Magnesium in PDB 5lri: Photosynthetic Reaction Center Mutant with GLUL212 Replaced with Trp (Chain L, EL212W)

The structure of Photosynthetic Reaction Center Mutant with GLUL212 Replaced with Trp (Chain L, EL212W), PDB code: 5lri was solved by P.K.Fyfe, M.R.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.91 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.820, 139.820, 185.252, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 21.7

The structure of Photosynthetic Reaction Center Mutant with GLUL212 Replaced with Trp (Chain L, EL212W) also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Magnesium atom in the Photosynthetic Reaction Center Mutant with GLUL212 Replaced with Trp (Chain L, EL212W) (pdb code 5lri). 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 Mutant with GLUL212 Replaced with Trp (Chain L, EL212W), PDB code: 5lri:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Photosynthetic Reaction Center Mutant with GLUL212 Replaced with Trp (Chain L, EL212W)


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 Mutant with GLUL212 Replaced with Trp (Chain L, EL212W) within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg301 b:43.7 occ:1.00 MG L:BCL301 0.0 43.7 1.0 ND L:BCL301 2.0 41.3 1.0 NC L:BCL301 2.1 40.7 1.0 NB L:BCL301 2.1 39.1 1.0 NA L:BCL301 2.2 39.2 1.0 NE2 L:HIS173 2.4 38.2 1.0 C4D L:BCL301 2.9 43.6 1.0 C1D L:BCL301 3.1 41.4 1.0 C1C L:BCL301 3.1 38.5 1.0 C4C L:BCL301 3.1 39.0 1.0 C4B L:BCL301 3.1 40.4 1.0 C1B L:BCL301 3.1 37.4 1.0 C4A L:BCL301 3.1 38.5 1.0 C1A L:BCL301 3.2 40.0 1.0 CD2 L:HIS173 3.3 39.3 1.0 CHD L:BCL301 3.4 39.3 1.0 CE1 L:HIS173 3.4 38.7 1.0 CHC L:BCL301 3.4 38.6 1.0 CHB L:BCL301 3.4 38.4 1.0 CHA L:BCL301 3.5 41.1 1.0 CBB M:BCL705 3.7 40.9 1.0 OBB M:BCL705 3.7 45.6 1.0 CAB M:BCL705 3.7 41.9 1.0 C3D L:BCL301 4.1 40.1 1.0 C2D L:BCL301 4.2 43.5 1.0 C3B L:BCL301 4.3 37.6 1.0 C2B L:BCL301 4.3 38.2 1.0 C2C L:BCL301 4.4 36.5 1.0 C3C L:BCL301 4.4 37.8 1.0 C3A L:BCL301 4.4 40.7 1.0 CG L:HIS173 4.5 40.6 1.0 C3B M:BCL705 4.5 38.1 1.0 ND1 L:HIS173 4.5 38.6 1.0 C2A L:BCL301 4.5 40.1 1.0 CD2 L:PHE167 4.6 39.4 1.0 CBD L:BCL301 4.9 40.5 1.0 CMA L:BCL301 5.0 40.2 1.0

Magnesium binding site 2 out of 4 in the Photosynthetic Reaction Center Mutant with GLUL212 Replaced with Trp (Chain L, EL212W)


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 Mutant with GLUL212 Replaced with Trp (Chain L, EL212W) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg704 b:41.4 occ:1.00 MG M:BCL704 0.0 41.4 1.0 ND M:BCL704 2.0 39.5 1.0 NC M:BCL704 2.0 41.2 1.0 NB M:BCL704 2.1 42.1 1.0 NA M:BCL704 2.2 40.9 1.0 NE2 M:HIS182 2.4 47.8 1.0 C4D M:BCL704 2.9 40.2 1.0 C1D M:BCL704 3.0 39.7 1.0 C1C M:BCL704 3.0 43.8 1.0 C4C M:BCL704 3.1 41.7 1.0 C1B M:BCL704 3.1 43.6 1.0 C4B M:BCL704 3.1 44.5 1.0 C4A M:BCL704 3.1 41.4 1.0 CD2 M:HIS182 3.2 49.9 1.0 C1A M:BCL704 3.2 41.2 1.0 CHD M:BCL704 3.4 40.3 1.0 CHB M:BCL704 3.4 42.0 1.0 CHC M:BCL704 3.4 43.3 1.0 CHA M:BCL704 3.4 40.1 1.0 CE1 M:HIS182 3.5 48.1 1.0 C3D M:BCL704 4.1 38.9 1.0 C2D M:BCL704 4.2 39.9 1.0 C2B M:BCL704 4.3 44.8 1.0 C3B M:BCL704 4.3 44.1 1.0 C3C M:BCL704 4.4 43.5 1.0 C2C M:BCL704 4.4 42.4 1.0 CG M:HIS182 4.4 48.5 1.0 C3A M:BCL704 4.4 42.0 1.0 C2A M:BCL704 4.5 43.5 1.0 ND1 M:HIS182 4.6 49.4 1.0 CE2 L:PHE181 4.8 42.5 1.0 OBB M:BPH707 4.8 48.2 1.0 CBD M:BCL704 4.9 40.6 1.0

Magnesium binding site 3 out of 4 in the Photosynthetic Reaction Center Mutant with GLUL212 Replaced with Trp (Chain L, EL212W)


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 Mutant with GLUL212 Replaced with Trp (Chain L, EL212W) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg705 b:35.8 occ:1.00 MG M:BCL705 0.0 35.8 1.0 ND M:BCL705 2.0 33.6 1.0 NB M:BCL705 2.0 34.6 1.0 NC M:BCL705 2.1 34.8 1.0 NA M:BCL705 2.2 34.4 1.0 NE2 M:HIS202 2.5 39.7 1.0 C4D M:BCL705 2.9 36.6 1.0 C1C M:BCL705 3.0 36.6 1.0 C4B M:BCL705 3.0 38.1 1.0 C1B M:BCL705 3.0 36.6 1.0 C4C M:BCL705 3.1 35.8 1.0 C1D M:BCL705 3.1 36.0 1.0 C4A M:BCL705 3.1 35.0 1.0 C1A M:BCL705 3.2 35.6 1.0 CHC M:BCL705 3.3 36.6 1.0 CD2 M:HIS202 3.4 39.9 1.0 CHB M:BCL705 3.4 36.2 1.0 CHA M:BCL705 3.4 35.1 1.0 CE1 M:HIS202 3.5 41.1 1.0 CHD M:BCL705 3.5 36.1 1.0 CBB L:BCL301 3.7 43.3 1.0 OBB L:BCL301 3.7 41.5 1.0 CAB L:BCL301 3.7 40.7 1.0 C3D M:BCL705 4.2 36.4 1.0 C2B M:BCL705 4.2 36.7 1.0 C3B M:BCL705 4.2 38.1 1.0 C2D M:BCL705 4.3 35.3 1.0 C2C M:BCL705 4.4 39.3 1.0 C3C M:BCL705 4.4 39.1 1.0 C3B L:BCL301 4.5 37.6 1.0 C3A M:BCL705 4.5 39.0 1.0 C2A M:BCL705 4.5 38.6 1.0 CG M:HIS202 4.5 40.5 1.0 ND1 M:HIS202 4.6 41.2 1.0 CBD M:BCL705 4.9 37.9 1.0

Magnesium binding site 4 out of 4 in the Photosynthetic Reaction Center Mutant with GLUL212 Replaced with Trp (Chain L, EL212W)


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 Mutant with GLUL212 Replaced with Trp (Chain L, EL212W) within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg706 b:33.0 occ:1.00 MG M:BCL706 0.0 33.0 1.0 ND M:BCL706 2.0 27.0 1.0 NC M:BCL706 2.0 29.2 1.0 NB M:BCL706 2.0 29.1 1.0 NA M:BCL706 2.1 27.7 1.0 NE2 L:HIS153 2.5 46.1 1.0 C4D M:BCL706 2.9 28.2 1.0 C1C M:BCL706 3.0 32.3 1.0 C4C M:BCL706 3.0 31.6 1.0 C4A M:BCL706 3.0 29.2 1.0 C4B M:BCL706 3.0 31.5 1.0 C1B M:BCL706 3.1 29.2 1.0 C1D M:BCL706 3.1 29.3 1.0 C1A M:BCL706 3.1 30.7 1.0 CD2 L:HIS153 3.3 47.6 1.0 CHC M:BCL706 3.4 32.4 1.0 CHB M:BCL706 3.4 29.4 1.0 CHA M:BCL706 3.4 30.3 1.0 CHD M:BCL706 3.4 30.3 1.0 CE1 L:HIS153 3.6 49.1 1.0 C3D M:BCL706 4.2 27.8 1.0 C2D M:BCL706 4.2 28.7 1.0 C2B M:BCL706 4.3 30.9 1.0 C3B M:BCL706 4.3 31.3 1.0 C3C M:BCL706 4.3 33.4 1.0 C2C M:BCL706 4.3 34.5 1.0 C3A M:BCL706 4.3 32.1 1.0 OBB L:BPH302 4.4 49.4 1.0 CE2 M:TYR210 4.4 42.9 1.0 C2A M:BCL706 4.4 33.2 1.0 CG L:HIS153 4.5 49.0 1.0 ND1 L:HIS153 4.6 49.4 1.0 CBC M:BCL706 4.8 34.8 1.0 CBA M:BCL706 4.8 39.6 1.0 CD1 L:LEU154 4.9 46.5 1.0 CBD M:BCL706 4.9 33.9 1.0 C19 L:BPH302 5.0 43.3 1.0

V.M.Friebe, D.J.Swainsbury, P.K.Fyfe, W.Van Der Heijden, M.R.Jones, R.N.Frese. On the Mechanism of Ubiquinone Mediated Photocurrent Generation By A Reaction Center Based Photocathode. Biochim.Biophys.Acta V.1857 1925 2016.
ISSN: ISSN 0006-3002
PubMed: 27687473
DOI: 10.1016/J.BBABIO.2016.09.011