Magnesium in PDB 2wx5: Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre

The structure of Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre, PDB code: 2wx5 was solved by M.Marsh, D.Frolov, L.I.Crouch, P.K.Fyfe, B.Robert, R.Van Grondelle, M.R.Jones, A.T.Hadfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.40 / 2.63
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	140.180, 140.180, 185.401, 90.00, 90.00, 120.00
R / Rfree (%)	23.7 / 27.9

The structure of Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre (pdb code 2wx5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre, PDB code: 2wx5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg1282 b:54.7 occ:1.00 MG L:BCL1282 0.0 54.7 1.0 NB L:BCL1282 1.9 56.5 1.0 ND L:BCL1282 2.0 42.9 1.0 O L:HOH2073 2.0 59.0 1.0 NC L:BCL1282 2.0 45.2 1.0 NA L:BCL1282 2.0 49.9 1.0 NE2 M:HIS182 2.1 55.4 1.0 C4C L:BCL1282 3.0 52.0 1.0 C4A L:BCL1282 3.0 47.3 1.0 CD2 M:HIS182 3.0 57.9 1.0 C4D L:BCL1282 3.0 46.0 1.0 C1B L:BCL1282 3.0 56.6 1.0 C1C L:BCL1282 3.0 55.5 1.0 C4B L:BCL1282 3.0 58.3 1.0 C1A L:BCL1282 3.1 50.9 1.0 C1D L:BCL1282 3.1 44.4 1.0 CE1 M:HIS182 3.2 50.4 1.0 CHB L:BCL1282 3.3 50.5 1.0 CHC L:BCL1282 3.4 50.7 1.0 CHD L:BCL1282 3.4 45.1 1.0 NH2 L:ARG181 3.5 82.8 1.0 CHA L:BCL1282 3.5 49.4 1.0 CG M:HIS182 4.2 55.3 1.0 C2B L:BCL1282 4.2 54.1 1.0 C3B L:BCL1282 4.2 57.1 1.0 ND1 M:HIS182 4.2 60.1 1.0 C3D L:BCL1282 4.2 45.0 1.0 C2D L:BCL1282 4.3 45.7 1.0 C3C L:BCL1282 4.3 51.7 1.0 C3A L:BCL1282 4.3 52.6 1.0 C2C L:BCL1282 4.3 50.8 1.0 C2A L:BCL1282 4.4 59.1 1.0 CM5 M:SPN1315 4.7 52.5 1.0 CZ L:ARG181 4.8 75.5 1.0 OBB M:BPH1314 4.8 64.6 1.0 CBA L:BCL1282 5.0 79.8 1.0 CBD L:BCL1282 5.0 53.3 1.0 CMA L:BCL1282 5.0 55.7 1.0

Magnesium binding site 2 out of 4 in the Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg1283 b:63.8 occ:1.00 MG L:BCL1283 0.0 63.8 1.0 ND L:BCL1283 1.9 61.9 1.0 NB L:BCL1283 2.0 60.0 1.0 NC L:BCL1283 2.0 64.0 1.0 NA L:BCL1283 2.1 61.3 1.0 NE2 L:HIS173 2.1 42.1 1.0 C4D L:BCL1283 3.0 62.9 1.0 C4A L:BCL1283 3.0 50.7 1.0 C1C L:BCL1283 3.0 62.4 1.0 C4C L:BCL1283 3.0 53.3 1.0 C1B L:BCL1283 3.0 57.6 1.0 C1D L:BCL1283 3.1 59.8 1.0 C4B L:BCL1283 3.1 59.2 1.0 CE1 L:HIS173 3.1 39.3 1.0 CD2 L:HIS173 3.1 40.7 1.0 C1A L:BCL1283 3.1 55.8 1.0 CHC L:BCL1283 3.4 59.1 1.0 CHB L:BCL1283 3.4 50.9 1.0 CHD L:BCL1283 3.4 54.1 1.0 CHA L:BCL1283 3.5 54.0 1.0 OBB M:BCL1303 3.7 78.7 1.0 CAB M:BCL1303 3.9 72.4 1.0 CBB M:BCL1303 4.2 70.0 1.0 C3D L:BCL1283 4.2 57.7 1.0 C2D L:BCL1283 4.2 60.8 1.0 ND1 L:HIS173 4.2 39.0 1.0 C2B L:BCL1283 4.2 63.5 1.0 CG L:HIS173 4.2 45.0 1.0 C3B L:BCL1283 4.2 62.4 1.0 C3A L:BCL1283 4.3 53.8 1.0 C2C L:BCL1283 4.3 49.8 1.0 C3C L:BCL1283 4.3 46.7 1.0 C2A L:BCL1283 4.4 56.5 1.0 CD2 L:PHE167 4.5 59.5 1.0 C3B M:BCL1303 4.6 65.0 1.0 CMA L:BCL1283 4.8 53.9 1.0 CBD L:BCL1283 4.9 53.4 1.0

Magnesium binding site 3 out of 4 in the Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg1303 b:55.0 occ:1.00 MG M:BCL1303 0.0 55.0 1.0 NB M:BCL1303 2.0 57.6 1.0 ND M:BCL1303 2.0 45.8 1.0 NC M:BCL1303 2.0 50.6 1.0 NA M:BCL1303 2.1 52.5 1.0 NE2 M:HIS202 2.3 48.7 1.0 C1C M:BCL1303 3.0 54.8 1.0 C4D M:BCL1303 3.0 55.7 1.0 C4A M:BCL1303 3.0 47.3 1.0 C4B M:BCL1303 3.0 60.4 1.0 C4C M:BCL1303 3.0 49.0 1.0 C1B M:BCL1303 3.0 54.9 1.0 C1A M:BCL1303 3.1 41.4 1.0 C1D M:BCL1303 3.1 49.6 1.0 CE1 M:HIS202 3.3 48.4 1.0 CD2 M:HIS202 3.3 45.0 1.0 CHC M:BCL1303 3.3 55.3 1.0 CHB M:BCL1303 3.4 50.0 1.0 CHD M:BCL1303 3.5 56.2 1.0 CHA M:BCL1303 3.5 51.0 1.0 CBB L:BCL1283 3.8 63.6 1.0 CAB L:BCL1283 3.9 63.0 1.0 OBB L:BCL1283 4.0 61.5 1.0 C3B M:BCL1303 4.2 65.0 1.0 C2B M:BCL1303 4.2 60.4 1.0 C3D M:BCL1303 4.2 57.5 1.0 C2D M:BCL1303 4.3 49.8 1.0 C2C M:BCL1303 4.3 59.7 1.0 C3C M:BCL1303 4.3 54.7 1.0 C3A M:BCL1303 4.3 49.0 1.0 C2A M:BCL1303 4.4 49.3 1.0 ND1 M:HIS202 4.4 53.0 1.0 CG M:HIS202 4.4 44.4 1.0 C3B L:BCL1283 4.6 62.4 1.0 CMC M:BCL1303 4.9 58.4 1.0 CBD M:BCL1303 4.9 50.9 1.0 CD1 M:ILE206 4.9 58.7 1.0 O2D M:BCL1303 4.9 56.4 1.0

Magnesium binding site 4 out of 4 in the Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg1304 b:38.8 occ:1.00 MG M:BCL1304 0.0 38.8 1.0 NB M:BCL1304 1.9 28.4 1.0 ND M:BCL1304 2.0 14.7 1.0 NC M:BCL1304 2.0 23.4 1.0 NA M:BCL1304 2.0 28.2 1.0 NE2 L:HIS153 2.5 59.6 1.0 C4A M:BCL1304 2.9 34.3 1.0 C1C M:BCL1304 3.0 36.1 1.0 C4D M:BCL1304 3.0 29.3 1.0 C1B M:BCL1304 3.0 36.2 1.0 C4B M:BCL1304 3.0 40.6 1.0 C4C M:BCL1304 3.0 37.5 1.0 C1A M:BCL1304 3.1 39.4 1.0 C1D M:BCL1304 3.1 26.4 1.0 CD2 L:HIS153 3.3 57.0 1.0 CHC M:BCL1304 3.3 32.4 1.0 CHB M:BCL1304 3.4 26.1 1.0 CHA M:BCL1304 3.5 37.8 1.0 CHD M:BCL1304 3.6 24.1 1.0 CE1 L:HIS153 3.6 59.4 1.0 C2B M:BCL1304 4.2 38.9 1.0 C3B M:BCL1304 4.2 42.7 1.0 C3D M:BCL1304 4.3 28.4 1.0 C3A M:BCL1304 4.3 39.8 1.0 C2C M:BCL1304 4.3 38.4 1.0 C2D M:BCL1304 4.3 29.8 1.0 C3C M:BCL1304 4.4 34.2 1.0 C2A M:BCL1304 4.4 40.4 1.0 CG L:HIS153 4.5 69.8 1.0 ND1 L:HIS153 4.6 71.2 1.0 CE2 M:TYR210 4.6 60.2 1.0 CD2 L:LEU154 4.6 58.0 1.0 OBB L:BPH1288 4.7 69.0 1.0 CBC M:BCL1304 4.8 45.6 1.0 C19 L:BPH1288 4.8 59.9 1.0 CBD M:BCL1304 4.9 44.3 1.0 CBA M:BCL1304 5.0 62.9 1.0 CMA M:BCL1304 5.0 45.8 1.0

D.Frolov, M.Marsh, L.I.Crouch, P.K.Fyfe, B.Robert, R.Van Grondelle, A.T.Hadfield, M.R.Jones. Structural and Spectroscopic Consequences of Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre Biochemistry V. 49 1882 2010.
ISSN: ISSN 0006-2960
PubMed: 20112981
DOI: 10.1021/BI901922T