Magnesium in PDB 3i4d: Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1, PDB code: 3i4d was solved by R.Fujii, S.Adachi, A.W.Roszak, A.T.Gardiner, R.J.Cogdell, N.W.Isaacs, S.Koshihara, H.Hashimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.25 / 2.01
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.800, 138.800, 184.569, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 20.7

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Iron	(Fe)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 (pdb code 3i4d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1, PDB code: 3i4d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg602 b:29.8 occ:1.00 MG L:BCL602 0.0 29.8 1.0 ND L:BCL602 2.0 28.1 1.0 NB L:BCL602 2.1 29.9 1.0 NC L:BCL602 2.1 28.4 1.0 NE2 L:HIS173 2.2 27.5 1.0 NA L:BCL602 2.2 26.4 1.0 C4D L:BCL602 3.0 28.1 1.0 C1B L:BCL602 3.1 29.7 1.0 C1C L:BCL602 3.1 29.0 1.0 C4A L:BCL602 3.1 30.1 1.0 CE1 L:HIS173 3.1 31.5 1.0 C4B L:BCL602 3.1 29.1 1.0 C4C L:BCL602 3.1 30.8 1.0 C1D L:BCL602 3.1 27.9 1.0 CD2 L:HIS173 3.2 29.5 1.0 C1A L:BCL602 3.2 28.9 1.0 CHB L:BCL602 3.4 28.5 1.0 CHC L:BCL602 3.5 29.6 1.0 CHD L:BCL602 3.5 30.1 1.0 CHA L:BCL602 3.5 30.2 1.0 CBB M:BCL603 3.7 28.0 1.0 CAB M:BCL603 3.9 34.6 1.0 OBB M:BCL603 4.1 34.3 1.0 C3D L:BCL602 4.2 28.6 1.0 ND1 L:HIS173 4.2 29.8 1.0 C3B L:BCL602 4.3 29.2 1.0 C2B L:BCL602 4.3 29.3 1.0 CG L:HIS173 4.3 29.7 1.0 C2D L:BCL602 4.3 30.4 1.0 C3A L:BCL602 4.4 31.1 1.0 C2C L:BCL602 4.4 30.3 1.0 C3C L:BCL602 4.4 29.6 1.0 C2A L:BCL602 4.5 31.3 1.0 C3B M:BCL603 4.6 29.3 1.0 CD2 L:PHE167 4.7 33.0 1.0 CMA L:BCL602 4.9 26.5 1.0 CBD L:BCL602 5.0 28.0 1.0

Magnesium binding site 2 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg604 b:28.3 occ:1.00 MG L:BCL604 0.0 28.3 1.0 ND L:BCL604 2.1 27.0 1.0 NC L:BCL604 2.1 28.6 1.0 NB L:BCL604 2.1 26.7 1.0 NA L:BCL604 2.1 29.1 1.0 NE2 L:HIS153 2.2 29.4 1.0 C4D L:BCL604 3.0 26.4 1.0 C1C L:BCL604 3.0 27.7 1.0 CD2 L:HIS153 3.0 32.2 1.0 C4B L:BCL604 3.1 30.0 1.0 C1B L:BCL604 3.1 28.6 1.0 C4A L:BCL604 3.1 27.2 1.0 C4C L:BCL604 3.1 26.1 1.0 C1D L:BCL604 3.1 27.5 1.0 C1A L:BCL604 3.2 27.4 1.0 CE1 L:HIS153 3.2 32.9 1.0 CHC L:BCL604 3.4 28.0 1.0 CHA L:BCL604 3.4 30.5 1.0 CHB L:BCL604 3.4 27.8 1.0 CHD L:BCL604 3.5 28.2 1.0 C3D L:BCL604 4.2 24.6 1.0 CG L:HIS153 4.2 31.6 1.0 C3B L:BCL604 4.3 27.1 1.0 ND1 L:HIS153 4.3 31.4 1.0 C2B L:BCL604 4.3 27.5 1.0 C2D L:BCL604 4.3 29.8 1.0 CBB L:BPH402 4.4 23.5 1.0 C2C L:BCL604 4.4 25.4 1.0 C3C L:BCL604 4.4 27.1 1.0 C3A L:BCL604 4.4 29.6 1.0 C2A L:BCL604 4.5 26.9 1.0 CBC L:BCL604 4.7 29.3 1.0 CE2 M:TYR210 4.7 28.3 1.0 CD1 L:LEU154 4.9 39.4 1.0 C19 L:BPH402 4.9 30.4 1.0 CBD L:BCL604 4.9 30.9 1.0 CBA L:BCL604 5.0 28.8 1.0 CMC L:BCL604 5.0 28.8 1.0

Magnesium binding site 3 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg601 b:33.1 occ:1.00 MG M:BCL601 0.0 33.1 1.0 ND M:BCL601 2.0 29.1 1.0 NB M:BCL601 2.1 32.8 1.0 NC M:BCL601 2.1 30.9 1.0 NA M:BCL601 2.2 33.1 1.0 NE2 M:HIS182 2.3 29.3 1.0 C4D M:BCL601 2.9 31.1 1.0 C4B M:BCL601 3.1 31.6 1.0 C1D M:BCL601 3.1 29.4 1.0 CD2 M:HIS182 3.1 32.0 1.0 C1C M:BCL601 3.1 30.8 1.0 C1B M:BCL601 3.1 31.1 1.0 C4A M:BCL601 3.1 33.6 1.0 C4C M:BCL601 3.1 33.2 1.0 C1A M:BCL601 3.2 33.5 1.0 CE1 M:HIS182 3.3 34.4 1.0 CHC M:BCL601 3.4 30.6 1.0 CHB M:BCL601 3.4 33.5 1.0 CHA M:BCL601 3.4 33.1 1.0 CHD M:BCL601 3.5 29.9 1.0 C3D M:BCL601 4.1 29.2 1.0 C2D M:BCL601 4.2 29.0 1.0 C3B M:BCL601 4.3 32.8 1.0 C2B M:BCL601 4.3 33.3 1.0 CG M:HIS182 4.3 33.1 1.0 ND1 M:HIS182 4.4 35.9 1.0 C3A M:BCL601 4.4 33.4 1.0 C2C M:BCL601 4.4 34.5 1.0 C3C M:BCL601 4.4 34.1 1.0 C2A M:BCL601 4.5 34.2 1.0 CBB M:BPH401 4.5 31.4 1.0 CE2 L:PHE181 4.8 28.2 1.0 CBD M:BCL601 4.9 32.5 1.0 CMA M:BCL601 5.0 32.1 1.0

Magnesium binding site 4 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Photosynthetic Reaction Center From Rhodobacter Sphaeroides 2.4.1 within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg603 b:30.6 occ:1.00 MG M:BCL603 0.0 30.6 1.0 ND M:BCL603 2.0 28.3 1.0 NB M:BCL603 2.1 30.6 1.0 NC M:BCL603 2.1 29.1 1.0 NA M:BCL603 2.2 28.9 1.0 NE2 M:HIS202 2.3 30.6 1.0 C4D M:BCL603 2.9 33.5 1.0 C1C M:BCL603 3.0 30.7 1.0 C1B M:BCL603 3.1 29.8 1.0 C4B M:BCL603 3.1 31.4 1.0 C4C M:BCL603 3.1 31.0 1.0 C1D M:BCL603 3.1 31.7 1.0 C4A M:BCL603 3.1 30.4 1.0 CE1 M:HIS202 3.2 27.5 1.0 C1A M:BCL603 3.2 30.2 1.0 CD2 M:HIS202 3.3 31.2 1.0 CHC M:BCL603 3.4 30.1 1.0 CHB M:BCL603 3.4 28.1 1.0 CHA M:BCL603 3.4 29.5 1.0 CHD M:BCL603 3.4 29.1 1.0 CBB L:BCL602 3.6 28.0 1.0 CAB L:BCL602 3.8 33.0 1.0 OBB L:BCL602 4.0 31.9 1.0 C3D M:BCL603 4.2 29.2 1.0 C2D M:BCL603 4.3 31.8 1.0 C2B M:BCL603 4.3 28.1 1.0 ND1 M:HIS202 4.3 29.6 1.0 C3B M:BCL603 4.3 29.3 1.0 C2C M:BCL603 4.3 31.6 1.0 C3C M:BCL603 4.4 30.4 1.0 CG M:HIS202 4.4 27.6 1.0 C3A M:BCL603 4.5 28.7 1.0 C2A M:BCL603 4.5 29.6 1.0 C3B L:BCL602 4.6 29.2 1.0 CBD M:BCL603 4.9 29.0 1.0 CMC M:BCL603 4.9 29.8 1.0

R.Fujii, S.Adachi, A.W.Roszak, A.T.Gardiner, R.J.Cogdell, N.W.Isaacs, S.Koshihara, H.Hashimoto. Structure of the Carotenoid Bound to the Reaction Centre From Rhodobacter Sphaeroides 2.4.1 Revealed By Time-Resolved X-Ray Crystallography To Be Published.