Magnesium in PDB 2axt: Crystal Structure of Photosystem II From Thermosynechococcus Elongatus

The structure of Crystal Structure of Photosystem II From Thermosynechococcus Elongatus, PDB code: 2axt was solved by B.Loll, J.Kern, W.Saenger, A.Zouni, J.Biesiadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	127.692, 225.403, 306.106, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 28.6

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

Manganese	(Mn)	8 atoms
Calcium	(Ca)	4 atoms
Iron	(Fe)	6 atoms
Neon	(Ne)	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;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus (pdb code 2axt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 70 binding sites of Magnesium where determined in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus, PDB code: 2axt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 70 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg558 b:45.2 occ:1.00 MG A:CLA558 0.0 45.2 1.0 ND A:CLA558 2.0 48.4 1.0 NB A:CLA558 2.1 45.4 1.0 NC A:CLA558 2.1 44.7 1.0 NA A:CLA558 2.2 49.1 1.0 NE2 A:HIS198 2.3 45.2 1.0 CE1 A:HIS198 2.9 45.0 1.0 C4D A:CLA558 3.0 47.8 1.0 C1B A:CLA558 3.1 45.5 1.0 C4A A:CLA558 3.1 47.7 1.0 C4B A:CLA558 3.1 45.1 1.0 C1D A:CLA558 3.1 48.4 1.0 C1C A:CLA558 3.1 44.2 1.0 C4C A:CLA558 3.1 44.6 1.0 C1A A:CLA558 3.2 48.6 1.0 CHB A:CLA558 3.4 46.5 1.0 CHC A:CLA558 3.4 42.7 1.0 CHD A:CLA558 3.5 46.9 1.0 CD2 A:HIS198 3.5 47.9 1.0 CHA A:CLA558 3.5 45.9 1.0 CBB D:CLA354 3.9 43.5 1.0 CE A:MET183 4.1 52.8 1.0 ND1 A:HIS198 4.1 47.7 1.0 C3D A:CLA558 4.2 48.8 1.0 C2D A:CLA558 4.3 48.5 1.0 C2B A:CLA558 4.3 46.0 1.0 C3B A:CLA558 4.3 46.1 1.0 C2C A:CLA558 4.4 44.8 1.0 C3C A:CLA558 4.4 44.5 1.0 C3A A:CLA558 4.4 46.9 1.0 CG A:HIS198 4.4 47.8 1.0 C2A A:CLA558 4.5 47.9 1.0 CAB D:CLA354 4.9 40.9 1.0 CBD A:CLA558 5.0 47.0 1.0

Magnesium binding site 2 out of 70 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg559 b:41.4 occ:1.00 MG A:CLA559 0.0 41.4 1.0 ND A:CLA559 2.0 41.6 1.0 NB A:CLA559 2.1 42.7 1.0 NC A:CLA559 2.1 42.7 1.0 NA A:CLA559 2.1 41.7 1.0 C4D A:CLA559 3.0 42.1 1.0 C4A A:CLA559 3.1 41.4 1.0 C1B A:CLA559 3.1 41.7 1.0 C1D A:CLA559 3.1 43.4 1.0 C1C A:CLA559 3.1 42.0 1.0 C4B A:CLA559 3.1 41.5 1.0 C4C A:CLA559 3.1 42.0 1.0 C1A A:CLA559 3.1 40.4 1.0 CHB A:CLA559 3.4 41.2 1.0 CHD A:CLA559 3.5 41.0 1.0 CHA A:CLA559 3.5 41.6 1.0 CHC A:CLA559 3.5 40.4 1.0 C3D A:CLA559 4.2 43.1 1.0 CG2 A:THR179 4.3 56.7 1.0 C2D A:CLA559 4.3 44.1 1.0 C2B A:CLA559 4.3 42.1 1.0 C3B A:CLA559 4.4 42.2 1.0 C3C A:CLA559 4.4 41.8 1.0 C2C A:CLA559 4.4 42.6 1.0 C3A A:CLA559 4.4 39.4 1.0 C2A A:CLA559 4.4 39.7 1.0 OG1 A:THR179 4.8 57.9 1.0 CBB A:PHO561 4.9 52.4 1.0 CBD A:CLA559 4.9 42.2 1.0 CBA A:CLA559 5.0 44.1 1.0

Magnesium binding site 3 out of 70 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg560 b:54.7 occ:1.00 MG A:CLA560 0.0 54.7 1.0 ND A:CLA560 2.0 56.1 1.0 NB A:CLA560 2.1 56.5 1.0 NC A:CLA560 2.1 54.9 1.0 NA A:CLA560 2.2 56.3 1.0 C4D A:CLA560 3.0 56.0 1.0 C1B A:CLA560 3.1 57.1 1.0 C4A A:CLA560 3.1 57.1 1.0 C4B A:CLA560 3.1 57.3 1.0 C1D A:CLA560 3.1 54.2 1.0 C1C A:CLA560 3.1 55.1 1.0 C4C A:CLA560 3.1 54.8 1.0 C1A A:CLA560 3.2 56.0 1.0 CHB A:CLA560 3.4 57.3 1.0 CHC A:CLA560 3.5 57.6 1.0 CHD A:CLA560 3.5 54.7 1.0 CHA A:CLA560 3.5 54.3 1.0 C3D A:CLA560 4.2 53.4 1.0 C2D A:CLA560 4.3 53.2 1.0 C2B A:CLA560 4.3 57.9 1.0 C3B A:CLA560 4.3 58.2 1.0 C2C A:CLA560 4.4 54.2 1.0 C3C A:CLA560 4.4 54.4 1.0 C3A A:CLA560 4.4 57.2 1.0 C2A A:CLA560 4.5 56.9 1.0 C20 A:PHO562 4.6 65.9 1.0 CG1 D:ILE178 4.9 58.0 1.0 CBD A:CLA560 5.0 52.2 1.0

Magnesium binding site 4 out of 70 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg563 b:45.4 occ:1.00 MG A:CLA563 0.0 45.4 1.0 ND A:CLA563 2.0 45.3 1.0 NB A:CLA563 2.1 46.3 1.0 NC A:CLA563 2.1 44.9 1.0 NA A:CLA563 2.2 51.6 1.0 NE2 A:HIS118 2.6 66.8 1.0 C4D A:CLA563 3.0 47.3 1.0 CE1 A:HIS118 3.1 67.4 1.0 C4A A:CLA563 3.1 50.8 1.0 C1B A:CLA563 3.1 46.7 1.0 C1C A:CLA563 3.1 43.8 1.0 C4B A:CLA563 3.1 47.0 1.0 C1D A:CLA563 3.1 45.5 1.0 C4C A:CLA563 3.1 43.5 1.0 C1A A:CLA563 3.2 50.7 1.0 CHB A:CLA563 3.4 48.0 1.0 CHC A:CLA563 3.4 46.0 1.0 CHA A:CLA563 3.5 49.3 1.0 CHD A:CLA563 3.5 43.8 1.0 CD2 A:HIS118 3.9 65.8 1.0 C3D A:CLA563 4.2 46.4 1.0 C2D A:CLA563 4.3 45.4 1.0 C2B A:CLA563 4.3 47.1 1.0 C3B A:CLA563 4.3 47.3 1.0 C2C A:CLA563 4.4 44.0 1.0 ND1 A:HIS118 4.4 66.6 1.0 C3C A:CLA563 4.4 43.3 1.0 C3A A:CLA563 4.4 52.1 1.0 CG2 I:VAL12 4.4 66.9 1.0 C2A A:CLA563 4.4 53.1 1.0 CG1 I:VAL8 4.5 62.8 1.0 CG A:HIS118 4.8 64.6 1.0 CBD A:CLA563 4.9 50.7 1.0

Magnesium binding site 5 out of 70 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg511 b:90.4 occ:1.00 MG B:CLA511 0.0 90.4 1.0 ND B:CLA511 2.0 90.0 1.0 NB B:CLA511 2.1 90.5 1.0 NC B:CLA511 2.2 90.5 1.0 NA B:CLA511 2.2 88.5 1.0 C4D B:CLA511 3.0 90.9 1.0 C1B B:CLA511 3.1 90.0 1.0 C4A B:CLA511 3.1 89.4 1.0 C1D B:CLA511 3.1 90.4 1.0 C4B B:CLA511 3.1 90.4 1.0 C1C B:CLA511 3.2 90.3 1.0 C1A B:CLA511 3.2 89.8 1.0 C4C B:CLA511 3.2 90.0 1.0 O B:TRP185 3.2 71.4 1.0 CHB B:CLA511 3.4 88.7 1.0 CHA B:CLA511 3.5 90.9 1.0 CHD B:CLA511 3.5 89.0 1.0 CHC B:CLA511 3.5 89.4 1.0 C3D B:CLA511 4.3 91.3 1.0 C B:TRP185 4.3 70.4 1.0 C2D B:CLA511 4.3 90.9 1.0 C2B B:CLA511 4.3 90.3 1.0 C3B B:CLA511 4.4 90.3 1.0 C3A B:CLA511 4.4 89.7 1.0 C2C B:CLA511 4.4 90.3 1.0 C3C B:CLA511 4.5 90.0 1.0 C2A B:CLA511 4.5 89.9 1.0 CB B:TRP185 4.6 68.5 1.0 CBB B:CLA512 4.7 75.7 1.0 CA B:TRP185 4.9 70.0 1.0 CBD B:CLA511 5.0 93.0 1.0

Magnesium binding site 6 out of 70 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg512 b:74.6 occ:1.00 MG B:CLA512 0.0 74.6 1.0 ND B:CLA512 2.0 73.8 1.0 NB B:CLA512 2.1 75.2 1.0 ND1 B:HIS201 2.1 63.3 1.0 NC B:CLA512 2.1 76.4 1.0 NA B:CLA512 2.2 76.3 1.0 CE1 B:HIS201 2.9 63.0 1.0 C4D B:CLA512 3.0 75.2 1.0 C4A B:CLA512 3.1 76.5 1.0 C1B B:CLA512 3.1 75.6 1.0 C1D B:CLA512 3.1 74.9 1.0 C4B B:CLA512 3.1 75.1 1.0 C1C B:CLA512 3.1 75.8 1.0 C4C B:CLA512 3.2 75.2 1.0 C1A B:CLA512 3.2 76.0 1.0 CG B:HIS201 3.3 63.3 1.0 CHB B:CLA512 3.4 76.2 1.0 CHC B:CLA512 3.5 75.4 1.0 CHA B:CLA512 3.5 76.1 1.0 CHD B:CLA512 3.5 75.8 1.0 CB B:HIS201 3.8 62.8 1.0 NE2 B:HIS201 4.1 62.5 1.0 C3D B:CLA512 4.2 75.1 1.0 CZ H:PHE41 4.2 74.6 1.0 C2D B:CLA512 4.3 74.4 1.0 CD2 B:HIS201 4.3 63.0 1.0 C2B B:CLA512 4.3 75.4 1.0 C3A B:CLA512 4.4 76.3 1.0 C3B B:CLA512 4.4 75.6 1.0 C2C B:CLA512 4.4 75.7 1.0 C3C B:CLA512 4.4 75.0 1.0 CA B:HIS201 4.4 62.6 1.0 C2A B:CLA512 4.5 75.9 1.0 CBD B:CLA512 5.0 75.3 1.0

Magnesium binding site 7 out of 70 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg513 b:61.8 occ:1.00 MG B:CLA513 0.0 61.8 1.0 ND B:CLA513 2.0 58.5 1.0 NB B:CLA513 2.1 60.2 1.0 NE2 B:HIS202 2.1 57.4 1.0 NC B:CLA513 2.1 60.7 1.0 NA B:CLA513 2.2 60.4 1.0 CD2 B:HIS202 2.9 59.6 1.0 C4D B:CLA513 3.0 58.4 1.0 C1B B:CLA513 3.0 63.0 1.0 C4A B:CLA513 3.1 61.6 1.0 C1D B:CLA513 3.1 57.3 1.0 C4B B:CLA513 3.1 62.7 1.0 C1C B:CLA513 3.1 59.8 1.0 C4C B:CLA513 3.1 60.1 1.0 C1A B:CLA513 3.2 59.4 1.0 CE1 B:HIS202 3.2 57.4 1.0 CHB B:CLA513 3.4 62.3 1.0 CHD B:CLA513 3.5 59.5 1.0 CHC B:CLA513 3.5 61.2 1.0 CHA B:CLA513 3.5 59.4 1.0 C9 B:CLA515 4.1 72.9 1.0 CG B:HIS202 4.2 59.7 1.0 C3D B:CLA513 4.2 58.0 1.0 ND1 B:HIS202 4.3 58.8 1.0 C2D B:CLA513 4.3 56.9 1.0 C2B B:CLA513 4.3 64.9 1.0 C6 B:CLA515 4.3 69.7 1.0 C3B B:CLA513 4.3 64.8 1.0 C2C B:CLA513 4.4 59.7 1.0 C3A B:CLA513 4.4 61.1 1.0 C3C B:CLA513 4.4 60.6 1.0 C2A B:CLA513 4.5 60.5 1.0 CE2 B:PHE153 4.8 64.7 1.0 CBD B:CLA513 5.0 59.7 1.0

Magnesium binding site 8 out of 70 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg514 b:64.5 occ:1.00 MG B:CLA514 0.0 64.5 1.0 ND B:CLA514 2.1 63.8 1.0 NB B:CLA514 2.1 63.1 1.0 NC B:CLA514 2.1 63.3 1.0 NE2 B:HIS455 2.2 54.0 1.0 NA B:CLA514 2.2 62.9 1.0 C4D B:CLA514 3.0 63.3 1.0 C1B B:CLA514 3.1 62.3 1.0 C4B B:CLA514 3.1 63.7 1.0 C1C B:CLA514 3.1 64.4 1.0 C1D B:CLA514 3.1 63.5 1.0 CD2 B:HIS455 3.1 54.2 1.0 C4A B:CLA514 3.1 62.7 1.0 C4C B:CLA514 3.1 63.5 1.0 CE1 B:HIS455 3.2 54.7 1.0 C1A B:CLA514 3.2 63.1 1.0 CHB B:CLA514 3.4 61.8 1.0 CHC B:CLA514 3.4 63.8 1.0 CHD B:CLA514 3.5 63.6 1.0 CHA B:CLA514 3.5 63.5 1.0 C14 B:CLA522 3.7 61.7 1.0 C3D B:CLA514 4.2 63.6 1.0 ND1 B:HIS455 4.3 52.0 1.0 CG B:HIS455 4.3 50.9 1.0 C2D B:CLA514 4.3 64.0 1.0 C2B B:CLA514 4.3 63.0 1.0 C3B B:CLA514 4.3 63.5 1.0 C2C B:CLA514 4.4 65.3 1.0 C3C B:CLA514 4.4 65.2 1.0 C3A B:CLA514 4.4 62.7 1.0 C2A B:CLA514 4.5 63.9 1.0 C13 B:CLA522 4.6 60.0 1.0 C15 B:CLA522 4.8 57.0 1.0 CBD B:CLA514 5.0 63.8 1.0

Magnesium binding site 9 out of 70 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg515 b:66.0 occ:1.00 MG B:CLA515 0.0 66.0 1.0 ND B:CLA515 2.0 63.7 1.0 NB B:CLA515 2.1 67.4 1.0 NC B:CLA515 2.1 68.6 1.0 NA B:CLA515 2.2 64.2 1.0 NE2 B:HIS100 2.5 60.6 1.0 C4D B:CLA515 3.0 63.5 1.0 C4A B:CLA515 3.1 65.0 1.0 C1B B:CLA515 3.1 67.7 1.0 C1D B:CLA515 3.1 65.0 1.0 C1C B:CLA515 3.1 68.5 1.0 C4B B:CLA515 3.1 67.6 1.0 C4C B:CLA515 3.1 67.5 1.0 C1A B:CLA515 3.2 62.1 1.0 CE1 B:HIS100 3.2 60.0 1.0 CHB B:CLA515 3.4 66.3 1.0 CHD B:CLA515 3.5 65.9 1.0 CHA B:CLA515 3.5 62.8 1.0 CHC B:CLA515 3.5 67.5 1.0 CD2 B:HIS100 3.7 59.1 1.0 C1 B:CLA514 4.2 75.2 1.0 C3D B:CLA515 4.2 62.9 1.0 C2D B:CLA515 4.3 64.1 1.0 C2B B:CLA515 4.3 68.3 1.0 C2C B:CLA515 4.4 68.8 1.0 C3A B:CLA515 4.4 64.3 1.0 C3C B:CLA515 4.4 69.0 1.0 C3B B:CLA515 4.4 68.6 1.0 ND1 B:HIS100 4.4 58.5 1.0 C2A B:CLA515 4.5 62.4 1.0 CG B:HIS100 4.7 57.7 1.0 C4 B:CLA516 4.7 63.9 1.0 C2 B:CLA514 4.9 75.7 1.0 CBD B:CLA515 4.9 60.3 1.0 O1A B:CLA514 5.0 70.7 1.0

Magnesium binding site 10 out of 70 in the Crystal Structure of Photosystem II From Thermosynechococcus Elongatus


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 From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg516 b:77.3 occ:1.00 MG B:CLA516 0.0 77.3 1.0 ND B:CLA516 2.1 78.3 1.0 NB B:CLA516 2.1 76.6 1.0 NC B:CLA516 2.1 78.5 1.0 NA B:CLA516 2.2 73.4 1.0 CD2 B:HIS157 2.2 68.6 1.0 NE2 B:HIS157 2.9 68.3 1.0 C4D B:CLA516 3.0 77.3 1.0 C1B B:CLA516 3.1 76.2 1.0 C4B B:CLA516 3.1 77.2 1.0 C1C B:CLA516 3.1 77.5 1.0 C4A B:CLA516 3.1 73.1 1.0 C1D B:CLA516 3.1 78.0 1.0 C4C B:CLA516 3.1 77.4 1.0 C1A B:CLA516 3.2 73.1 1.0 CHB B:CLA516 3.4 75.0 1.0 CHC B:CLA516 3.4 77.9 1.0 CG B:HIS157 3.5 69.7 1.0 CHD B:CLA516 3.5 77.2 1.0 CHA B:CLA516 3.5 75.8 1.0 CE1 B:HIS157 4.1 67.8 1.0 C3D B:CLA516 4.3 77.5 1.0 CB B:HIS157 4.3 71.8 1.0 C2B B:CLA516 4.3 76.2 1.0 C2D B:CLA516 4.3 77.5 1.0 C3B B:CLA516 4.3 76.7 1.0 C2C B:CLA516 4.4 76.7 1.0 C3C B:CLA516 4.4 76.9 1.0 ND1 B:HIS157 4.4 67.3 1.0 C3A B:CLA516 4.4 71.8 1.0 C2A B:CLA516 4.5 71.3 1.0 CD B:PRO164 4.9 70.5 1.0 CBD B:CLA516 5.0 76.8 1.0

B.Loll, J.Kern, W.Saenger, A.Zouni, J.Biesiadka. Towards Complete Cofactor Arrangement in the 3.0 A Resolution Structure of Photosystem II Nature V. 438 1040 2005.
ISSN: ISSN 0028-0836
PubMed: 16355230
DOI: 10.1038/NATURE04224