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Sodium in PDB 2pya: Ultra-High Resolution Structure of P. Abyssi Rubredoxin W4L/R5S/A44S

Protein crystallography data

The structure of Ultra-High Resolution Structure of P. Abyssi Rubredoxin W4L/R5S/A44S, PDB code: 2pya was solved by H.Boenisch, R.Ladenstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 0.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.385, 39.812, 45.117, 90.00, 90.00, 90.00
R / Rfree (%) 9.8 / 10.5

Other elements in 2pya:

The structure of Ultra-High Resolution Structure of P. Abyssi Rubredoxin W4L/R5S/A44S also contains other interesting chemical elements:

Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Ultra-High Resolution Structure of P. Abyssi Rubredoxin W4L/R5S/A44S (pdb code 2pya). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ultra-High Resolution Structure of P. Abyssi Rubredoxin W4L/R5S/A44S, PDB code: 2pya:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2pya

Go back to Sodium Binding Sites List in 2pya
Sodium binding site 1 out of 2 in the Ultra-High Resolution Structure of P. Abyssi Rubredoxin W4L/R5S/A44S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ultra-High Resolution Structure of P. Abyssi Rubredoxin W4L/R5S/A44S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na200

b:4.7
occ:0.50
O A:HOH220 1.5 6.1 0.5
O A:HOH230 2.3 10.6 1.0
O A:HOH205 2.4 4.6 1.0
O A:HOH220 2.4 4.4 0.5
OD1 A:ASN22 2.4 4.9 1.0
O A:HOH254 2.5 8.5 0.5
HD22 A:ASN22 3.0 4.8 1.0
CG A:ASN22 3.2 3.9 1.0
O A:HOH254 3.4 2.6 0.5
ND2 A:ASN22 3.4 4.0 1.0
O A:HOH265 3.8 52.8 0.5
O A:HOH215 3.9 6.8 0.5
HA A:PRO40 4.0 3.5 1.0
O A:HOH206 4.1 4.8 1.0
O A:HOH207 4.2 5.5 1.0
HD21 A:ASN22 4.2 4.8 1.0
HB3 A:PRO40 4.3 5.3 0.6
O A:PRO40 4.4 9.8 1.0
CB A:ASN22 4.6 3.6 1.0
HB3 A:ASN22 4.6 4.3 1.0
HB3 A:PRO40 4.7 3.9 0.4
O A:HOH202 4.8 4.0 1.0
CA A:PRO40 4.9 2.9 1.0

Sodium binding site 2 out of 2 in 2pya

Go back to Sodium Binding Sites List in 2pya
Sodium binding site 2 out of 2 in the Ultra-High Resolution Structure of P. Abyssi Rubredoxin W4L/R5S/A44S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ultra-High Resolution Structure of P. Abyssi Rubredoxin W4L/R5S/A44S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:10.9
occ:1.00
O A:GLU31 2.2 6.4 1.0
O A:HOH224 2.3 12.4 1.0
O A:HOH271 2.3 19.9 1.0
O A:HOH270 2.4 28.1 1.0
O A:HOH250 2.4 12.5 1.0
O A:HOH238 2.6 20.3 1.0
C A:GLU31 3.5 4.4 1.0
HA A:ASP32 3.5 5.0 1.0
HB2 A:GLU31 4.1 5.7 1.0
N A:ASP32 4.3 3.5 1.0
CA A:ASP32 4.3 4.1 1.0
HA A:GLU31 4.3 4.9 1.0
O A:HOH239 4.4 15.1 1.0
O A:HOH236 4.4 12.2 1.0
CA A:GLU31 4.5 4.0 1.0
OD1 A:ASP32 4.5 9.2 1.0
HZ1 A:LYS46 4.6 7.2 1.0
HZ3 A:LYS46 4.6 7.2 1.0
O A:LEU33 4.7 4.7 1.0
O A:HOH293 4.8 64.4 1.0
CB A:GLU31 4.8 4.7 1.0
HZ2 A:LYS46 4.9 7.2 1.0
NZ A:LYS46 4.9 4.8 1.0
C A:ASP32 5.0 4.3 1.0

Reference:

H.Bonisch, C.L.Schmidt, P.Bianco, R.Ladenstein. Ultrahigh-Resolution Study on Pyrococcus Abyssi Rubredoxin: II. Introduction of An O-H...Sgamma-Fe Hydrogen Bond Increased the Reduction Potential By 65 Mv. J.Biol.Inorg.Chem. V. 12 1163 2007.
ISSN: ISSN 0949-8257
PubMed: 17712580
DOI: 10.1007/S00775-007-0289-8
Page generated: Tue Dec 15 05:54:17 2020

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