Sodium 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:

Magnesium	(Mg)	4 atoms
Iron	(Fe)	1 atom

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre, PDB code: 2wx5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Hexa-Coordination of A Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 H:Na1252 b:45.1 occ:1.00 O H:HOH2074 2.5 59.4 1.0 O H:ALA137 2.5 63.5 1.0 O H:HOH2075 2.6 64.1 1.0 O H:PHE140 2.8 58.9 1.0 O H:MET134 2.8 51.8 1.0 C H:ALA137 3.6 67.6 1.0 N H:PHE140 3.7 65.0 1.0 C H:PHE140 3.8 56.2 1.0 C H:MET134 3.8 60.9 1.0 N H:GLY139 3.9 70.2 1.0 CA H:PHE140 4.1 58.6 1.0 O H:LYS135 4.2 64.9 1.0 N H:ALA137 4.3 62.6 1.0 CG H:MET134 4.3 63.4 1.0 CB H:PHE140 4.4 62.0 1.0 CA H:ALA137 4.4 66.1 1.0 C H:GLY139 4.4 70.2 1.0 C H:LYS135 4.6 58.7 1.0 N H:ALA138 4.6 69.4 1.0 N H:LYS135 4.6 58.8 1.0 CA H:GLY139 4.6 70.2 1.0 C H:ALA138 4.7 72.8 1.0 CA H:LYS135 4.7 60.4 1.0 CB H:ALA137 4.8 65.6 1.0 CA H:MET134 4.8 61.8 1.0 CA H:ALA138 4.8 73.1 1.0 CB H:MET134 5.0 63.4 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 M:Na1311 b:71.9 occ:1.00 O M:HOH2026 1.7 56.3 1.0 O M:HOH2025 2.3 83.5 1.0 OG M:SER54 2.8 99.9 1.0 ND2 M:ASN28 3.3 68.8 1.0 N M:SER54 3.5 87.4 1.0 CB M:SER54 4.1 91.7 1.0 CA M:GLY53 4.1 82.9 1.0 C M:GLY53 4.2 84.8 1.0 CG M:ASN28 4.3 83.6 1.0 CA M:SER54 4.4 90.1 1.0 OD1 M:ASN28 4.5 81.6 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