Magnesium in PDB 4il6: Structure of Sr-Substituted Photosystem II

All present enzymatic activity of Structure of Sr-Substituted Photosystem II:
1.10.3.9;

The structure of Structure of Sr-Substituted Photosystem II, PDB code: 4il6 was solved by F.H.M.Koua, Y.Umena, K.Kawakami, N.Kamiya, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	121.860, 228.790, 285.760, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.5

The structure of Structure of Sr-Substituted Photosystem II also contains other interesting chemical elements:

Strontium	(Sr)	2 atoms
Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Chlorine	(Cl)	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; Page 8, Binding sites: 71 - 74;

Binding sites:

The binding sites of Magnesium atom in the Structure of Sr-Substituted Photosystem II (pdb code 4il6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 74 binding sites of Magnesium where determined in the Structure of Sr-Substituted Photosystem II, PDB code: 4il6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 74 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Sr-Substituted Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:20.0 occ:1.00 MG A:CLA1005 0.0 20.0 1.0 ND A:CLA1005 2.0 19.8 1.0 NB A:CLA1005 2.1 19.6 1.0 NA A:CLA1005 2.1 19.6 1.0 NE2 A:HIS198 2.3 20.7 1.0 NC A:CLA1005 2.3 19.1 1.0 C4D A:CLA1005 2.9 20.0 1.0 C1A A:CLA1005 3.0 20.2 1.0 C1B A:CLA1005 3.1 19.1 1.0 C4A A:CLA1005 3.1 19.8 1.0 C4B A:CLA1005 3.1 19.0 1.0 C1D A:CLA1005 3.2 19.4 1.0 C1C A:CLA1005 3.2 19.2 1.0 CE1 A:HIS198 3.2 20.6 1.0 CD2 A:HIS198 3.2 20.6 1.0 C4C A:CLA1005 3.3 18.8 1.0 CHA A:CLA1005 3.4 19.8 1.0 CHB A:CLA1005 3.4 19.3 1.0 CHC A:CLA1005 3.5 19.1 1.0 CHD A:CLA1005 3.7 19.0 1.0 CE A:MET183 4.1 19.7 1.0 C3D A:CLA1005 4.1 19.7 1.0 CAB D:CLA402 4.4 19.3 1.0 ND1 A:HIS198 4.4 20.7 1.0 C3B A:CLA1005 4.4 18.7 1.0 C2A A:CLA1005 4.4 20.1 1.0 C2D A:CLA1005 4.4 20.1 1.0 C3A A:CLA1005 4.4 19.7 1.0 C2B A:CLA1005 4.4 19.0 1.0 CG A:HIS198 4.4 21.4 1.0 C2C A:CLA1005 4.6 18.2 1.0 C3C A:CLA1005 4.6 18.3 1.0 CBD A:CLA1005 4.8 20.1 1.0

Magnesium binding site 2 out of 74 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Sr-Substituted Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1006 b:23.2 occ:1.00 MG A:CLA1006 0.0 23.2 1.0 O A:HOH1128 2.0 24.4 1.0 NB A:CLA1006 2.0 23.2 1.0 ND A:CLA1006 2.1 22.9 1.0 NC A:CLA1006 2.1 22.7 1.0 NA A:CLA1006 2.2 23.2 1.0 C4D A:CLA1006 2.9 23.0 1.0 C4B A:CLA1006 3.0 23.4 1.0 C1B A:CLA1006 3.1 22.9 1.0 C1C A:CLA1006 3.1 22.8 1.0 C1A A:CLA1006 3.1 23.4 1.0 C4A A:CLA1006 3.2 23.6 1.0 C1D A:CLA1006 3.2 22.0 1.0 C4C A:CLA1006 3.2 22.3 1.0 CHC A:CLA1006 3.4 22.8 1.0 CHA A:CLA1006 3.4 23.2 1.0 CHB A:CLA1006 3.5 23.6 1.0 CHD A:CLA1006 3.7 22.2 1.0 CBB D:PHO404 3.9 22.4 1.0 O A:HOH1113 4.1 23.0 1.0 C3D A:CLA1006 4.2 22.9 1.0 C3B A:CLA1006 4.3 24.0 1.0 C2B A:CLA1006 4.4 24.0 1.0 C2D A:CLA1006 4.4 22.7 1.0 C2C A:CLA1006 4.4 22.1 1.0 C2A A:CLA1006 4.5 23.8 1.0 C3C A:CLA1006 4.5 22.6 1.0 C3A A:CLA1006 4.5 23.4 1.0 CG2 D:ILE178 4.5 21.0 1.0 C20 D:PHO404 4.9 23.9 1.0 CE1 A:PHE206 4.9 23.9 1.0 CBD A:CLA1006 4.9 23.6 1.0 CBA A:CLA1006 4.9 25.8 1.0 CG1 D:ILE178 5.0 21.6 1.0

Magnesium binding site 3 out of 74 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Sr-Substituted Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1008 b:27.6 occ:1.00 MG A:CLA1008 0.0 27.6 1.0 ND A:CLA1008 2.0 27.0 1.0 NB A:CLA1008 2.0 26.5 1.0 NC A:CLA1008 2.2 27.1 1.0 NE2 A:HIS118 2.2 24.9 1.0 NA A:CLA1008 2.3 27.8 1.0 C4D A:CLA1008 2.9 26.8 1.0 C4B A:CLA1008 3.0 26.2 1.0 C1B A:CLA1008 3.1 26.4 1.0 C1C A:CLA1008 3.1 27.4 1.0 C1D A:CLA1008 3.1 26.8 1.0 CE1 A:HIS118 3.2 25.7 1.0 C4A A:CLA1008 3.2 27.8 1.0 C1A A:CLA1008 3.2 27.6 1.0 CD2 A:HIS118 3.2 25.6 1.0 C4C A:CLA1008 3.3 26.8 1.0 CHC A:CLA1008 3.4 26.8 1.0 CHB A:CLA1008 3.5 26.8 1.0 CHA A:CLA1008 3.5 26.6 1.0 CHD A:CLA1008 3.6 26.6 1.0 C3D A:CLA1008 4.2 26.6 1.0 ND1 A:HIS118 4.3 25.9 1.0 C3B A:CLA1008 4.3 26.2 1.0 CG1 I:VAL8 4.3 30.3 1.0 C2D A:CLA1008 4.4 26.4 1.0 C2B A:CLA1008 4.4 25.6 1.0 CG A:HIS118 4.4 25.8 1.0 CG2 I:VAL12 4.5 35.3 1.0 C3A A:CLA1008 4.5 28.6 1.0 C2C A:CLA1008 4.5 27.3 1.0 C2A A:CLA1008 4.5 29.0 1.0 C3C A:CLA1008 4.5 26.9 1.0 CBD A:CLA1008 5.0 26.7 1.0

Magnesium binding site 4 out of 74 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Sr-Substituted Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:38.6 occ:1.00 MG B:CLA601 0.0 38.6 1.0 ND B:CLA601 2.0 40.3 1.0 O B:HOH750 2.0 37.3 1.0 NB B:CLA601 2.1 38.7 1.0 NA B:CLA601 2.2 40.0 1.0 NC B:CLA601 2.3 37.6 1.0 C4D B:CLA601 2.9 41.8 1.0 C4B B:CLA601 3.1 38.2 1.0 C1B B:CLA601 3.1 38.2 1.0 C1A B:CLA601 3.1 42.5 1.0 C1D B:CLA601 3.2 39.7 1.0 C1C B:CLA601 3.2 37.3 1.0 C4A B:CLA601 3.2 41.2 1.0 C4C B:CLA601 3.3 37.4 1.0 CHA B:CLA601 3.4 42.4 1.0 CHC B:CLA601 3.4 37.5 1.0 CHB B:CLA601 3.5 39.7 1.0 CHD B:CLA601 3.7 38.7 1.0 C10 B:CLA601 3.9 61.9 1.0 C3D B:CLA601 4.1 42.0 1.0 O B:TRP185 4.2 34.8 1.0 CE2 B:PHE190 4.2 33.2 1.0 C12 B:CLA601 4.3 60.6 1.0 C3B B:CLA601 4.4 37.4 1.0 C2D B:CLA601 4.4 41.0 1.0 C2B B:CLA601 4.4 37.9 1.0 CBB B:CLA602 4.5 31.1 1.0 CZ B:PHE190 4.5 33.3 1.0 C2A B:CLA601 4.5 45.2 1.0 C11 B:CLA601 4.5 60.4 1.0 C3A B:CLA601 4.5 43.2 1.0 C2C B:CLA601 4.5 36.4 1.0 C3C B:CLA601 4.6 36.9 1.0 O B:HOH747 4.8 34.6 1.0 CBD B:CLA601 4.9 42.7 1.0 C8 B:CLA601 4.9 63.9 1.0 C7 B:CLA601 4.9 65.2 1.0 CBA B:CLA601 5.0 54.1 1.0

Magnesium binding site 5 out of 74 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Sr-Substituted Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:27.7 occ:1.00 MG B:CLA602 0.0 27.7 1.0 ND B:CLA602 2.1 27.1 1.0 NB B:CLA602 2.1 28.4 1.0 NA B:CLA602 2.2 26.8 1.0 ND1 B:HIS201 2.2 24.8 1.0 NC B:CLA602 2.3 27.7 1.0 C4D B:CLA602 3.0 27.2 1.0 CE1 B:HIS201 3.0 24.8 1.0 C4B B:CLA602 3.1 28.7 1.0 C1B B:CLA602 3.1 28.4 1.0 C4A B:CLA602 3.1 27.7 1.0 C1A B:CLA602 3.1 26.9 1.0 C1C B:CLA602 3.2 27.8 1.0 C1D B:CLA602 3.2 27.1 1.0 C4C B:CLA602 3.3 27.7 1.0 CG B:HIS201 3.3 25.1 1.0 CHC B:CLA602 3.4 28.1 1.0 CHB B:CLA602 3.4 27.7 1.0 CHA B:CLA602 3.4 26.7 1.0 CHD B:CLA602 3.7 27.5 1.0 CB B:HIS201 3.8 26.4 1.0 CZ H:PHE41 3.8 28.8 1.0 C3D B:CLA602 4.2 27.4 1.0 NE2 B:HIS201 4.3 25.3 1.0 CE2 H:PHE41 4.3 28.6 1.0 C3B B:CLA602 4.4 29.1 1.0 CA B:HIS201 4.4 27.1 1.0 CD2 B:HIS201 4.4 25.1 1.0 C2B B:CLA602 4.4 28.9 1.0 C3A B:CLA602 4.4 26.8 1.0 C2A B:CLA602 4.5 26.5 1.0 C2D B:CLA602 4.5 27.3 1.0 C2C B:CLA602 4.6 28.3 1.0 C3C B:CLA602 4.6 27.4 1.0 CBD B:CLA602 4.9 27.7 1.0 CE1 H:PHE41 4.9 29.0 1.0

Magnesium binding site 6 out of 74 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Sr-Substituted Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:26.8 occ:1.00 MG B:CLA603 0.0 26.8 1.0 NB B:CLA603 1.9 26.0 1.0 ND B:CLA603 2.1 27.1 1.0 NC B:CLA603 2.2 27.2 1.0 NA B:CLA603 2.2 26.3 1.0 NE2 B:HIS202 2.3 28.1 1.0 C4B B:CLA603 2.9 26.1 1.0 C1B B:CLA603 2.9 25.9 1.0 C4D B:CLA603 3.0 26.3 1.0 CD2 B:HIS202 3.1 28.3 1.0 C4A B:CLA603 3.1 26.2 1.0 C1C B:CLA603 3.1 27.3 1.0 C1A B:CLA603 3.2 26.1 1.0 C1D B:CLA603 3.3 26.8 1.0 C4C B:CLA603 3.3 27.2 1.0 CHC B:CLA603 3.3 26.5 1.0 CHB B:CLA603 3.3 25.9 1.0 CE1 B:HIS202 3.4 29.3 1.0 CHA B:CLA603 3.5 26.0 1.0 CHD B:CLA603 3.7 26.9 1.0 C3B B:CLA603 4.2 25.7 1.0 C2B B:CLA603 4.3 25.4 1.0 C3D B:CLA603 4.3 26.6 1.0 CG B:HIS202 4.3 28.6 1.0 ND1 B:HIS202 4.4 28.8 1.0 C3A B:CLA603 4.5 26.4 1.0 C2C B:CLA603 4.5 27.3 1.0 C2A B:CLA603 4.5 25.9 1.0 C5 B:CLA605 4.5 31.0 1.0 C2D B:CLA603 4.5 26.4 1.0 C3C B:CLA603 4.6 27.4 1.0 C4 B:CLA605 4.6 30.9 1.0 NE2 B:HIS201 4.6 25.3 1.0 CD2 B:HIS201 4.7 25.1 1.0 C7 B:CLA605 4.7 31.9 1.0 C6 B:CLA605 4.8 31.4 1.0 C3 B:CLA605 4.9 31.0 1.0

Magnesium binding site 7 out of 74 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Sr-Substituted Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:23.0 occ:1.00 MG B:CLA604 0.0 23.0 1.0 NB B:CLA604 2.0 23.1 1.0 ND B:CLA604 2.1 23.2 1.0 NC B:CLA604 2.2 22.7 1.0 NE2 B:HIS455 2.3 21.2 1.0 NA B:CLA604 2.3 23.6 1.0 C4B B:CLA604 3.0 23.1 1.0 C4D B:CLA604 3.0 23.5 1.0 CD2 B:HIS455 3.0 21.5 1.0 C1B B:CLA604 3.1 23.1 1.0 C1C B:CLA604 3.1 22.6 1.0 C1D B:CLA604 3.2 22.6 1.0 C4A B:CLA604 3.2 23.6 1.0 C4C B:CLA604 3.2 22.7 1.0 C1A B:CLA604 3.3 24.2 1.0 CHC B:CLA604 3.3 22.6 1.0 CE1 B:HIS455 3.4 21.2 1.0 CHB B:CLA604 3.4 23.1 1.0 CHA B:CLA604 3.6 23.9 1.0 CHD B:CLA604 3.6 22.8 1.0 C14 B:CLA612 4.0 28.8 1.0 C3D B:CLA604 4.3 23.3 1.0 CG B:HIS455 4.3 21.5 1.0 C3B B:CLA604 4.3 23.3 1.0 C2B B:CLA604 4.4 23.2 1.0 ND1 B:HIS455 4.4 21.2 1.0 C2C B:CLA604 4.4 22.6 1.0 C2D B:CLA604 4.4 23.3 1.0 C3C B:CLA604 4.5 22.6 1.0 C3A B:CLA604 4.6 23.9 1.0 C2A B:CLA604 4.6 24.3 1.0 C13 B:CLA612 4.8 29.6 1.0 C15 B:CLA612 5.0 29.8 1.0

Magnesium binding site 8 out of 74 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Sr-Substituted Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:26.1 occ:1.00 MG B:CLA605 0.0 26.1 1.0 NB B:CLA605 2.0 26.4 1.0 ND B:CLA605 2.1 26.0 1.0 NC B:CLA605 2.2 26.1 1.0 NA B:CLA605 2.3 25.9 1.0 NE2 B:HIS100 2.3 24.5 1.0 C4B B:CLA605 3.0 26.5 1.0 C1B B:CLA605 3.0 25.6 1.0 C4D B:CLA605 3.0 25.1 1.0 C1C B:CLA605 3.1 26.1 1.0 C4A B:CLA605 3.2 25.9 1.0 CD2 B:HIS100 3.2 24.3 1.0 C1A B:CLA605 3.2 25.4 1.0 C1D B:CLA605 3.2 25.8 1.0 C4C B:CLA605 3.3 26.3 1.0 CE1 B:HIS100 3.3 23.8 1.0 CHC B:CLA605 3.4 26.0 1.0 CHB B:CLA605 3.4 25.5 1.0 CHA B:CLA605 3.5 25.1 1.0 CHD B:CLA605 3.7 25.8 1.0 C1 B:CLA604 4.0 35.4 1.0 C2 B:CLA604 4.2 39.0 1.0 C3D B:CLA605 4.3 25.9 1.0 C3B B:CLA605 4.3 26.6 1.0 C2B B:CLA605 4.3 26.4 1.0 CG B:HIS100 4.4 24.4 1.0 ND1 B:HIS100 4.4 23.8 1.0 C2C B:CLA605 4.5 26.0 1.0 C2D B:CLA605 4.5 25.2 1.0 C3A B:CLA605 4.5 25.6 1.0 C2A B:CLA605 4.5 25.2 1.0 C3C B:CLA605 4.6 25.9 1.0 C4 B:CLA606 4.9 29.5 1.0 CBD B:CLA605 5.0 25.1 1.0

Magnesium binding site 9 out of 74 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Sr-Substituted Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:29.3 occ:1.00 MG B:CLA606 0.0 29.3 1.0 ND B:CLA606 2.0 30.9 1.0 NB B:CLA606 2.1 29.5 1.0 NC B:CLA606 2.2 30.4 1.0 ND1 B:HIS157 2.2 28.0 1.0 NA B:CLA606 2.3 29.8 1.0 C4D B:CLA606 3.0 30.9 1.0 CE1 B:HIS157 3.0 28.2 1.0 C1B B:CLA606 3.1 28.9 1.0 C4B B:CLA606 3.1 29.7 1.0 C1D B:CLA606 3.1 31.2 1.0 C4A B:CLA606 3.2 29.5 1.0 C1C B:CLA606 3.2 30.7 1.0 C4C B:CLA606 3.2 31.0 1.0 C1A B:CLA606 3.3 30.0 1.0 CG B:HIS157 3.4 29.1 1.0 CHB B:CLA606 3.4 29.3 1.0 CHC B:CLA606 3.5 29.6 1.0 CHD B:CLA606 3.5 30.9 1.0 CHA B:CLA606 3.6 30.8 1.0 CB B:HIS157 3.8 29.8 1.0 C3D B:CLA606 4.2 31.4 1.0 C8 B:UNL625 4.2 45.1 1.0 NE2 B:HIS157 4.3 28.3 1.0 C7 B:UNL625 4.3 46.4 1.0 C3B B:CLA606 4.4 29.0 1.0 C2B B:CLA606 4.4 29.5 1.0 C2D B:CLA606 4.4 31.7 1.0 CD2 B:HIS157 4.4 28.7 1.0 C9 B:UNL625 4.5 44.9 1.0 C2C B:CLA606 4.5 30.9 1.0 C3C B:CLA606 4.5 31.2 1.0 C3A B:CLA606 4.6 29.1 1.0 C2A B:CLA606 4.6 29.3 1.0 CD B:PRO164 4.9 31.8 1.0 CA B:HIS157 4.9 30.1 1.0 C6 B:UNL625 5.0 47.0 1.0

Magnesium binding site 10 out of 74 in the Structure of Sr-Substituted Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Sr-Substituted Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:22.2 occ:1.00 MG B:CLA607 0.0 22.2 1.0 ND B:CLA607 2.0 22.2 1.0 NB B:CLA607 2.1 21.8 1.0 O B:HOH708 2.1 19.6 1.0 NC B:CLA607 2.2 22.4 1.0 NA B:CLA607 2.3 22.1 1.0 C4D B:CLA607 3.0 22.1 1.0 C4B B:CLA607 3.1 22.0 1.0 C1B B:CLA607 3.1 21.6 1.0 C1D B:CLA607 3.1 22.6 1.0 C1C B:CLA607 3.2 22.5 1.0 C4C B:CLA607 3.2 22.9 1.0 C4A B:CLA607 3.2 21.7 1.0 C1A B:CLA607 3.3 22.1 1.0 CHC B:CLA607 3.4 21.9 1.0 CHB B:CLA607 3.5 21.4 1.0 CHD B:CLA607 3.5 22.3 1.0 CHA B:CLA607 3.6 22.0 1.0 C12 B:LMG622 3.7 44.2 1.0 O B:HOH755 4.1 19.0 1.0 C3D B:CLA607 4.2 21.9 1.0 SD B:MET37 4.3 24.8 1.0 C3B B:CLA607 4.4 21.5 1.0 C2D B:CLA607 4.4 22.2 1.0 C2B B:CLA607 4.4 21.7 1.0 C14 B:LMG622 4.5 41.8 1.0 C2C B:CLA607 4.5 23.0 1.0 C3C B:CLA607 4.5 22.8 1.0 C3A B:CLA607 4.6 21.6 1.0 C2A B:CLA607 4.6 22.1 1.0 C13 B:LMG622 4.6 43.1 1.0 CD2 B:PHE61 4.7 24.6 1.0 O9 B:LMG622 4.7 48.9 1.0 CE B:MET37 4.7 23.2 1.0 C11 B:LMG622 4.7 45.0 1.0 CB B:PHE61 4.7 24.1 1.0 CG B:PHE61 4.9 24.5 1.0

F.H.Koua, Y.Umena, K.Kawakami, J.R.Shen. Structure of Sr-Substituted Photosystem II at 2.1 A Resolution and Its Implications in the Mechanism of Water Oxidation Proc.Natl.Acad.Sci.Usa V. 110 3889 2013.
ISSN: ISSN 0027-8424
PubMed: 23426624
DOI: 10.1073/PNAS.1219922110