0 CG B:HIS157 4.2 55.2 1.0 C5 B:LMT521 4.2 20.0 1.0 C3B B:CLA506 4.2 51.5 1.0 C2B B:CLA506 4.3 51.5 1.0 C2D B:CLA506 4.3 51.5 1.0 C2C B:CLA506 4.4 51.5 1.0 C3C B:CLA506 4.4 51.5 1.0 C3A B:CLA506 4.5 51.5 1.0 C2A B:CLA506 4.5 51.5 1.0 O1A B:CLA506 4.5 51.5 1.0 CB B:HIS157 4.7 55.2 1.0 NE2 B:HIS157 4.8 55.2 1.0 C8 B:LMT521 4.8 20.0 1.0 C3 B:LMT521 4.9 20.0 1.0 CBD B:CLA506 4.9 51.5 1.0

Magnesium binding site 10 out of 35 in the Cryo-Em Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii


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 Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg507 b:37.9 occ:1.00 MG B:CLA507 0.0 37.9 1.0 ND B:CLA507 2.0 37.9 1.0 NB B:CLA507 2.0 37.9 1.0 NC B:CLA507 2.1 37.9 1.0 NA B:CLA507 2.2 37.9 1.0 C4D B:CLA507 2.9 37.9 1.0 C4B B:CLA507 3.0 37.9 1.0 C1C B:CLA507 3.0 37.9 1.0 C1B B:CLA507 3.1 37.9 1.0 C1D B:CLA507 3.1 37.9 1.0 C4A B:CLA507 3.2 37.9 1.0 C1A B:CLA507 3.2 37.9 1.0 C4C B:CLA507 3.2 37.9 1.0 CHC B:CLA507 3.3 37.9 1.0 CE B:MET37 3.4 39.1 1.0 C12 B:LMG519 3.4 39.8 1.0 CHB B:CLA507 3.4 37.9 1.0 CHA B:CLA507 3.5 37.9 1.0 CHD B:CLA507 3.5 37.9 1.0 C3D B:CLA507 4.2 37.9 1.0 C15 B:LMG519 4.2 39.8 1.0 O1A B:CLA507 4.2 37.9 1.0 C3B B:CLA507 4.2 37.9 1.0 C2B B:CLA507 4.3 37.9 1.0 C2D B:CLA507 4.3 37.9 1.0 C14 B:LMG519 4.3 39.8 1.0 C2C B:CLA507 4.4 37.9 1.0 C11 B:LMG519 4.4 39.8 1.0 C3C B:CLA507 4.4 37.9 1.0 C13 B:LMG519 4.5 39.8 1.0 C3A B:CLA507 4.5 37.9 1.0 C2A B:CLA507 4.5 37.9 1.0 C10 B:LMG519 4.8 39.8 1.0 C16 B:LMG519 4.8 39.8 1.0 SD B:MET37 4.8 39.1 1.0 CBD B:CLA507 4.9 37.9 1.0 O9 B:LMG519 5.0 39.8 1.0

M.Fadeeva, D.Klaiman, E.Kandiah, N.Nelson. Structure of Native Photosystem II Assembly Intermediate From Chlamydomonas Reinhardtii Front Plant Sci V. 14 2024.
ISSN: ESSN 1664-462X
DOI: 10.3389/FPLS.2023.1334608