Magnesium in PDB 3duq: E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides

The structure of E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides, PDB code: 3duq was solved by P.R.Pokkuluri, M.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.300, 141.300, 187.400, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 21.7

The structure of E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Magnesium atom in the E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides (pdb code 3duq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides, PDB code: 3duq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg502 b:31.9 occ:1.00 MG L:BCL502 0.0 31.9 1.0 ND L:BCL502 2.0 35.5 1.0 NB L:BCL502 2.1 31.3 1.0 NC L:BCL502 2.1 30.1 1.0 NA L:BCL502 2.2 34.1 1.0 NE2 L:HIS173 2.3 22.3 1.0 C4D L:BCL502 3.0 37.4 1.0 C1B L:BCL502 3.1 30.5 1.0 C4B L:BCL502 3.1 30.0 1.0 C1D L:BCL502 3.1 33.9 1.0 C4A L:BCL502 3.1 34.0 1.0 C1C L:BCL502 3.1 30.7 1.0 C4C L:BCL502 3.2 30.3 1.0 CD2 L:HIS173 3.2 17.9 1.0 C1A L:BCL502 3.2 34.8 1.0 CE1 L:HIS173 3.3 24.1 1.0 CHB L:BCL502 3.5 32.3 1.0 CHC L:BCL502 3.5 28.7 1.0 CHD L:BCL502 3.5 31.4 1.0 CHA L:BCL502 3.5 35.9 1.0 OBB M:BCL502 3.6 42.5 1.0 CAB M:BCL502 3.8 37.6 1.0 CBB M:BCL502 4.0 36.7 1.0 C3D L:BCL502 4.2 34.6 1.0 C2B L:BCL502 4.3 32.8 1.0 C2D L:BCL502 4.3 36.1 1.0 C3B L:BCL502 4.3 33.3 1.0 CG L:HIS173 4.3 26.3 1.0 ND1 L:HIS173 4.4 23.5 1.0 C3A L:BCL502 4.4 36.4 1.0 C2C L:BCL502 4.4 25.2 1.0 C3C L:BCL502 4.5 24.3 1.0 C2A L:BCL502 4.5 35.5 1.0 C3B M:BCL502 4.5 33.1 1.0 CD2 L:PHE167 4.7 37.4 1.0 CMA L:BCL502 4.9 29.8 1.0 CBD L:BCL502 5.0 36.9 1.0

Magnesium binding site 2 out of 4 in the E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg501 b:19.6 occ:1.00 MG L:BCL501 0.0 19.6 1.0 ND L:BCL501 2.0 17.8 1.0 NB L:BCL501 2.1 23.3 1.0 NC L:BCL501 2.1 20.3 1.0 NA L:BCL501 2.2 19.3 1.0 NE2 L:HIS153 2.3 49.9 1.0 C4D L:BCL501 3.0 21.2 1.0 C1D L:BCL501 3.0 21.2 1.0 C1B L:BCL501 3.1 22.6 1.0 C1C L:BCL501 3.1 25.2 1.0 C4B L:BCL501 3.1 26.5 1.0 C4C L:BCL501 3.1 22.6 1.0 C4A L:BCL501 3.1 24.1 1.0 C1A L:BCL501 3.2 22.7 1.0 CD2 L:HIS153 3.3 48.8 1.0 CE1 L:HIS153 3.3 48.9 1.0 CHC L:BCL501 3.4 23.3 1.0 CHD L:BCL501 3.4 18.8 1.0 CHB L:BCL501 3.4 20.4 1.0 CHA L:BCL501 3.5 20.1 1.0 C3D L:BCL501 4.2 20.0 1.0 C2D L:BCL501 4.3 23.2 1.0 C2B L:BCL501 4.3 24.2 1.0 CBB L:BPH503 4.3 35.1 1.0 C3B L:BCL501 4.3 28.2 1.0 C3C L:BCL501 4.4 27.0 1.0 C2C L:BCL501 4.4 27.3 1.0 CG L:HIS153 4.4 47.7 1.0 C3A L:BCL501 4.4 23.8 1.0 ND1 L:HIS153 4.4 49.2 1.0 C2A L:BCL501 4.5 27.1 1.0 CE2 M:TYR210 4.6 42.4 1.0 CBA L:BCL501 4.9 34.6 1.0 CD2 L:LEU154 4.9 39.1 1.0 CAC L:BCL501 4.9 33.0 1.0 CBD L:BCL501 5.0 28.8 1.0

Magnesium binding site 3 out of 4 in the E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg501 b:30.4 occ:1.00 MG M:BCL501 0.0 30.4 1.0 ND M:BCL501 2.0 27.1 1.0 NB M:BCL501 2.1 32.7 1.0 NC M:BCL501 2.1 26.7 1.0 NA M:BCL501 2.2 28.7 1.0 NE2 M:HIS182 2.2 44.7 1.0 C4D M:BCL501 3.0 27.9 1.0 C1B M:BCL501 3.1 33.4 1.0 CD2 M:HIS182 3.1 44.2 1.0 C1D M:BCL501 3.1 29.9 1.0 C4B M:BCL501 3.1 31.7 1.0 C4C M:BCL501 3.1 26.2 1.0 C1C M:BCL501 3.1 28.2 1.0 C4A M:BCL501 3.2 30.5 1.0 C1A M:BCL501 3.2 30.9 1.0 CE1 M:HIS182 3.2 45.0 1.0 CHB M:BCL501 3.5 28.9 1.0 CHA M:BCL501 3.5 32.6 1.0 CHD M:BCL501 3.5 28.2 1.0 CHC M:BCL501 3.5 29.4 1.0 C3D M:BCL501 4.2 31.6 1.0 CG M:HIS182 4.3 42.0 1.0 C2B M:BCL501 4.3 35.6 1.0 C2D M:BCL501 4.3 34.3 1.0 ND1 M:HIS182 4.3 43.5 1.0 C3B M:BCL501 4.3 35.4 1.0 C2C M:BCL501 4.4 29.3 1.0 C3C M:BCL501 4.4 25.6 1.0 C3A M:BCL501 4.5 32.1 1.0 C2A M:BCL501 4.5 35.4 1.0 CBB M:BPH503 4.8 42.5 1.0 CE2 L:PHE181 4.8 39.1 1.0 CBD M:BCL501 5.0 35.8 1.0 CBA M:BCL501 5.0 47.8 1.0

Magnesium binding site 4 out of 4 in the E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E(L212)A, D(L213)A, N(M5)D Triple Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg502 b:28.9 occ:1.00 MG M:BCL502 0.0 28.9 1.0 ND M:BCL502 2.0 29.1 1.0 NB M:BCL502 2.1 30.0 1.0 NC M:BCL502 2.1 33.0 1.0 NA M:BCL502 2.2 30.6 1.0 NE2 M:HIS202 2.2 27.3 1.0 C4D M:BCL502 3.0 32.2 1.0 C1B M:BCL502 3.1 31.6 1.0 C4B M:BCL502 3.1 28.7 1.0 C1C M:BCL502 3.1 32.3 1.0 C1D M:BCL502 3.1 27.5 1.0 CE1 M:HIS202 3.1 26.8 1.0 C4C M:BCL502 3.1 29.4 1.0 CD2 M:HIS202 3.1 27.5 1.0 C4A M:BCL502 3.1 31.2 1.0 C1A M:BCL502 3.2 31.4 1.0 CHC M:BCL502 3.4 29.0 1.0 CHB M:BCL502 3.5 30.1 1.0 CHA M:BCL502 3.5 32.0 1.0 CHD M:BCL502 3.5 27.6 1.0 CBB L:BCL502 3.7 33.9 1.0 CAB L:BCL502 4.0 33.9 1.0 OBB L:BCL502 4.2 33.5 1.0 C3D M:BCL502 4.2 31.5 1.0 ND1 M:HIS202 4.3 24.3 1.0 CG M:HIS202 4.3 26.5 1.0 C2B M:BCL502 4.3 30.1 1.0 C3B M:BCL502 4.3 33.1 1.0 C2D M:BCL502 4.3 29.0 1.0 C2C M:BCL502 4.3 31.7 1.0 C3C M:BCL502 4.4 33.6 1.0 C2A M:BCL502 4.4 34.2 1.0 C3A M:BCL502 4.4 31.6 1.0 C3B L:BCL502 4.5 33.3 1.0 CBD M:BCL502 4.9 31.4 1.0 O2D M:BCL502 4.9 37.4 1.0 CMC M:BCL502 5.0 30.7 1.0

P.R.Pokkuluri, P.D.Laible, S.L.Ginell, D.K.Hanson, M.Schiffer. Structural Description of Compensatory Mutations That Restore Proton Transfer Pathways to the L212A-L213A Mutant Bacterial Reaction Center To Be Published.