Magnesium in PDB 1izl: Crystal Structure of Photosystem II

The structure of Crystal Structure of Photosystem II, PDB code: 1izl was solved by N.Kamiya, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 3.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	129.377, 225.192, 308.672, 90.00, 90.00, 90.00
R / Rfree (%)	53 / n/a

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

Manganese	(Mn)	8 atoms
Iron	(Fe)	6 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 - 72;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Photosystem II (pdb code 1izl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 72 binding sites of Magnesium where determined in the Crystal Structure of Photosystem II, PDB code: 1izl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 72 in the Crystal Structure of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg365 b:46.9 occ:1.00 MG A:CLA365 0.0 46.9 1.0 ND A:CLA365 2.0 46.9 1.0 NB A:CLA365 2.1 46.9 1.0 NC A:CLA365 2.1 46.9 1.0 NA A:CLA365 2.2 46.9 1.0 C4D A:CLA365 3.0 46.9 1.0 C1D A:CLA365 3.1 46.9 1.0 C1B A:CLA365 3.1 46.9 1.0 C4A A:CLA365 3.1 46.9 1.0 C4C A:CLA365 3.1 46.9 1.0 C1C A:CLA365 3.1 46.9 1.0 C4B A:CLA365 3.1 46.9 1.0 C1A A:CLA365 3.2 46.9 1.0 CHB A:CLA365 3.4 46.9 1.0 CHD A:CLA365 3.4 46.9 1.0 CHC A:CLA365 3.5 46.9 1.0 CHA A:CLA365 3.6 46.9 1.0 C3D A:CLA365 4.2 46.9 1.0 C2D A:CLA365 4.3 46.9 1.0 C2B A:CLA365 4.3 46.9 1.0 C3C A:CLA365 4.4 46.9 1.0 C2C A:CLA365 4.4 46.9 1.0 C3B A:CLA365 4.4 46.9 1.0 C3A A:CLA365 4.4 46.9 1.0 C2A A:CLA365 4.5 46.9 1.0 CAB D:CLA354 4.6 46.9 1.0 CMA A:CLA365 4.9 46.9 1.0 CBD A:CLA365 4.9 46.9 1.0

Magnesium binding site 2 out of 72 in the Crystal Structure of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg366 b:46.9 occ:1.00 MG A:CLA366 0.0 46.9 1.0 ND A:CLA366 2.0 46.9 1.0 NB A:CLA366 2.1 46.9 1.0 NC A:CLA366 2.1 46.9 1.0 NA A:CLA366 2.2 46.9 1.0 C4D A:CLA366 2.9 46.9 1.0 C1D A:CLA366 3.1 46.9 1.0 C1B A:CLA366 3.1 46.9 1.0 C4A A:CLA366 3.1 46.9 1.0 C4C A:CLA366 3.1 46.9 1.0 C1C A:CLA366 3.1 46.9 1.0 C4B A:CLA366 3.2 46.9 1.0 C1A A:CLA366 3.2 46.9 1.0 CHB A:CLA366 3.4 46.9 1.0 CHA A:CLA366 3.5 46.9 1.0 CHD A:CLA366 3.5 46.9 1.0 CHC A:CLA366 3.5 46.9 1.0 C3D A:CLA366 4.2 46.9 1.0 O A:GLY178 4.2 46.9 1.0 C2D A:CLA366 4.2 46.9 1.0 C2B A:CLA366 4.3 46.9 1.0 C3C A:CLA366 4.3 46.9 1.0 C2C A:CLA366 4.3 46.9 1.0 C3B A:CLA366 4.4 46.9 1.0 C3A A:CLA366 4.4 46.9 1.0 C2A A:CLA366 4.5 46.9 1.0 CB A:THR179 4.8 46.9 1.0 CBD A:CLA366 4.9 46.9 1.0

Magnesium binding site 3 out of 72 in the Crystal Structure of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg368 b:46.9 occ:1.00 MG A:CLA368 0.0 46.9 1.0 NB A:CLA368 1.9 46.9 1.0 NC A:CLA368 2.1 46.9 1.0 NA A:CLA368 2.2 46.9 1.0 ND A:CLA368 2.2 46.9 1.0 C1B A:CLA368 2.9 46.9 1.0 C4B A:CLA368 2.9 46.9 1.0 C1C A:CLA368 3.0 46.9 1.0 C4A A:CLA368 3.1 46.9 1.0 C4D A:CLA368 3.1 46.9 1.0 C4C A:CLA368 3.2 46.9 1.0 C1A A:CLA368 3.2 46.9 1.0 C1D A:CLA368 3.2 46.9 1.0 CHB A:CLA368 3.3 46.9 1.0 CHC A:CLA368 3.3 46.9 1.0 CHD A:CLA368 3.6 46.9 1.0 CHA A:CLA368 3.6 46.9 1.0 CE1 A:HIS118 3.9 46.9 1.0 C2B A:CLA368 4.1 46.9 1.0 C3B A:CLA368 4.1 46.9 1.0 C2C A:CLA368 4.3 46.9 1.0 C3D A:CLA368 4.3 46.9 1.0 C3C A:CLA368 4.4 46.9 1.0 C3A A:CLA368 4.4 46.9 1.0 C2D A:CLA368 4.4 46.9 1.0 C2A A:CLA368 4.5 46.9 1.0 NE2 A:HIS118 4.8 46.9 1.0 ND1 A:HIS118 4.9 46.9 1.0 CB A:PRO95 4.9 46.9 1.0

Magnesium binding site 4 out of 72 in the Crystal Structure of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg369 b:46.9 occ:1.00 MG A:CLA369 0.0 46.9 1.0 NB A:CLA369 1.9 46.9 1.0 NC A:CLA369 2.1 46.9 1.0 ND A:CLA369 2.2 46.9 1.0 NA A:CLA369 2.2 46.9 1.0 C1B A:CLA369 2.9 46.9 1.0 C4B A:CLA369 2.9 46.9 1.0 C1C A:CLA369 3.0 46.9 1.0 C4A A:CLA369 3.1 46.9 1.0 C4D A:CLA369 3.1 46.9 1.0 C4C A:CLA369 3.2 46.9 1.0 C1A A:CLA369 3.2 46.9 1.0 C1D A:CLA369 3.2 46.9 1.0 CHB A:CLA369 3.3 46.9 1.0 CHC A:CLA369 3.3 46.9 1.0 CHA A:CLA369 3.6 46.9 1.0 CHD A:CLA369 3.6 46.9 1.0 C2B A:CLA369 4.1 46.9 1.0 C3B A:CLA369 4.1 46.9 1.0 C2C A:CLA369 4.3 46.9 1.0 C3D A:CLA369 4.3 46.9 1.0 C3C A:CLA369 4.4 46.9 1.0 C3A A:CLA369 4.4 46.9 1.0 C2D A:CLA369 4.4 46.9 1.0 C2A A:CLA369 4.5 46.9 1.0

Magnesium binding site 5 out of 72 in the Crystal Structure of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1107 b:46.9 occ:1.00 MG B:CLA1107 0.0 46.9 1.0 NB B:CLA1107 1.9 46.9 1.0 NC B:CLA1107 2.1 46.9 1.0 NA B:CLA1107 2.2 46.9 1.0 ND B:CLA1107 2.2 46.9 1.0 C1B B:CLA1107 2.9 46.9 1.0 C4B B:CLA1107 2.9 46.9 1.0 C1C B:CLA1107 3.0 46.9 1.0 C4A B:CLA1107 3.1 46.9 1.0 C4D B:CLA1107 3.1 46.9 1.0 C4C B:CLA1107 3.2 46.9 1.0 C1A B:CLA1107 3.2 46.9 1.0 C1D B:CLA1107 3.2 46.9 1.0 CHB B:CLA1107 3.3 46.9 1.0 CHC B:CLA1107 3.3 46.9 1.0 CHA B:CLA1107 3.6 46.9 1.0 CHD B:CLA1107 3.6 46.9 1.0 C2B B:CLA1107 4.1 46.9 1.0 C3B B:CLA1107 4.1 46.9 1.0 C2C B:CLA1107 4.3 46.9 1.0 C3D B:CLA1107 4.3 46.9 1.0 C3C B:CLA1107 4.4 46.9 1.0 C3A B:CLA1107 4.4 46.9 1.0 C2D B:CLA1107 4.4 46.9 1.0 C2A B:CLA1107 4.5 46.9 1.0

Magnesium binding site 6 out of 72 in the Crystal Structure of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1108 b:46.9 occ:1.00 MG B:CLA1108 0.0 46.9 1.0 NB B:CLA1108 1.9 46.9 1.0 NC B:CLA1108 2.1 46.9 1.0 NA B:CLA1108 2.2 46.9 1.0 ND B:CLA1108 2.2 46.9 1.0 C1B B:CLA1108 2.9 46.9 1.0 C4B B:CLA1108 2.9 46.9 1.0 C1C B:CLA1108 3.0 46.9 1.0 C4A B:CLA1108 3.1 46.9 1.0 C4D B:CLA1108 3.1 46.9 1.0 C4C B:CLA1108 3.2 46.9 1.0 C1A B:CLA1108 3.2 46.9 1.0 C1D B:CLA1108 3.2 46.9 1.0 CHB B:CLA1108 3.3 46.9 1.0 CHC B:CLA1108 3.3 46.9 1.0 CHD B:CLA1108 3.6 46.9 1.0 CHA B:CLA1108 3.6 46.9 1.0 C2B B:CLA1108 4.1 46.9 1.0 C3B B:CLA1108 4.1 46.9 1.0 C2C B:CLA1108 4.3 46.9 1.0 C3D B:CLA1108 4.3 46.9 1.0 C3C B:CLA1108 4.4 46.9 1.0 C3A B:CLA1108 4.4 46.9 1.0 C2D B:CLA1108 4.4 46.9 1.0 C2A B:CLA1108 4.5 46.9 1.0 CMA B:CLA1109 4.9 46.9 1.0

Magnesium binding site 7 out of 72 in the Crystal Structure of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1109 b:46.9 occ:1.00 MG B:CLA1109 0.0 46.9 1.0 NB B:CLA1109 1.9 46.9 1.0 NC B:CLA1109 2.1 46.9 1.0 NA B:CLA1109 2.2 46.9 1.0 ND B:CLA1109 2.2 46.9 1.0 C1B B:CLA1109 2.9 46.9 1.0 C4B B:CLA1109 2.9 46.9 1.0 C1C B:CLA1109 3.0 46.9 1.0 C4A B:CLA1109 3.0 46.9 1.0 C4D B:CLA1109 3.1 46.9 1.0 C4C B:CLA1109 3.2 46.9 1.0 C1A B:CLA1109 3.2 46.9 1.0 C1D B:CLA1109 3.2 46.9 1.0 CHB B:CLA1109 3.3 46.9 1.0 CHC B:CLA1109 3.3 46.9 1.0 CHA B:CLA1109 3.6 46.9 1.0 CHD B:CLA1109 3.6 46.9 1.0 C2B B:CLA1109 4.1 46.9 1.0 C3B B:CLA1109 4.1 46.9 1.0 C2C B:CLA1109 4.3 46.9 1.0 C3D B:CLA1109 4.3 46.9 1.0 C3C B:CLA1109 4.4 46.9 1.0 C3A B:CLA1109 4.4 46.9 1.0 C2D B:CLA1109 4.4 46.9 1.0 C2A B:CLA1109 4.5 46.9 1.0

Magnesium binding site 8 out of 72 in the Crystal Structure of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1110 b:46.9 occ:1.00 MG B:CLA1110 0.0 46.9 1.0 NB B:CLA1110 1.9 46.9 1.0 NC B:CLA1110 2.1 46.9 1.0 ND B:CLA1110 2.2 46.9 1.0 NA B:CLA1110 2.2 46.9 1.0 C1B B:CLA1110 2.9 46.9 1.0 C4B B:CLA1110 2.9 46.9 1.0 C1C B:CLA1110 3.0 46.9 1.0 C4A B:CLA1110 3.0 46.9 1.0 C4D B:CLA1110 3.1 46.9 1.0 C4C B:CLA1110 3.2 46.9 1.0 C1A B:CLA1110 3.2 46.9 1.0 C1D B:CLA1110 3.2 46.9 1.0 CHB B:CLA1110 3.3 46.9 1.0 CHC B:CLA1110 3.3 46.9 1.0 CHA B:CLA1110 3.6 46.9 1.0 CHD B:CLA1110 3.6 46.9 1.0 C2B B:CLA1110 4.1 46.9 1.0 C3B B:CLA1110 4.1 46.9 1.0 C2C B:CLA1110 4.3 46.9 1.0 C3D B:CLA1110 4.3 46.9 1.0 C3C B:CLA1110 4.4 46.9 1.0 C3A B:CLA1110 4.4 46.9 1.0 C2D B:CLA1110 4.4 46.9 1.0 C2A B:CLA1110 4.5 46.9 1.0 CZ3 B:TRP450 4.7 46.9 1.0 CE3 B:TRP450 4.9 46.9 1.0 CB B:MET60 5.0 46.9 1.0

Magnesium binding site 9 out of 72 in the Crystal Structure of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1111 b:46.9 occ:1.00 MG B:CLA1111 0.0 46.9 1.0 NB B:CLA1111 1.9 46.9 1.0 NC B:CLA1111 2.1 46.9 1.0 NA B:CLA1111 2.2 46.9 1.0 ND B:CLA1111 2.2 46.9 1.0 C1B B:CLA1111 2.9 46.9 1.0 C4B B:CLA1111 2.9 46.9 1.0 C1C B:CLA1111 3.0 46.9 1.0 C4A B:CLA1111 3.1 46.9 1.0 C4D B:CLA1111 3.1 46.9 1.0 C4C B:CLA1111 3.2 46.9 1.0 C1A B:CLA1111 3.2 46.9 1.0 C1D B:CLA1111 3.2 46.9 1.0 CHB B:CLA1111 3.3 46.9 1.0 CHC B:CLA1111 3.3 46.9 1.0 CHD B:CLA1111 3.6 46.9 1.0 CHA B:CLA1111 3.6 46.9 1.0 C2B B:CLA1111 4.1 46.9 1.0 C3B B:CLA1111 4.1 46.9 1.0 C2C B:CLA1111 4.3 46.9 1.0 C3D B:CLA1111 4.3 46.9 1.0 C3C B:CLA1111 4.4 46.9 1.0 C3A B:CLA1111 4.4 46.9 1.0 C2D B:CLA1111 4.4 46.9 1.0 C2A B:CLA1111 4.5 46.9 1.0

Magnesium binding site 10 out of 72 in the Crystal Structure of Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1112 b:46.9 occ:1.00 MG B:CLA1112 0.0 46.9 1.0 NB B:CLA1112 1.9 46.9 1.0 NC B:CLA1112 2.1 46.9 1.0 NA B:CLA1112 2.2 46.9 1.0 ND B:CLA1112 2.2 46.9 1.0 C1B B:CLA1112 2.9 46.9 1.0 C4B B:CLA1112 2.9 46.9 1.0 C1C B:CLA1112 3.0 46.9 1.0 C4A B:CLA1112 3.1 46.9 1.0 C4D B:CLA1112 3.1 46.9 1.0 C4C B:CLA1112 3.2 46.9 1.0 C1A B:CLA1112 3.2 46.9 1.0 C1D B:CLA1112 3.2 46.9 1.0 CHB B:CLA1112 3.3 46.9 1.0 CHC B:CLA1112 3.3 46.9 1.0 CHA B:CLA1112 3.6 46.9 1.0 CHD B:CLA1112 3.6 46.9 1.0 C2B B:CLA1112 4.1 46.9 1.0 C3B B:CLA1112 4.1 46.9 1.0 C2C B:CLA1112 4.3 46.9 1.0 C3D B:CLA1112 4.3 46.9 1.0 C3C B:CLA1112 4.4 46.9 1.0 C3A B:CLA1112 4.4 46.9 1.0 C2D B:CLA1112 4.4 46.9 1.0 C2A B:CLA1112 4.5 46.9 1.0

N.Kamiya, J.-R.Shen. Crystal Structure of Oxygen-Evolving Photosystem II From Thermosynechococcus Vulcanus at 3.7-A Resolution Proc.Natl.Acad.Sci.Usa V. 100 98 2003.
ISSN: ISSN 0027-8424
PubMed: 12518057
DOI: 10.1073/PNAS.0135651100