Atomistry » Sodium » PDB 2woi-2x2v » 2wx5
Atomistry »
  Sodium »
    PDB 2woi-2x2v »
      2wx5 »

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

Protein crystallography data

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

Other elements in 2wx5:

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

Sodium Binding Sites:

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 2wx5

Go back to Sodium Binding Sites List in 2wx5
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 2wx5

Go back to Sodium Binding Sites List in 2wx5
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

Reference:

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
Page generated: Tue Dec 15 05:58:34 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy