Atomistry » Sodium » PDB 4nxz-4obo » 4nyo
Atomistry »
  Sodium »
    PDB 4nxz-4obo »
      4nyo »

Sodium in PDB 4nyo: The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3

Protein crystallography data

The structure of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3, PDB code: 4nyo was solved by B.Bagautdinov, T.H.Tahirov, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.10 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.085, 124.250, 50.458, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.5

Other elements in 4nyo:

The structure of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 (pdb code 4nyo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3, PDB code: 4nyo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4nyo

Go back to Sodium Binding Sites List in 4nyo
Sodium binding site 1 out of 2 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:39.4
occ:1.00
O A:HOH307 2.2 29.7 1.0
O B:HOH308 2.2 27.7 1.0
O B:HOH314 2.3 34.6 1.0
O C:HOH310 2.3 30.2 1.0
O A:HOH335 2.5 29.0 1.0
O C:HOH329 2.5 30.0 1.0
O B:HOH324 4.0 35.8 1.0
OD2 B:ASP86 4.1 22.1 1.0
OD2 A:ASP86 4.1 19.2 1.0
O A:ASP84 4.3 19.7 1.0
OD1 B:ASP86 4.3 21.8 1.0
OD1 A:ASP86 4.3 24.9 1.0
OD2 C:ASP86 4.4 21.3 1.0
OD1 C:ASP86 4.5 20.6 1.0
O C:ASP84 4.5 18.4 1.0
O B:ASP84 4.6 22.0 1.0
CG B:ASP86 4.6 22.6 1.0
CG A:ASP86 4.6 22.6 1.0
CG C:ASP86 4.8 20.7 1.0

Sodium binding site 2 out of 2 in 4nyo

Go back to Sodium Binding Sites List in 4nyo
Sodium binding site 2 out of 2 in the The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The 1.8 Angstrom Crystal Structure of the Periplasmic Divalent Cation Tolerance Protein Cuta From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3001

b:38.7
occ:0.33
O F:HOH307 2.3 26.9 1.0
O E:HOH4115 2.3 19.4 1.0
O D:HOH3138 2.4 34.3 1.0
O D:HOH3142 2.4 29.6 1.0
O F:HOH375 2.4 42.3 1.0
O E:HOH4144 2.4 24.0 1.0
O E:HOH4215 3.6 32.3 1.0
O F:HOH356 3.9 45.7 1.0
OD2 F:ASP86 4.1 18.6 1.0
OD2 D:ASP86 4.2 21.5 1.0
OD2 E:ASP86 4.2 20.7 1.0
O E:ASP84 4.4 18.8 1.0
OD1 F:ASP86 4.4 20.5 1.0
OD1 E:ASP86 4.4 22.0 1.0
OD1 D:ASP86 4.5 20.8 1.0
O F:ASP84 4.5 16.5 1.0
O D:ASP84 4.5 19.6 1.0
CG F:ASP86 4.7 19.7 1.0
O F:HOH320 4.7 27.1 1.0
CG E:ASP86 4.7 19.4 1.0
CG D:ASP86 4.8 20.4 1.0

Reference:

B.Bagautdinov, B.Bagautdinov, T.H.Tahirov, Riken Structural Genomics/Proteomicsinitiative (Rsgi). N/A N/A.
ISSN: ISSN 2053-230X
PubMed: 24699729
DOI: 10.1107/S2053230X14003422
Page generated: Tue Dec 15 06:56:09 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