Magnesium in PDB 4fby: Fs X-Ray Diffraction of Photosystem II

All present enzymatic activity of Fs X-Ray Diffraction of Photosystem II:
1.10.3.9;

The structure of Fs X-Ray Diffraction of Photosystem II, PDB code: 4fby was solved by J.Kern, R.Alonso-Mori, J.Hellmich, R.Tran, J.Hattne, H.Laksmono, C.Gloeckner, N.Echols, R.G.Sierra, J.Sellberg, B.Lassalle-Kaiser, R.J.Gildea, P.Glatzel, R.W.Grosse-Kunstleve, M.J.Latimer, T.A.Mcqueen, D.Difiore, A.R.Fry, M.M.Messerschmidt, A.Miahnahri, D.W.Schafer, M.M.Seibert, D.Sokaras, T.-C.Weng, P.H.Zwart, W.E.White, P.D.Adams, M.J.Bogan, S.Boutet, G.J.Williams, J.Messinger, N.K.Sauter, A.Zouni, U.Bergmann, J.Yano, V.K.Yachandra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.89 / 6.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	130.783, 227.764, 308.630, 90.00, 90.00, 90.00
R / Rfree (%)	36.6 / 38.5

The structure of Fs X-Ray Diffraction of Photosystem II also contains other interesting chemical elements:

Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Chlorine	(Cl)	2 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 - 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 Fs X-Ray Diffraction of Photosystem II (pdb code 4fby). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 70 binding sites of Magnesium where determined in the Fs X-Ray Diffraction of Photosystem II, PDB code: 4fby:
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 Fs X-Ray Diffraction 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 Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:0.9 occ:1.00 MG A:CLA401 0.0 0.9 1.0 ND A:CLA401 2.0 0.8 1.0 NB A:CLA401 2.0 0.0 1.0 NC A:CLA401 2.0 0.1 1.0 NA A:CLA401 2.1 0.7 1.0 C4D A:CLA401 2.9 0.2 1.0 C1B A:CLA401 2.9 0.4 1.0 NE2 A:HIS198 2.9 0.2 1.0 C4A A:CLA401 3.0 0.3 1.0 C1C A:CLA401 3.0 0.9 1.0 C4B A:CLA401 3.0 0.3 1.0 C4C A:CLA401 3.1 0.9 1.0 C1D A:CLA401 3.1 0.5 1.0 C1A A:CLA401 3.1 0.2 1.0 CHB A:CLA401 3.3 0.1 1.0 CHC A:CLA401 3.4 0.2 1.0 CHA A:CLA401 3.4 1.0 1.0 CHD A:CLA401 3.5 0.9 1.0 CE1 A:HIS198 3.8 0.7 1.0 CD2 A:HIS198 4.0 0.4 1.0 C3D A:CLA401 4.1 0.9 1.0 C2B A:CLA401 4.1 0.2 1.0 C3B A:CLA401 4.2 0.4 1.0 C2D A:CLA401 4.2 0.8 1.0 CAB D:CLA401 4.3 0.9 1.0 C2C A:CLA401 4.3 0.2 1.0 C3A A:CLA401 4.3 1.0 1.0 C3C A:CLA401 4.3 0.7 1.0 C2A A:CLA401 4.4 0.1 1.0 SD A:MET183 4.8 0.4 1.0 CBD A:CLA401 4.9 0.7 1.0 CHC D:CLA401 4.9 0.5 1.0 ND1 A:HIS198 5.0 0.5 1.0

Magnesium binding site 2 out of 70 in the Fs X-Ray Diffraction 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 Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:0.4 occ:1.00 MG A:CLA402 0.0 0.4 1.0 ND A:CLA402 2.0 0.7 1.0 NB A:CLA402 2.0 0.6 1.0 NC A:CLA402 2.0 0.8 1.0 NA A:CLA402 2.1 0.0 1.0 C4D A:CLA402 2.9 0.2 1.0 C1B A:CLA402 2.9 0.7 1.0 C4A A:CLA402 3.0 0.7 1.0 C1C A:CLA402 3.0 0.8 1.0 C4B A:CLA402 3.0 0.6 1.0 C4C A:CLA402 3.1 0.4 1.0 C1D A:CLA402 3.1 0.7 1.0 C1A A:CLA402 3.1 0.1 1.0 CHB A:CLA402 3.3 0.2 1.0 CHC A:CLA402 3.4 0.5 1.0 CHA A:CLA402 3.4 0.9 1.0 CHD A:CLA402 3.5 0.7 1.0 O1A A:CLA402 4.0 0.6 1.0 C3D A:CLA402 4.1 0.3 1.0 C2B A:CLA402 4.1 0.9 1.0 C3B A:CLA402 4.2 0.5 1.0 C2D A:CLA402 4.2 0.6 1.0 CBB A:PHO404 4.3 0.5 1.0 C2C A:CLA402 4.3 0.8 1.0 C3A A:CLA402 4.3 0.8 1.0 C3C A:CLA402 4.3 0.6 1.0 C2A A:CLA402 4.4 0.1 1.0 C20 A:PHO404 4.9 0.5 1.0 CBD A:CLA402 4.9 1.0 1.0 CG2 A:THR179 5.0 0.0 1.0

Magnesium binding site 3 out of 70 in the Fs X-Ray Diffraction 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 Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:0.2 occ:1.00 MG A:CLA403 0.0 0.2 1.0 ND A:CLA403 2.0 0.4 1.0 NB A:CLA403 2.0 0.5 1.0 NC A:CLA403 2.0 0.6 1.0 NA A:CLA403 2.1 0.1 1.0 C4D A:CLA403 2.9 0.5 1.0 C1B A:CLA403 2.9 0.1 1.0 C4A A:CLA403 3.0 0.3 1.0 C1C A:CLA403 3.0 0.7 1.0 C4B A:CLA403 3.0 0.6 1.0 C4C A:CLA403 3.1 0.6 1.0 C1D A:CLA403 3.1 0.6 1.0 C1A A:CLA403 3.1 0.2 1.0 CHB A:CLA403 3.3 0.8 1.0 CHC A:CLA403 3.4 0.9 1.0 CHA A:CLA403 3.4 0.5 1.0 CHD A:CLA403 3.5 0.6 1.0 CBB D:PHO402 3.9 0.8 1.0 C3D A:CLA403 4.1 0.6 1.0 C2B A:CLA403 4.1 0.7 1.0 C3B A:CLA403 4.2 0.2 1.0 C2D A:CLA403 4.2 0.4 1.0 C2C A:CLA403 4.3 0.5 1.0 C3A A:CLA403 4.3 0.9 1.0 C3C A:CLA403 4.3 0.0 1.0 C2A A:CLA403 4.4 0.0 1.0 C20 D:PHO402 4.6 0.1 1.0 CE1 A:PHE206 4.6 0.5 1.0 CBA A:CLA403 4.8 1.0 1.0 CBD A:CLA403 4.9 0.2 1.0

Magnesium binding site 4 out of 70 in the Fs X-Ray Diffraction 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 Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:0.1 occ:1.00 MG A:CLA405 0.0 0.1 1.0 ND A:CLA405 2.0 0.1 1.0 NB A:CLA405 2.0 0.7 1.0 NC A:CLA405 2.0 0.1 1.0 NA A:CLA405 2.1 0.1 1.0 NE2 A:HIS118 2.9 0.4 1.0 C4D A:CLA405 2.9 0.9 1.0 C1B A:CLA405 2.9 0.9 1.0 C4A A:CLA405 3.0 0.9 1.0 C4B A:CLA405 3.0 0.7 1.0 C1C A:CLA405 3.0 0.1 1.0 C4C A:CLA405 3.1 0.4 1.0 C1D A:CLA405 3.1 0.9 1.0 C1A A:CLA405 3.1 0.3 1.0 CHB A:CLA405 3.3 0.1 1.0 CHC A:CLA405 3.4 0.2 1.0 CHA A:CLA405 3.4 0.5 1.0 CHD A:CLA405 3.5 0.0 1.0 CE1 A:HIS118 3.6 0.6 1.0 CD2 A:HIS118 4.0 0.4 1.0 CG2 I:VAL12 4.1 0.9 1.0 C3D A:CLA405 4.1 0.7 1.0 C2B A:CLA405 4.1 0.5 1.0 C3B A:CLA405 4.2 0.3 1.0 CG1 I:VAL8 4.2 0.5 1.0 C2D A:CLA405 4.2 0.4 1.0 C2C A:CLA405 4.3 0.4 1.0 C3A A:CLA405 4.3 0.3 1.0 C3C A:CLA405 4.3 0.1 1.0 C2A A:CLA405 4.4 0.9 1.0 ND1 A:HIS118 4.8 0.1 1.0 CBD A:CLA405 4.9 0.0 1.0 CG A:HIS118 5.0 0.9 1.0

Magnesium binding site 5 out of 70 in the Fs X-Ray Diffraction 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 Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:0.9 occ:1.00 MG B:CLA601 0.0 0.9 1.0 ND B:CLA601 2.0 0.2 1.0 NB B:CLA601 2.0 1.0 1.0 NC B:CLA601 2.0 1.0 1.0 NA B:CLA601 2.1 0.4 1.0 C4D B:CLA601 2.9 0.0 1.0 C1B B:CLA601 2.9 0.7 1.0 C4A B:CLA601 3.0 0.6 1.0 C1C B:CLA601 3.0 0.9 1.0 C4B B:CLA601 3.0 0.4 1.0 C4C B:CLA601 3.1 0.4 1.0 C1D B:CLA601 3.1 0.5 1.0 C1A B:CLA601 3.1 0.1 1.0 CHB B:CLA601 3.3 0.5 1.0 CHC B:CLA601 3.4 0.0 1.0 CHA B:CLA601 3.4 0.1 1.0 CHD B:CLA601 3.5 0.3 1.0 O B:TRP185 3.9 0.5 1.0 C3D B:CLA601 4.1 0.3 1.0 C2B B:CLA601 4.1 0.0 1.0 C3B B:CLA601 4.2 0.9 1.0 C2D B:CLA601 4.2 0.4 1.0 C2C B:CLA601 4.3 0.6 1.0 C3A B:CLA601 4.3 1.0 1.0 C3C B:CLA601 4.3 0.6 1.0 C2A B:CLA601 4.4 0.6 1.0 CBD B:CLA601 4.9 0.4 1.0 CE1 B:PHE190 4.9 0.1 1.0

Magnesium binding site 6 out of 70 in the Fs X-Ray Diffraction 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 Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:0.8 occ:1.00 MG B:CLA602 0.0 0.8 1.0 ND B:CLA602 2.0 0.9 1.0 NB B:CLA602 2.0 0.8 1.0 NC B:CLA602 2.0 0.1 1.0 NA B:CLA602 2.1 0.7 1.0 ND1 B:HIS201 2.8 0.9 1.0 C4D B:CLA602 2.9 0.5 1.0 C1B B:CLA602 2.9 0.5 1.0 C4A B:CLA602 3.0 0.5 1.0 C1C B:CLA602 3.0 0.4 1.0 C4B B:CLA602 3.0 0.4 1.0 C4C B:CLA602 3.1 0.2 1.0 C1D B:CLA602 3.1 0.3 1.0 C1A B:CLA602 3.1 0.7 1.0 CHB B:CLA602 3.3 0.7 1.0 CHC B:CLA602 3.4 0.4 1.0 CHA B:CLA602 3.4 0.0 1.0 CHD B:CLA602 3.5 0.5 1.0 CE1 B:HIS201 3.7 0.9 1.0 CZ H:PHE41 3.8 0.8 1.0 CG B:HIS201 3.9 0.7 1.0 C3D B:CLA602 4.1 0.9 1.0 C2B B:CLA602 4.1 0.9 1.0 CB B:HIS201 4.2 0.1 1.0 C3B B:CLA602 4.2 0.6 1.0 C2D B:CLA602 4.2 0.6 1.0 C2C B:CLA602 4.3 0.3 1.0 C3A B:CLA602 4.3 0.0 1.0 C3C B:CLA602 4.3 0.8 1.0 C2A B:CLA602 4.4 0.1 1.0 CE1 H:PHE41 4.6 1.0 1.0 CE2 H:PHE41 4.6 0.3 1.0 CA B:HIS201 4.7 0.7 1.0 CE2 B:PHE190 4.7 0.4 1.0 NE2 B:HIS201 4.8 0.4 1.0 CBD B:CLA602 4.9 0.8 1.0 CD2 B:HIS201 5.0 0.1 1.0

Magnesium binding site 7 out of 70 in the Fs X-Ray Diffraction 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 Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:0.3 occ:1.00 MG B:CLA603 0.0 0.3 1.0 ND B:CLA603 2.0 0.0 1.0 NB B:CLA603 2.0 0.5 1.0 NC B:CLA603 2.0 0.6 1.0 NA B:CLA603 2.1 0.3 1.0 C4D B:CLA603 2.9 0.1 1.0 C1B B:CLA603 2.9 0.6 1.0 C4A B:CLA603 3.0 0.2 1.0 C1C B:CLA603 3.0 0.9 1.0 C4B B:CLA603 3.0 0.1 1.0 C4C B:CLA603 3.1 0.8 1.0 C1D B:CLA603 3.1 0.8 1.0 C1A B:CLA603 3.1 0.5 1.0 NE2 B:HIS202 3.2 0.7 1.0 CHB B:CLA603 3.3 0.5 1.0 CHC B:CLA603 3.4 0.5 1.0 CHA B:CLA603 3.4 0.9 1.0 CHD B:CLA603 3.5 0.8 1.0 C7 B:CLA605 3.6 0.4 1.0 C5 B:CLA605 3.9 0.1 1.0 CD2 B:HIS202 3.9 0.7 1.0 CE1 B:HIS202 4.1 0.9 1.0 C3D B:CLA603 4.1 0.6 1.0 C2B B:CLA603 4.1 0.3 1.0 C3B B:CLA603 4.2 0.5 1.0 C2D B:CLA603 4.2 0.4 1.0 C6 B:CLA605 4.3 0.3 1.0 C3A B:CLA603 4.3 0.8 1.0 C2C B:CLA603 4.3 0.8 1.0 C3C B:CLA603 4.3 0.4 1.0 C2A B:CLA603 4.4 0.0 1.0 C8 B:CLA605 4.9 0.2 1.0 CBD B:CLA603 4.9 0.1 1.0 NE2 B:HIS201 4.9 0.4 1.0 O2A B:CLA603 5.0 0.6 1.0 CBA B:CLA603 5.0 0.4 1.0

Magnesium binding site 8 out of 70 in the Fs X-Ray Diffraction 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 Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:0.3 occ:1.00 MG B:CLA604 0.0 0.3 1.0 ND B:CLA604 2.0 0.9 1.0 NB B:CLA604 2.0 0.3 1.0 NC B:CLA604 2.0 0.3 1.0 NA B:CLA604 2.1 0.9 1.0 C4D B:CLA604 2.9 0.2 1.0 C1B B:CLA604 2.9 0.1 1.0 NE2 B:HIS455 3.0 0.5 1.0 C4A B:CLA604 3.0 0.6 1.0 C4B B:CLA604 3.0 0.3 1.0 C1C B:CLA604 3.0 0.5 1.0 C4C B:CLA604 3.1 0.9 1.0 C1D B:CLA604 3.1 0.0 1.0 C1A B:CLA604 3.1 0.5 1.0 CHB B:CLA604 3.3 0.5 1.0 CHC B:CLA604 3.4 0.4 1.0 CHA B:CLA604 3.4 0.1 1.0 CHD B:CLA604 3.5 0.3 1.0 CD2 B:HIS455 3.7 0.2 1.0 C14 B:CLA612 3.8 0.3 1.0 CE1 B:HIS455 4.1 0.2 1.0 C2B B:CLA604 4.1 0.1 1.0 C3D B:CLA604 4.1 0.6 1.0 C3B B:CLA604 4.2 1.0 1.0 C2D B:CLA604 4.2 0.7 1.0 C15 B:CLA612 4.3 0.5 1.0 C3A B:CLA604 4.3 0.5 1.0 C2C B:CLA604 4.3 1.0 1.0 C3C B:CLA604 4.3 0.7 1.0 C13 B:CLA612 4.4 0.5 1.0 C2A B:CLA604 4.4 0.9 1.0 CBD B:CLA604 4.9 0.4 1.0 CG B:HIS455 4.9 0.2 1.0 CAB B:CLA613 5.0 0.1 1.0

Magnesium binding site 9 out of 70 in the Fs X-Ray Diffraction 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 Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:0.0 occ:1.00 MG B:CLA605 0.0 0.0 1.0 ND B:CLA605 2.0 0.4 1.0 NB B:CLA605 2.0 0.5 1.0 NC B:CLA605 2.0 1.0 1.0 NA B:CLA605 2.1 0.5 1.0 C4D B:CLA605 2.9 1.0 1.0 C1B B:CLA605 3.0 0.2 1.0 C4A B:CLA605 3.0 0.8 1.0 C1C B:CLA605 3.0 0.6 1.0 C4B B:CLA605 3.0 0.6 1.0 C4C B:CLA605 3.1 0.6 1.0 NE2 B:HIS100 3.1 0.8 1.0 C1D B:CLA605 3.1 0.8 1.0 C1A B:CLA605 3.1 0.7 1.0 CHB B:CLA605 3.3 0.6 1.0 CHC B:CLA605 3.4 0.5 1.0 CHA B:CLA605 3.4 0.2 1.0 CHD B:CLA605 3.5 0.3 1.0 CD2 B:HIS100 3.9 0.2 1.0 C1 B:CLA604 3.9 0.1 1.0 C2 B:CLA604 4.0 0.6 1.0 CE1 B:HIS100 4.1 0.5 1.0 C3D B:CLA605 4.1 0.6 1.0 C2B B:CLA605 4.1 0.9 1.0 C3B B:CLA605 4.2 0.7 1.0 C2D B:CLA605 4.2 0.1 1.0 C2C B:CLA605 4.3 0.9 1.0 C3A B:CLA605 4.3 0.2 1.0 C3C B:CLA605 4.3 0.2 1.0 C2A B:CLA605 4.4 0.8 1.0 O2A B:CLA604 4.7 0.4 1.0 C3 B:CLA604 4.8 0.7 1.0 CBD B:CLA605 4.9 0.2 1.0 O1A B:CLA604 4.9 0.1 1.0

Magnesium binding site 10 out of 70 in the Fs X-Ray Diffraction 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 Fs X-Ray Diffraction of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg606 b:0.1 occ:1.00 MG B:CLA606 0.0 0.1 1.0 ND B:CLA606 2.0 0.9 1.0 NB B:CLA606 2.0 0.3 1.0 NC B:CLA606 2.0 0.7 1.0 NA B:CLA606 2.1 0.8 1.0 C4D B:CLA606 2.9 1.0 1.0 C1B B:CLA606 2.9 0.8 1.0 ND1 B:HIS157 3.0 0.1 1.0 C4A B:CLA606 3.0 0.8 1.0 C1C B:CLA606 3.0 1.0 1.0 C4B B:CLA606 3.0 0.9 1.0 C4C B:CLA606 3.1 0.7 1.0 C1D B:CLA606 3.1 0.7 1.0 C1A B:CLA606 3.1 0.1 1.0 CHB B:CLA606 3.3 0.7 1.0 CE1 B:HIS157 3.3 0.2 1.0 CHC B:CLA606 3.4 0.1 1.0 CHA B:CLA606 3.4 0.5 1.0 CHD B:CLA606 3.5 0.9 1.0 C6 B:LMT625 3.8 0.4 1.0 C4 B:LMT625 3.8 0.2 1.0 C5 B:LMT625 3.9 0.8 1.0 C3D B:CLA606 4.1 0.1 1.0 C2B B:CLA606 4.1 0.5 1.0 C3B B:CLA606 4.2 0.6 1.0 C2D B:CLA606 4.2 0.5 1.0 CG B:HIS157 4.2 0.3 1.0 C2C B:CLA606 4.3 0.1 1.0 C3A B:CLA606 4.3 0.3 1.0 C3C B:CLA606 4.3 0.6 1.0 C2A B:CLA606 4.4 0.2 1.0 NE2 B:HIS157 4.6 0.8 1.0 CB B:HIS157 4.9 0.1 1.0 CBD B:CLA606 4.9 0.6 1.0

J.Kern, R.Alonso-Mori, J.Hellmich, R.Tran, J.Hattne, H.Laksmono, C.Glockner, N.Echols, R.G.Sierra, J.Sellberg, B.Lassalle-Kaiser, R.J.Gildea, P.Glatzel, R.W.Grosse-Kunstleve, M.J.Latimer, T.A.Mcqueen, D.Difiore, A.R.Fry, M.Messerschmidt, A.Miahnahri, D.W.Schafer, M.M.Seibert, D.Sokaras, T.C.Weng, P.H.Zwart, W.E.White, P.D.Adams, M.J.Bogan, S.Boutet, G.J.Williams, J.Messinger, N.K.Sauter, A.Zouni, U.Bergmann, J.Yano, V.K.Yachandra. Room Temperature Femtosecond X-Ray Diffraction of Photosystem II Microcrystals. Proc.Natl.Acad.Sci.Usa V. 109 9721 2012.
ISSN: ISSN 0027-8424
PubMed: 22665786
DOI: 10.1073/PNAS.1204598109