Magnesium in PDB 3a0h: Crystal Structure of I-Substituted Photosystem II Complex

The structure of Crystal Structure of I-Substituted Photosystem II Complex, PDB code: 3a0h was solved by K.Kawakami, Y.Umena, N.Kamiya, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 4.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	128.499, 224.702, 304.919, 90.00, 90.00, 90.00
R / Rfree (%)	29 / 32.6

The structure of Crystal Structure of I-Substituted Photosystem II Complex also contains other interesting chemical elements:

Manganese	(Mn)	8 atoms
Iodine	(I)	10 atoms
Iron	(Fe)	6 atoms
Calcium	(Ca)	2 atoms

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>>> 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 I-Substituted Photosystem II Complex (pdb code 3a0h). 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 I-Substituted Photosystem II Complex, PDB code: 3a0h:
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 I-Substituted Photosystem II Complex


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:0.6 occ:1.00 MG A:CLA1003 0.0 0.6 1.0 NA A:CLA1003 2.0 0.7 1.0 ND A:CLA1003 2.0 0.3 1.0 NB A:CLA1003 2.1 0.7 1.0 NC A:CLA1003 2.1 1.0 1.0 C4D A:CLA1003 3.0 0.6 1.0 C1A A:CLA1003 3.0 0.2 1.0 C4A A:CLA1003 3.0 0.8 1.0 NE2 A:HIS198 3.1 0.9 1.0 C1B A:CLA1003 3.1 0.9 1.0 C4B A:CLA1003 3.1 0.8 1.0 C1C A:CLA1003 3.1 0.2 1.0 C4C A:CLA1003 3.1 0.7 1.0 C1D A:CLA1003 3.2 0.6 1.0 CHB A:CLA1003 3.4 0.2 1.0 CHA A:CLA1003 3.4 0.1 1.0 CHC A:CLA1003 3.4 0.6 1.0 CBC D:CLA1005 3.5 1.0 1.0 CHD A:CLA1003 3.6 0.6 1.0 CD2 A:HIS198 3.7 0.8 1.0 CBB D:CLA1004 3.8 0.5 1.0 CE1 A:HIS198 4.2 0.4 1.0 C3D A:CLA1003 4.2 0.0 1.0 CAB D:CLA1004 4.3 0.3 1.0 C2A A:CLA1003 4.3 0.9 1.0 C3A A:CLA1003 4.3 0.5 1.0 CAC D:CLA1005 4.3 0.8 1.0 C3B A:CLA1003 4.4 0.5 1.0 C2B A:CLA1003 4.4 0.1 1.0 C2C A:CLA1003 4.4 0.1 1.0 C2D A:CLA1003 4.4 0.0 1.0 C3C A:CLA1003 4.4 0.6 1.0 CE A:MET183 4.8 0.5 1.0 CBD A:CLA1003 4.9 0.9 1.0

Magnesium binding site 2 out of 70 in the Crystal Structure of I-Substituted Photosystem II Complex


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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1005 b:0.4 occ:1.00 MG D:CLA1005 0.0 0.4 1.0 NA D:CLA1005 2.0 0.1 1.0 ND D:CLA1005 2.0 0.7 1.0 NB D:CLA1005 2.1 0.5 1.0 NC D:CLA1005 2.1 0.6 1.0 C4D D:CLA1005 3.0 0.7 1.0 C1A D:CLA1005 3.0 0.6 1.0 C4A D:CLA1005 3.0 0.1 1.0 C1B D:CLA1005 3.1 0.3 1.0 C4B D:CLA1005 3.1 0.2 1.0 C1C D:CLA1005 3.1 0.7 1.0 C4C D:CLA1005 3.1 0.6 1.0 C1D D:CLA1005 3.2 0.7 1.0 CHB D:CLA1005 3.4 0.1 1.0 CHA D:CLA1005 3.4 0.5 1.0 CHC D:CLA1005 3.4 0.2 1.0 CHD D:CLA1005 3.6 0.1 1.0 O1A D:CLA1005 3.6 0.6 1.0 C3D D:CLA1005 4.2 0.0 1.0 C2A D:CLA1005 4.3 0.8 1.0 C3A D:CLA1005 4.3 0.1 1.0 C3B D:CLA1005 4.4 0.1 1.0 C2B D:CLA1005 4.4 0.2 1.0 C2C D:CLA1005 4.4 0.4 1.0 C2D D:CLA1005 4.4 0.4 1.0 C3C D:CLA1005 4.4 0.8 1.0 CGA D:CLA1005 4.7 0.1 1.0 CG2 A:THR179 4.8 0.5 1.0 CBD D:CLA1005 4.9 0.6 1.0 OG1 A:THR179 5.0 0.6 1.0

Magnesium binding site 3 out of 70 in the Crystal Structure of I-Substituted Photosystem II Complex


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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1006 b:0.1 occ:1.00 MG A:CLA1006 0.0 0.1 1.0 NA A:CLA1006 2.0 0.3 1.0 ND A:CLA1006 2.0 0.2 1.0 NB A:CLA1006 2.1 0.8 1.0 NC A:CLA1006 2.1 0.8 1.0 C4D A:CLA1006 3.0 0.8 1.0 C1A A:CLA1006 3.0 0.7 1.0 C4A A:CLA1006 3.0 0.7 1.0 C1B A:CLA1006 3.1 0.4 1.0 C4B A:CLA1006 3.1 1.0 1.0 C1C A:CLA1006 3.1 0.2 1.0 C4C A:CLA1006 3.1 0.6 1.0 C1D A:CLA1006 3.2 0.7 1.0 CHB A:CLA1006 3.4 0.9 1.0 CHA A:CLA1006 3.4 0.9 1.0 CHC A:CLA1006 3.4 0.6 1.0 CHD A:CLA1006 3.6 0.1 1.0 C3D A:CLA1006 4.2 0.4 1.0 C2A A:CLA1006 4.3 0.6 1.0 C3A A:CLA1006 4.3 0.7 1.0 C3B A:CLA1006 4.4 0.3 1.0 C2B A:CLA1006 4.4 0.1 1.0 C2C A:CLA1006 4.4 0.7 1.0 C2D A:CLA1006 4.4 0.7 1.0 C3C A:CLA1006 4.4 0.5 1.0 CBD A:CLA1006 4.9 0.4 1.0

Magnesium binding site 4 out of 70 in the Crystal Structure of I-Substituted Photosystem II Complex


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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1007 b:0.4 occ:1.00 MG A:CLA1007 0.0 0.4 1.0 NA A:CLA1007 2.0 0.5 1.0 ND A:CLA1007 2.0 0.1 1.0 NB A:CLA1007 2.1 0.9 1.0 NC A:CLA1007 2.1 0.4 1.0 C4D A:CLA1007 3.0 0.8 1.0 C1A A:CLA1007 3.0 0.5 1.0 C4A A:CLA1007 3.0 0.9 1.0 NE2 A:HIS118 3.0 0.0 1.0 C1B A:CLA1007 3.1 0.2 1.0 C4B A:CLA1007 3.1 1.0 1.0 C1C A:CLA1007 3.1 0.1 1.0 C4C A:CLA1007 3.1 0.9 1.0 C1D A:CLA1007 3.2 1.0 1.0 CE1 A:HIS118 3.2 0.4 1.0 CHB A:CLA1007 3.4 0.0 1.0 CHA A:CLA1007 3.4 0.4 1.0 CHC A:CLA1007 3.4 0.3 1.0 CHD A:CLA1007 3.6 0.3 1.0 C3D A:CLA1007 4.2 0.2 1.0 C2A A:CLA1007 4.3 0.3 1.0 C3A A:CLA1007 4.3 0.0 1.0 CD2 A:HIS118 4.3 0.3 1.0 C3B A:CLA1007 4.4 0.6 1.0 C2B A:CLA1007 4.4 0.6 1.0 C2C A:CLA1007 4.4 0.3 1.0 C2D A:CLA1007 4.4 0.3 1.0 C3C A:CLA1007 4.4 0.4 1.0 ND1 A:HIS118 4.5 0.2 1.0 CG2 I:VAL12 4.6 0.6 1.0 CBA A:CLA1007 4.8 0.1 1.0 CBD A:CLA1007 4.9 0.4 1.0

Magnesium binding site 5 out of 70 in the Crystal Structure of I-Substituted Photosystem II Complex


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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1009 b:0.9 occ:1.00 MG B:CLA1009 0.0 0.9 1.0 NA B:CLA1009 2.0 0.0 1.0 ND B:CLA1009 2.0 0.7 1.0 NB B:CLA1009 2.0 0.6 1.0 NC B:CLA1009 2.1 0.9 1.0 O1A B:CLA1009 2.7 0.9 1.0 C4D B:CLA1009 2.9 0.8 1.0 C1A B:CLA1009 3.0 0.7 1.0 C4A B:CLA1009 3.0 0.4 1.0 C1B B:CLA1009 3.1 0.8 1.0 C4B B:CLA1009 3.1 0.9 1.0 C1C B:CLA1009 3.1 0.8 1.0 C4C B:CLA1009 3.1 0.4 1.0 C1D B:CLA1009 3.2 0.6 1.0 CHB B:CLA1009 3.4 0.2 1.0 CHA B:CLA1009 3.4 0.8 1.0 CHC B:CLA1009 3.4 0.1 1.0 CHD B:CLA1009 3.6 0.7 1.0 CGA B:CLA1009 3.6 0.2 1.0 C3D B:CLA1009 4.2 0.3 1.0 O B:TRP185 4.3 0.1 1.0 C2A B:CLA1009 4.3 0.8 1.0 C3A B:CLA1009 4.3 0.7 1.0 C3B B:CLA1009 4.4 0.5 1.0 O2A B:CLA1009 4.4 0.3 1.0 C2B B:CLA1009 4.4 0.2 1.0 C2D B:CLA1009 4.4 0.3 1.0 C2C B:CLA1009 4.4 0.1 1.0 C3C B:CLA1009 4.4 0.9 1.0 CBA B:CLA1009 4.7 0.9 1.0 CBD B:CLA1009 4.9 0.6 1.0

Magnesium binding site 6 out of 70 in the Crystal Structure of I-Substituted Photosystem II Complex


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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1010 b:0.4 occ:1.00 MG B:CLA1010 0.0 0.4 1.0 NA B:CLA1010 2.0 0.2 1.0 ND B:CLA1010 2.0 0.3 1.0 NB B:CLA1010 2.1 0.8 1.0 NC B:CLA1010 2.1 0.9 1.0 ND1 B:HIS201 2.5 0.8 1.0 C4D B:CLA1010 2.9 0.1 1.0 C1A B:CLA1010 3.0 0.3 1.0 C4A B:CLA1010 3.0 0.3 1.0 CE1 B:HIS201 3.0 0.7 1.0 C1B B:CLA1010 3.1 0.4 1.0 C4B B:CLA1010 3.1 0.4 1.0 C1C B:CLA1010 3.1 0.8 1.0 C4C B:CLA1010 3.1 0.5 1.0 C1D B:CLA1010 3.2 0.8 1.0 CZ H:PHE41 3.3 0.4 1.0 CHB B:CLA1010 3.4 0.9 1.0 CHA B:CLA1010 3.4 0.1 1.0 CHC B:CLA1010 3.4 0.8 1.0 CHD B:CLA1010 3.6 0.6 1.0 CG B:HIS201 3.7 0.8 1.0 CE2 H:PHE41 3.8 0.9 1.0 C3D B:CLA1010 4.2 0.7 1.0 NE2 B:HIS201 4.3 0.2 1.0 CB B:HIS201 4.3 0.2 1.0 C2A B:CLA1010 4.3 0.0 1.0 C3A B:CLA1010 4.3 0.7 1.0 C3B B:CLA1010 4.4 0.7 1.0 CE1 H:PHE41 4.4 0.9 1.0 C2B B:CLA1010 4.4 0.2 1.0 C2C B:CLA1010 4.4 0.1 1.0 C2D B:CLA1010 4.4 0.9 1.0 C3C B:CLA1010 4.4 0.3 1.0 CD2 B:HIS201 4.6 0.7 1.0 CD1 H:ILE45 4.7 0.5 1.0 CBD B:CLA1010 4.9 0.9 1.0

Magnesium binding site 7 out of 70 in the Crystal Structure of I-Substituted Photosystem II Complex


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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1011 b:0.1 occ:1.00 MG B:CLA1011 0.0 0.1 1.0 NA B:CLA1011 2.0 0.4 1.0 ND B:CLA1011 2.0 1.0 1.0 NB B:CLA1011 2.0 0.6 1.0 NC B:CLA1011 2.1 1.0 1.0 NE2 B:HIS202 2.6 0.6 1.0 C4D B:CLA1011 3.0 0.2 1.0 C1A B:CLA1011 3.0 0.5 1.0 C4A B:CLA1011 3.0 0.1 1.0 CE1 B:HIS202 3.1 0.7 1.0 C1B B:CLA1011 3.1 0.5 1.0 C4B B:CLA1011 3.1 0.6 1.0 C1C B:CLA1011 3.1 0.5 1.0 C4C B:CLA1011 3.1 0.8 1.0 C1D B:CLA1011 3.2 0.8 1.0 CHB B:CLA1011 3.4 0.7 1.0 CHA B:CLA1011 3.4 0.5 1.0 CHC B:CLA1011 3.4 0.0 1.0 CHD B:CLA1011 3.6 0.2 1.0 C5 B:CLA1013 3.7 0.0 1.0 CD2 B:HIS202 3.8 0.5 1.0 C1 B:CLA1011 4.1 0.3 1.0 C3D B:CLA1011 4.2 0.2 1.0 ND1 B:HIS202 4.3 0.3 1.0 C9 B:CLA1013 4.3 0.7 1.0 C2A B:CLA1011 4.3 0.5 1.0 C3A B:CLA1011 4.3 0.9 1.0 C3 B:CLA1013 4.3 0.7 1.0 C3B B:CLA1011 4.4 0.8 1.0 C2B B:CLA1011 4.4 0.2 1.0 C2D B:CLA1011 4.4 0.2 1.0 C2C B:CLA1011 4.4 0.3 1.0 C3C B:CLA1011 4.4 0.1 1.0 C6 B:CLA1013 4.5 0.7 1.0 C2 B:CLA1013 4.6 0.8 1.0 C8 B:CLA1013 4.6 0.5 1.0 CG B:HIS202 4.7 0.7 1.0 CBD B:CLA1011 4.9 0.8 1.0 O2A B:CLA1011 5.0 0.3 1.0

Magnesium binding site 8 out of 70 in the Crystal Structure of I-Substituted Photosystem II Complex


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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1012 b:0.1 occ:1.00 MG B:CLA1012 0.0 0.1 1.0 NA B:CLA1012 2.0 0.0 1.0 ND B:CLA1012 2.0 0.9 1.0 NB B:CLA1012 2.1 0.2 1.0 NC B:CLA1012 2.1 0.9 1.0 C4D B:CLA1012 3.0 1.0 1.0 C1A B:CLA1012 3.0 0.5 1.0 C4A B:CLA1012 3.0 0.1 1.0 NE2 B:HIS455 3.0 0.3 1.0 C1B B:CLA1012 3.1 0.5 1.0 C4B B:CLA1012 3.1 0.4 1.0 C1C B:CLA1012 3.1 0.8 1.0 C4C B:CLA1012 3.1 0.8 1.0 C1D B:CLA1012 3.2 0.4 1.0 CHB B:CLA1012 3.4 0.6 1.0 CHA B:CLA1012 3.4 0.1 1.0 CHC B:CLA1012 3.4 0.8 1.0 CD2 B:HIS455 3.5 0.1 1.0 CHD B:CLA1012 3.6 0.8 1.0 C3D B:CLA1012 4.2 0.1 1.0 CE1 B:HIS455 4.3 0.0 1.0 C2A B:CLA1012 4.3 0.3 1.0 C3A B:CLA1012 4.3 0.3 1.0 C3B B:CLA1012 4.4 0.8 1.0 C2B B:CLA1012 4.4 0.1 1.0 C2C B:CLA1012 4.4 0.0 1.0 C2D B:CLA1012 4.4 0.1 1.0 C3C B:CLA1012 4.4 0.9 1.0 C15 B:CLA1020 4.5 0.8 1.0 CG B:HIS455 4.8 0.2 1.0 C20 B:CLA1020 4.8 0.8 1.0 CBD B:CLA1012 4.9 0.3 1.0 C14 B:CLA1020 5.0 0.1 1.0

Magnesium binding site 9 out of 70 in the Crystal Structure of I-Substituted Photosystem II Complex


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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1013 b:0.6 occ:1.00 MG B:CLA1013 0.0 0.6 1.0 NA B:CLA1013 2.0 0.9 1.0 ND B:CLA1013 2.0 0.4 1.0 NB B:CLA1013 2.1 0.2 1.0 NC B:CLA1013 2.1 0.6 1.0 NE2 B:HIS100 2.8 0.7 1.0 C4D B:CLA1013 3.0 0.5 1.0 C1A B:CLA1013 3.0 0.3 1.0 C4A B:CLA1013 3.0 0.5 1.0 C1B B:CLA1013 3.1 0.8 1.0 C4B B:CLA1013 3.1 0.4 1.0 C1C B:CLA1013 3.1 0.6 1.0 C4C B:CLA1013 3.1 0.7 1.0 C1D B:CLA1013 3.2 0.9 1.0 CHB B:CLA1013 3.4 0.0 1.0 CD2 B:HIS100 3.4 0.5 1.0 CHA B:CLA1013 3.4 0.4 1.0 CHC B:CLA1013 3.4 0.6 1.0 CHD B:CLA1013 3.6 0.1 1.0 CE1 B:HIS100 3.9 1.0 1.0 C3D B:CLA1013 4.2 0.6 1.0 C2 B:CLA1012 4.2 1.0 1.0 C2A B:CLA1013 4.3 0.2 1.0 C3A B:CLA1013 4.3 0.2 1.0 C3B B:CLA1013 4.4 0.3 1.0 C2B B:CLA1013 4.4 0.2 1.0 C2C B:CLA1013 4.4 0.5 1.0 C2D B:CLA1013 4.4 0.2 1.0 C3C B:CLA1013 4.4 0.9 1.0 CG B:HIS100 4.7 0.5 1.0 O2A B:CLA1012 4.7 0.6 1.0 CBA B:CLA1013 4.8 0.5 1.0 C5 B:CLA1012 4.9 0.0 1.0 ND1 B:HIS100 4.9 0.2 1.0 CBD B:CLA1013 4.9 0.9 1.0

Magnesium binding site 10 out of 70 in the Crystal Structure of I-Substituted Photosystem II Complex


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 I-Substituted Photosystem II Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1014 b:0.4 occ:1.00 MG B:CLA1014 0.0 0.4 1.0 NA B:CLA1014 2.0 1.0 1.0 ND B:CLA1014 2.0 1.0 1.0 NB B:CLA1014 2.1 0.2 1.0 NC B:CLA1014 2.1 0.8 1.0 C4D B:CLA1014 3.0 0.9 1.0 C1A B:CLA1014 3.0 0.2 1.0 C4A B:CLA1014 3.0 0.6 1.0 C1B B:CLA1014 3.1 1.0 1.0 C4B B:CLA1014 3.1 0.1 1.0 C1C B:CLA1014 3.1 0.0 1.0 C4C B:CLA1014 3.1 0.9 1.0 C1D B:CLA1014 3.2 0.7 1.0 CE1 B:HIS157 3.3 0.8 1.0 ND1 B:HIS157 3.3 0.5 1.0 CHB B:CLA1014 3.4 0.7 1.0 CHA B:CLA1014 3.4 0.7 1.0 CHC B:CLA1014 3.4 0.7 1.0 CHD B:CLA1014 3.6 0.9 1.0 O1A B:CLA1014 3.8 0.0 1.0 C3D B:CLA1014 4.2 0.8 1.0 C2A B:CLA1014 4.3 1.0 1.0 C3A B:CLA1014 4.3 0.9 1.0 C3B B:CLA1014 4.4 0.7 1.0 C2B B:CLA1014 4.4 0.6 1.0 C2C B:CLA1014 4.4 0.1 1.0 C2D B:CLA1014 4.4 0.6 1.0 C3C B:CLA1014 4.4 0.7 1.0 NE2 B:HIS157 4.6 0.9 1.0 CG B:HIS157 4.7 0.0 1.0 CGA B:CLA1014 4.7 0.7 1.0 CBA B:CLA1014 4.8 0.0 1.0 CMB B:CLA1013 4.8 0.1 1.0 CBD B:CLA1014 4.9 0.3 1.0

K.Kawakami, Y.Umena, N.Kamiya, J.-R.Shen. Location of Chloride and Its Possible Functions in Oxygen-Evolving Photosystem II Revealed By X-Ray Crystallography Proc.Natl.Acad.Sci.Usa V. 106 8567 2009.
ISSN: ISSN 0027-8424
PubMed: 19433803
DOI: 10.1073/PNAS.0812797106