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Sodium in PDB 1tko: Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States

Protein crystallography data

The structure of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States, PDB code: 1tko was solved by K.Zeth, S.Offermann, L.O.Essen, D.Oesterhelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.90
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.110, 91.110, 150.040, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 26.3

Other elements in 1tko:

The structure of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States also contains other interesting chemical elements:

Iron (Fe) 38 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States (pdb code 1tko). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States, PDB code: 1tko:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1tko

Go back to Sodium Binding Sites List in 1tko
Sodium binding site 1 out of 2 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:19.2
occ:0.33
OE1 C:GLU59 2.9 42.3 1.0
CG C:GLU59 3.6 39.6 1.0
CD C:GLU59 3.7 41.8 1.0
CG2 C:VAL176 4.0 36.0 1.0
CB C:ALA58 4.2 32.1 1.0
OE2 C:GLU59 4.9 43.3 1.0
OG1 C:THR174 4.9 30.4 1.0

Sodium binding site 2 out of 2 in 1tko

Go back to Sodium Binding Sites List in 1tko
Sodium binding site 2 out of 2 in the Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Iron-Oxo Clusters Biomineralizing on Protein Surfaces. Structural Analysis of H.Salinarum Dpsa in Its Low and High Iron States within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:28.7
occ:1.00
OE1 D:GLU59 2.9 40.1 1.0
OE1 A:GLU59 3.0 44.4 1.0
CG D:GLU59 3.5 40.5 1.0
CG A:GLU59 3.6 40.8 1.0
CD D:GLU59 3.6 40.9 1.0
CD A:GLU59 3.7 43.9 1.0
CG2 A:VAL176 4.2 33.4 1.0
CB D:ALA58 4.2 33.6 1.0
CG2 D:VAL176 4.2 35.0 1.0
CB A:ALA58 4.3 35.6 1.0
OE2 D:GLU59 4.8 43.2 1.0
CB D:GLU59 4.9 36.5 1.0
OE2 A:GLU59 4.9 45.6 1.0
CB A:GLU59 4.9 36.7 1.0
N D:GLU59 4.9 34.6 1.0
OG1 A:THR174 5.0 31.0 1.0
C D:ALA58 5.0 34.0 1.0

Reference:

K.Zeth, S.Offermann, L.O.Essen, D.Oesterhelt. Iron-Oxo Clusters Biomineralizing on Protein Surfaces: Structural Analysis of Halobacterium Salinarum Dpsa in Its Low- and High-Iron States. Proc.Natl.Acad.Sci.Usa V. 101 13780 2004.
ISSN: ISSN 0027-8424
PubMed: 15365182
DOI: 10.1073/PNAS.0401821101
Page generated: Tue Dec 15 05:36:30 2020

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