Magnesium in PDB 3kzi: Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II

The structure of Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II, PDB code: 3kzi was solved by A.Gabdulkhakov, A.Guskov, M.Broser, J.Kern, A.Zouni, W.Saenger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.87 / 3.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	119.890, 224.690, 337.280, 90.00, 90.00, 90.00
R / Rfree (%)	29.7 / 30.8

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

Manganese	(Mn)	4 atoms
Iron	(Fe)	3 atoms
Calcium	(Ca)	4 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 Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II (pdb code 3kzi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 35 binding sites of Magnesium where determined in the Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II, PDB code: 3kzi:
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 Crystal Structure of Monomeric Form of Cyanobacterial 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 Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg362 b:0.2 occ:1.00 MG A:CLA362 0.0 0.2 1.0 ND A:CLA362 2.0 0.1 1.0 NC A:CLA362 2.1 0.1 1.0 NB A:CLA362 2.1 0.1 1.0 NA A:CLA362 2.2 0.7 1.0 NE2 A:HIS198 2.6 0.1 1.0 C4D A:CLA362 3.0 1.0 1.0 C1D A:CLA362 3.1 0.7 1.0 C1B A:CLA362 3.1 0.4 1.0 C4C A:CLA362 3.1 0.4 1.0 C1C A:CLA362 3.1 0.7 1.0 C4A A:CLA362 3.1 0.3 1.0 C4B A:CLA362 3.1 0.2 1.0 C1A A:CLA362 3.2 0.8 1.0 CHB A:CLA362 3.4 0.5 1.0 CHD A:CLA362 3.5 0.7 1.0 CE1 A:HIS198 3.5 0.3 1.0 CHC A:CLA362 3.5 0.5 1.0 CHA A:CLA362 3.5 0.2 1.0 CD2 A:HIS198 3.6 0.7 1.0 C3D A:CLA362 4.3 1.0 1.0 C2B A:CLA362 4.3 0.8 1.0 C2D A:CLA362 4.3 0.2 1.0 C3C A:CLA362 4.4 0.8 1.0 C2C A:CLA362 4.4 0.3 1.0 C3B A:CLA362 4.4 0.7 1.0 C3A A:CLA362 4.4 0.4 1.0 CBB D:CLA354 4.4 0.7 1.0 C2A A:CLA362 4.5 0.8 1.0 ND1 A:HIS198 4.6 0.5 1.0 CG A:HIS198 4.7 0.7 1.0 SD A:MET183 4.9 0.0 1.0

Magnesium binding site 2 out of 35 in the Crystal Structure of Monomeric Form of Cyanobacterial 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 Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg363 b:0.7 occ:1.00 MG A:CLA363 0.0 0.7 1.0 ND A:CLA363 2.0 0.4 1.0 NA A:CLA363 2.1 0.8 1.0 NB A:CLA363 2.1 0.7 1.0 NC A:CLA363 2.1 0.1 1.0 C4D A:CLA363 3.0 0.8 1.0 C4A A:CLA363 3.0 0.9 1.0 C1B A:CLA363 3.1 0.2 1.0 C4C A:CLA363 3.1 0.1 1.0 C1C A:CLA363 3.1 0.7 1.0 C1D A:CLA363 3.1 0.6 1.0 C1A A:CLA363 3.1 0.9 1.0 C4B A:CLA363 3.1 0.4 1.0 CHB A:CLA363 3.4 0.1 1.0 CHA A:CLA363 3.4 0.7 1.0 CHC A:CLA363 3.5 0.6 1.0 CHD A:CLA363 3.5 0.2 1.0 CBB A:PHO365 4.1 0.1 1.0 C3D A:CLA363 4.2 0.1 1.0 C2B A:CLA363 4.3 0.6 1.0 C2D A:CLA363 4.3 0.2 1.0 C3A A:CLA363 4.3 0.2 1.0 C3C A:CLA363 4.4 0.0 1.0 C2A A:CLA363 4.4 0.9 1.0 C2C A:CLA363 4.4 0.0 1.0 C3B A:CLA363 4.4 0.5 1.0 CG2 A:THR179 4.9 0.1 1.0 CBD A:CLA363 5.0 0.8 1.0

Magnesium binding site 3 out of 35 in the Crystal Structure of Monomeric Form of Cyanobacterial 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 Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg366 b:0.8 occ:1.00 MG A:CLA366 0.0 0.8 1.0 ND A:CLA366 2.0 1.0 1.0 NA A:CLA366 2.1 0.4 1.0 NB A:CLA366 2.1 0.9 1.0 NC A:CLA366 2.2 0.4 1.0 NE2 A:HIS118 2.8 0.0 1.0 C4D A:CLA366 2.9 0.7 1.0 C4A A:CLA366 3.1 0.1 1.0 C1B A:CLA366 3.1 0.8 1.0 C1D A:CLA366 3.1 0.2 1.0 C1A A:CLA366 3.1 0.8 1.0 C1C A:CLA366 3.2 0.2 1.0 C4B A:CLA366 3.2 0.7 1.0 C4C A:CLA366 3.2 0.7 1.0 CHB A:CLA366 3.4 0.7 1.0 CHA A:CLA366 3.5 0.3 1.0 CHD A:CLA366 3.5 0.8 1.0 CHC A:CLA366 3.5 0.8 1.0 CE1 A:HIS118 3.6 0.0 1.0 CD2 A:HIS118 3.8 0.1 1.0 CG2 I:VAL12 3.9 0.0 1.0 C3D A:CLA366 4.2 1.0 1.0 C2B A:CLA366 4.3 0.3 1.0 C2D A:CLA366 4.3 0.4 1.0 C3A A:CLA366 4.4 0.8 1.0 C2A A:CLA366 4.4 0.2 1.0 C3B A:CLA366 4.4 0.7 1.0 C2C A:CLA366 4.5 0.1 1.0 C3C A:CLA366 4.5 0.6 1.0 CG1 I:VAL8 4.6 0.5 1.0 ND1 A:HIS118 4.7 0.2 1.0 CG A:HIS118 4.9 0.8 1.0

Magnesium binding site 4 out of 35 in the Crystal Structure of Monomeric Form of Cyanobacterial 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 Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg511 b:0.0 occ:1.00 MG B:CLA511 0.0 0.0 1.0 ND B:CLA511 2.0 0.0 1.0 NB B:CLA511 2.1 0.0 1.0 NC B:CLA511 2.2 0.0 1.0 NA B:CLA511 2.2 0.4 1.0 C4D B:CLA511 3.0 0.4 1.0 C1B B:CLA511 3.1 0.0 1.0 C1D B:CLA511 3.1 0.0 1.0 C4A B:CLA511 3.1 0.0 1.0 C4C B:CLA511 3.2 0.0 1.0 C4B B:CLA511 3.2 0.0 1.0 C1C B:CLA511 3.2 0.0 1.0 C1A B:CLA511 3.3 0.8 1.0 CHB B:CLA511 3.4 0.1 1.0 CHD B:CLA511 3.5 0.0 1.0 CHC B:CLA511 3.6 0.9 1.0 CHA B:CLA511 3.6 0.5 1.0 O B:TRP185 3.7 0.6 1.0 C3D B:CLA511 4.3 0.0 1.0 C2B B:CLA511 4.3 0.0 1.0 C2D B:CLA511 4.3 0.0 1.0 C3B B:CLA511 4.4 0.0 1.0 C3A B:CLA511 4.5 0.0 1.0 C2C B:CLA511 4.5 0.0 1.0 C3C B:CLA511 4.5 0.0 1.0 C2A B:CLA511 4.6 0.9 1.0 C B:TRP185 4.9 0.4 1.0

Magnesium binding site 5 out of 35 in the Crystal Structure of Monomeric Form of Cyanobacterial 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 Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg512 b:0.3 occ:1.00 MG B:CLA512 0.0 0.3 1.0 ND B:CLA512 2.0 0.3 1.0 NB B:CLA512 2.1 0.4 1.0 NA B:CLA512 2.1 0.5 1.0 NC B:CLA512 2.1 0.1 1.0 ND1 B:HIS201 2.8 0.5 1.0 C4D B:CLA512 3.0 0.3 1.0 C1B B:CLA512 3.1 1.0 1.0 C4A B:CLA512 3.1 1.0 1.0 C1D B:CLA512 3.1 0.5 1.0 C1C B:CLA512 3.1 0.4 1.0 C4B B:CLA512 3.1 0.6 1.0 C4C B:CLA512 3.1 0.8 1.0 C1A B:CLA512 3.1 0.5 1.0 CHB B:CLA512 3.4 1.0 1.0 CHA B:CLA512 3.5 0.9 1.0 CHC B:CLA512 3.5 0.6 1.0 CE1 B:HIS201 3.5 0.2 1.0 CHD B:CLA512 3.5 0.0 1.0 CZ H:PHE41 3.7 0.8 1.0 CG B:HIS201 3.9 0.1 1.0 C3D B:CLA512 4.2 0.5 1.0 C2B B:CLA512 4.3 0.1 1.0 C2D B:CLA512 4.3 0.1 1.0 CB B:HIS201 4.3 0.1 1.0 C3B B:CLA512 4.4 0.0 1.0 C3A B:CLA512 4.4 0.1 1.0 C2C B:CLA512 4.4 0.5 1.0 C2A B:CLA512 4.4 0.5 1.0 C3C B:CLA512 4.4 0.0 1.0 CE2 H:PHE41 4.5 0.8 1.0 CE1 H:PHE41 4.6 0.2 1.0 NE2 B:HIS201 4.7 0.7 1.0 CE2 B:PHE190 4.8 0.8 1.0 CA B:HIS201 4.9 0.4 1.0 CD2 B:HIS201 4.9 0.9 1.0

Magnesium binding site 6 out of 35 in the Crystal Structure of Monomeric Form of Cyanobacterial 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 Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg513 b:0.1 occ:1.00 MG B:CLA513 0.0 0.1 1.0 ND B:CLA513 2.0 0.8 1.0 NA B:CLA513 2.0 0.5 1.0 NB B:CLA513 2.1 0.8 1.0 NC B:CLA513 2.1 0.1 1.0 NE2 B:HIS202 2.8 0.5 1.0 C4A B:CLA513 3.0 0.8 1.0 C4D B:CLA513 3.0 0.1 1.0 C1B B:CLA513 3.0 0.2 1.0 C1D B:CLA513 3.1 0.7 1.0 C4C B:CLA513 3.1 0.2 1.0 C1A B:CLA513 3.1 0.1 1.0 C1C B:CLA513 3.2 0.1 1.0 C4B B:CLA513 3.2 0.6 1.0 CHB B:CLA513 3.3 1.0 1.0 CHD B:CLA513 3.5 0.9 1.0 CHA B:CLA513 3.5 0.3 1.0 CHC B:CLA513 3.5 0.1 1.0 CD2 B:HIS202 3.7 0.9 1.0 CE1 B:HIS202 3.8 0.6 1.0 C6 B:CLA515 3.9 0.0 1.0 C3D B:CLA513 4.3 0.3 1.0 C3A B:CLA513 4.3 0.8 1.0 C2B B:CLA513 4.3 0.7 1.0 C2D B:CLA513 4.3 0.6 1.0 C2A B:CLA513 4.4 0.6 1.0 C3B B:CLA513 4.4 0.7 1.0 C3C B:CLA513 4.4 0.6 1.0 C2C B:CLA513 4.5 0.3 1.0 C8 B:CLA515 4.5 0.4 1.0 C7 B:CLA515 4.6 0.9 1.0 CG B:HIS202 4.8 0.0 1.0 C5 B:CLA515 4.8 0.7 1.0 ND1 B:HIS202 4.8 0.9 1.0 NE2 B:HIS201 5.0 0.7 1.0

Magnesium binding site 7 out of 35 in the Crystal Structure of Monomeric Form of Cyanobacterial 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 Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg514 b:0.7 occ:1.00 MG B:CLA514 0.0 0.7 1.0 ND B:CLA514 2.0 0.3 1.0 NA B:CLA514 2.1 0.7 1.0 NB B:CLA514 2.1 0.4 1.0 NC B:CLA514 2.1 1.0 1.0 NE2 B:HIS455 2.7 0.6 1.0 C4D B:CLA514 2.9 0.2 1.0 C4A B:CLA514 3.0 0.5 1.0 C1B B:CLA514 3.0 0.4 1.0 C1D B:CLA514 3.1 0.1 1.0 C4B B:CLA514 3.1 0.3 1.0 C1A B:CLA514 3.1 0.4 1.0 C1C B:CLA514 3.1 1.0 1.0 C4C B:CLA514 3.1 0.3 1.0 C14 B:CLA522 3.2 0.6 1.0 CHB B:CLA514 3.4 0.7 1.0 CD2 B:HIS455 3.4 0.5 1.0 CHA B:CLA514 3.4 0.4 1.0 CHC B:CLA514 3.5 0.1 1.0 CHD B:CLA514 3.5 0.4 1.0 CE1 B:HIS455 3.8 0.7 1.0 C3D B:CLA514 4.2 0.4 1.0 C2B B:CLA514 4.3 0.3 1.0 C2D B:CLA514 4.3 0.3 1.0 C3B B:CLA514 4.4 0.1 1.0 C3A B:CLA514 4.4 0.8 1.0 C2A B:CLA514 4.4 0.9 1.0 C2C B:CLA514 4.4 1.0 1.0 C3C B:CLA514 4.5 0.3 1.0 C13 B:CLA522 4.5 0.2 1.0 CBB B:CLA523 4.6 0.7 1.0 CG B:HIS455 4.7 0.7 1.0 ND1 B:HIS455 4.8 0.5 1.0 C15 B:CLA522 4.9 0.1 1.0 CBD B:CLA514 5.0 0.2 1.0

Magnesium binding site 8 out of 35 in the Crystal Structure of Monomeric Form of Cyanobacterial 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 Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg515 b:0.2 occ:1.00 MG B:CLA515 0.0 0.2 1.0 ND B:CLA515 2.0 0.8 1.0 NA B:CLA515 2.1 0.6 1.0 NB B:CLA515 2.1 0.8 1.0 NC B:CLA515 2.1 0.1 1.0 NE2 B:HIS100 2.8 0.2 1.0 C4D B:CLA515 3.0 0.5 1.0 C4A B:CLA515 3.1 1.0 1.0 C1B B:CLA515 3.1 0.9 1.0 C1A B:CLA515 3.1 0.8 1.0 C1C B:CLA515 3.1 0.7 1.0 C4B B:CLA515 3.1 0.5 1.0 C1D B:CLA515 3.1 0.2 1.0 C4C B:CLA515 3.2 0.1 1.0 CHB B:CLA515 3.4 0.6 1.0 CHA B:CLA515 3.5 0.2 1.0 CHC B:CLA515 3.5 0.6 1.0 CHD B:CLA515 3.5 0.8 1.0 CD2 B:HIS100 3.6 0.1 1.0 CE1 B:HIS100 3.7 0.5 1.0 C2 B:CLA514 4.2 0.1 1.0 C3D B:CLA515 4.3 0.6 1.0 C2B B:CLA515 4.3 0.6 1.0 C2D B:CLA515 4.4 0.4 1.0 C3A B:CLA515 4.4 0.4 1.0 C2A B:CLA515 4.4 0.8 1.0 C3B B:CLA515 4.4 0.4 1.0 C2C B:CLA515 4.4 0.1 1.0 C3C B:CLA515 4.4 0.4 1.0 O1A B:CLA514 4.6 0.6 1.0 CG B:HIS100 4.7 0.8 1.0 ND1 B:HIS100 4.8 0.1 1.0 C5 B:CLA514 4.8 0.0 1.0 C6 B:CLA514 5.0 0.9 1.0 CBD B:CLA515 5.0 0.1 1.0 C3 B:CLA514 5.0 0.3 1.0

Magnesium binding site 9 out of 35 in the Crystal Structure of Monomeric Form of Cyanobacterial 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 Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg516 b:0.6 occ:1.00 MG B:CLA516 0.0 0.6 1.0 ND B:CLA516 2.0 0.7 1.0 NA B:CLA516 2.1 0.3 1.0 NB B:CLA516 2.1 0.4 1.0 NC B:CLA516 2.2 1.0 1.0 ND1 B:HIS157 2.8 0.9 1.0 C4D B:CLA516 2.9 0.9 1.0 C4A B:CLA516 3.1 0.3 1.0 C1B B:CLA516 3.1 0.4 1.0 C1D B:CLA516 3.1 0.3 1.0 C4B B:CLA516 3.1 0.5 1.0 C1A B:CLA516 3.1 0.4 1.0 C1C B:CLA516 3.2 0.8 1.0 C4C B:CLA516 3.2 0.7 1.0 CE1 B:HIS157 3.2 0.9 1.0 CHB B:CLA516 3.4 0.4 1.0 CHA B:CLA516 3.5 0.8 1.0 CHD B:CLA516 3.5 0.8 1.0 CHC B:CLA516 3.5 0.1 1.0 C8 B:LMT535 4.0 0.5 1.0 CG B:HIS157 4.0 0.5 1.0 C3D B:CLA516 4.2 0.3 1.0 C10 B:LMT535 4.3 0.2 1.0 C2B B:CLA516 4.3 0.7 1.0 C2D B:CLA516 4.3 0.8 1.0 C3A B:CLA516 4.3 0.9 1.0 C2A B:CLA516 4.4 0.5 1.0 C3B B:CLA516 4.4 0.3 1.0 C9 B:LMT535 4.5 0.9 1.0 NE2 B:HIS157 4.5 0.1 1.0 C2C B:CLA516 4.5 0.7 1.0 C3C B:CLA516 4.5 0.7 1.0 CB B:HIS157 4.7 0.6 1.0 CD2 B:HIS157 4.9 0.1 1.0 CBD B:CLA516 5.0 0.5 1.0

Magnesium binding site 10 out of 35 in the Crystal Structure of Monomeric Form of Cyanobacterial 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 Monomeric Form of Cyanobacterial Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg517 b:0.9 occ:1.00 MG B:CLA517 0.0 0.9 1.0 ND B:CLA517 2.0 0.5 1.0 NC B:CLA517 2.1 0.3 1.0 NB B:CLA517 2.1 0.4 1.0 NA B:CLA517 2.2 0.2 1.0 C4D B:CLA517 3.0 0.5 1.0 C1D B:CLA517 3.1 1.0 1.0 C4C B:CLA517 3.1 0.6 1.0 C1C B:CLA517 3.1 0.8 1.0 C1B B:CLA517 3.1 0.0 1.0 C4B B:CLA517 3.1 0.5 1.0 C4A B:CLA517 3.1 1.0 1.0 C4B B:DGD533 3.2 0.4 1.0 C1A B:CLA517 3.3 0.8 1.0 CE B:MET37 3.4 0.8 1.0 CHD B:CLA517 3.4 0.5 1.0 CHB B:CLA517 3.4 0.8 1.0 CHC B:CLA517 3.5 0.1 1.0 CHA B:CLA517 3.6 0.5 1.0 C6B B:DGD533 4.0 0.4 1.0 C5B B:DGD533 4.1 0.0 1.0 C3D B:CLA517 4.3 0.8 1.0 C2B B:CLA517 4.3 0.2 1.0 C2D B:CLA517 4.3 0.2 1.0 C3C B:CLA517 4.4 0.6 1.0 C2C B:CLA517 4.4 0.9 1.0 C3B B:CLA517 4.4 0.7 1.0 C3B B:DGD533 4.4 0.8 1.0 C3A B:CLA517 4.5 0.5 1.0 C2A B:CLA517 4.5 0.8 1.0 C2B B:DGD533 4.7 0.8 1.0 SD B:MET37 4.9 0.1 1.0

M.Broser, A.Gabdulkhakov, J.Kern, A.Guskov, F.Muh, W.Saenger, A.Zouni. Crystal Structure of Monomeric Photosystem II From Thermosynechococcus Elongatus at 3.6-A Resolution J.Biol.Chem. V. 285 26255 2010.
ISSN: ISSN 0021-9258
PubMed: 20558739
DOI: 10.1074/JBC.M110.127589