Magnesium in PDB 1ry5: Photosynthetic Reaction Center Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn

The structure of Photosynthetic Reaction Center Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn, PDB code: 1ry5 was solved by Q.Xu, H.L.Axelrod, E.C.Abresch, M.L.Paddock, M.Y.Okamura, G.Feher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.23 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.071, 139.071, 184.599, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 22.6

The structure of Photosynthetic Reaction Center Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn also contains other interesting chemical elements:

Potassium	(K)	1 atom
Iron	(Fe)	1 atom

The binding sites of Magnesium atom in the Photosynthetic Reaction Center Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn (pdb code 1ry5). 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 From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn, PDB code: 1ry5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Photosynthetic Reaction Center Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn


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 From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg851 b:26.3 occ:1.00 MG L:BCL851 0.0 26.3 1.0 NB L:BCL851 2.0 28.1 1.0 NC L:BCL851 2.0 27.1 1.0 NA L:BCL851 2.1 27.0 1.0 ND L:BCL851 2.1 25.4 1.0 NE2 M:HIS182 2.3 25.4 1.0 C4B L:BCL851 3.0 27.5 1.0 C1C L:BCL851 3.0 27.5 1.0 C1B L:BCL851 3.0 27.2 1.0 C4D L:BCL851 3.0 25.8 1.0 C4C L:BCL851 3.1 27.6 1.0 C4A L:BCL851 3.1 30.1 1.0 CD2 M:HIS182 3.1 26.6 1.0 C1D L:BCL851 3.2 24.8 1.0 C1A L:BCL851 3.2 28.7 1.0 CHC L:BCL851 3.3 27.7 1.0 CHB L:BCL851 3.4 28.1 1.0 CE1 M:HIS182 3.5 27.3 1.0 CHA L:BCL851 3.5 27.2 1.0 CHD L:BCL851 3.5 24.7 1.0 C3D L:BCL851 4.2 24.5 1.0 C3B L:BCL851 4.3 29.1 1.0 C2B L:BCL851 4.3 28.0 1.0 C3C L:BCL851 4.3 30.6 1.0 C2C L:BCL851 4.3 30.3 1.0 CG M:HIS182 4.4 27.6 1.0 C2D L:BCL851 4.4 25.0 1.0 CBB M:BPH855 4.5 32.0 1.0 C3A L:BCL851 4.5 31.6 1.0 ND1 M:HIS182 4.5 26.4 1.0 C2A L:BCL851 4.5 31.6 1.0 CE2 L:PHE181 4.8 25.7 1.0 CAC L:BCL851 4.9 34.5 1.0 CBD L:BCL851 5.0 27.6 1.0

Magnesium binding site 2 out of 4 in the Photosynthetic Reaction Center Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn


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 From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg852 b:23.1 occ:1.00 MG L:BCL852 0.0 23.1 1.0 NB L:BCL852 2.0 24.5 1.0 NC L:BCL852 2.0 23.8 1.0 NA L:BCL852 2.1 24.9 1.0 ND L:BCL852 2.2 25.7 1.0 NE2 L:HIS173 2.3 23.7 1.0 C4B L:BCL852 3.0 25.7 1.0 C1B L:BCL852 3.0 23.8 1.0 C1C L:BCL852 3.0 23.9 1.0 C4D L:BCL852 3.1 27.4 1.0 C4A L:BCL852 3.1 24.6 1.0 C4C L:BCL852 3.1 24.5 1.0 CE1 L:HIS173 3.1 22.0 1.0 C1D L:BCL852 3.2 26.6 1.0 C1A L:BCL852 3.2 25.3 1.0 CHC L:BCL852 3.3 24.4 1.0 CHB L:BCL852 3.4 23.5 1.0 CD2 L:HIS173 3.4 23.0 1.0 CHD L:BCL852 3.5 25.5 1.0 CHA L:BCL852 3.5 26.6 1.0 CBB M:BCL853 3.6 24.5 1.0 CAB M:BCL853 3.7 25.9 1.0 OBB M:BCL853 3.8 29.9 1.0 C3D L:BCL852 4.3 26.8 1.0 C3B L:BCL852 4.3 24.7 1.0 C2B L:BCL852 4.3 25.6 1.0 ND1 L:HIS173 4.3 23.7 1.0 C2C L:BCL852 4.4 23.9 1.0 C3C L:BCL852 4.4 24.1 1.0 C2D L:BCL852 4.4 28.9 1.0 CG L:HIS173 4.4 23.2 1.0 C3B M:BCL853 4.5 23.6 1.0 C3A L:BCL852 4.5 26.5 1.0 C2A L:BCL852 4.5 26.0 1.0 CD2 L:PHE167 4.6 29.3 1.0 CBD L:BCL852 5.0 26.2 1.0

Magnesium binding site 3 out of 4 in the Photosynthetic Reaction Center Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn


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 From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg854 b:26.4 occ:1.00 MG L:BCL854 0.0 26.4 1.0 NB L:BCL854 1.9 23.5 1.0 NC L:BCL854 2.0 22.4 1.0 NA L:BCL854 2.1 25.1 1.0 ND L:BCL854 2.2 24.4 1.0 NE2 L:HIS153 2.4 26.1 1.0 C4B L:BCL854 2.9 25.6 1.0 C1B L:BCL854 3.0 24.4 1.0 C1C L:BCL854 3.0 25.6 1.0 C4D L:BCL854 3.1 23.0 1.0 C4C L:BCL854 3.1 23.9 1.0 C4A L:BCL854 3.1 25.0 1.0 CD2 L:HIS153 3.2 26.8 1.0 C1D L:BCL854 3.2 22.3 1.0 C1A L:BCL854 3.3 23.3 1.0 CHC L:BCL854 3.3 24.9 1.0 CHB L:BCL854 3.3 23.8 1.0 CE1 L:HIS153 3.5 27.4 1.0 CHD L:BCL854 3.5 23.2 1.0 CHA L:BCL854 3.5 23.8 1.0 CBB L:BPH856 4.2 26.7 1.0 C3B L:BCL854 4.2 26.6 1.0 C3D L:BCL854 4.3 22.9 1.0 C2B L:BCL854 4.3 24.1 1.0 C2C L:BCL854 4.3 26.1 1.0 C3C L:BCL854 4.3 26.4 1.0 C2D L:BCL854 4.4 25.1 1.0 CG L:HIS153 4.4 27.2 1.0 C3A L:BCL854 4.5 28.1 1.0 ND1 L:HIS153 4.6 27.0 1.0 C2A L:BCL854 4.6 27.9 1.0 CE2 M:TYR210 4.7 25.6 1.0 C19 L:BPH856 4.7 37.7 1.0

Magnesium binding site 4 out of 4 in the Photosynthetic Reaction Center Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn


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 From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg853 b:23.4 occ:1.00 MG M:BCL853 0.0 23.4 1.0 NB M:BCL853 2.0 22.5 1.0 NC M:BCL853 2.0 23.9 1.0 NA M:BCL853 2.1 24.1 1.0 ND M:BCL853 2.1 23.7 1.0 NE2 M:HIS202 2.3 23.6 1.0 C4B M:BCL853 2.9 25.0 1.0 C1B M:BCL853 3.0 23.3 1.0 C1C M:BCL853 3.0 22.6 1.0 C4D M:BCL853 3.0 27.6 1.0 C4A M:BCL853 3.1 23.1 1.0 C4C M:BCL853 3.1 25.0 1.0 C1D M:BCL853 3.2 27.2 1.0 C1A M:BCL853 3.2 24.4 1.0 CHC M:BCL853 3.3 24.0 1.0 CE1 M:HIS202 3.3 20.2 1.0 CHB M:BCL853 3.3 22.2 1.0 CBB L:BCL852 3.4 25.6 1.0 CD2 M:HIS202 3.4 22.2 1.0 CHA M:BCL853 3.5 25.2 1.0 CHD M:BCL853 3.5 24.5 1.0 CAB L:BCL852 3.7 26.6 1.0 OBB L:BCL852 3.9 25.6 1.0 C3D M:BCL853 4.2 25.6 1.0 C3B M:BCL853 4.3 23.6 1.0 C2B M:BCL853 4.3 22.0 1.0 C2C M:BCL853 4.3 26.2 1.0 C2D M:BCL853 4.4 26.0 1.0 C3C M:BCL853 4.4 24.1 1.0 C3B L:BCL852 4.5 24.7 1.0 ND1 M:HIS202 4.5 22.1 1.0 CG M:HIS202 4.5 19.7 1.0 C3A M:BCL853 4.5 23.6 1.0 C2A M:BCL853 4.5 25.8 1.0 CBD M:BCL853 5.0 26.0 1.0

Q.Xu, H.L.Axelrod, E.C.Abresch, M.L.Paddock, M.Y.Okamura, G.Feher. X-Ray Structure Determination of Three Mutants of the Bacterial Photosynthetic Reaction Centers From Rb. Sphaeroides; Altered Proton Transfer Pathways. Structure V. 12 703 2004.
ISSN: ISSN 0969-2126
PubMed: 15062092
DOI: 10.1016/J.STR.2004.03.001