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Sodium in PDB 2gyq: Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.

Protein crystallography data

The structure of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris., PDB code: 2gyq was solved by J.Osipiuk, E.Evdokimova, M.Kudritska, A.Savchenko, A.Edwards, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.70 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 33.451, 101.125, 103.802, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 17.6

Other elements in 2gyq:

The structure of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. also contains other interesting chemical elements:

Iron (Fe) 5 atoms
Zinc (Zn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. (pdb code 2gyq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris., PDB code: 2gyq:

Sodium binding site 1 out of 1 in 2gyq

Go back to Sodium Binding Sites List in 2gyq
Sodium binding site 1 out of 1 in the Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ycfi, A Putative Structural Protein From Rhodopseudomonas Palustris. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:11.8
occ:1.00
OD2 A:ASP7 2.1 25.1 1.0
O A:HOH547 2.2 46.0 1.0
OD1 A:ASP7 2.4 24.8 1.0
CG A:ASP7 2.6 22.6 1.0
CB A:ASP7 4.1 19.0 1.0
O A:SER5 4.2 19.8 1.0
O A:HOH548 4.4 51.0 1.0
O A:PHE3 4.6 25.6 1.0
CA A:PHE4 4.7 20.2 0.6
CA A:PHE4 4.8 20.9 0.4
C A:PHE4 4.9 19.9 1.0
N A:SER5 4.9 19.6 1.0
CA A:ASP7 5.0 16.9 1.0

Reference:

J.Osipiuk, E.Evdokimova, M.Kudritska, A.Savchenko, A.Edwards, A.Joachimiak. X-Ray Crystal Structure of Ycfi Protein, A Putative Structural Protein From Rhodopseudomonas Palustris. To Be Published.
Page generated: Tue Dec 15 05:50:19 2020

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