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Sodium in PDB 2dek: Crystal Structure of Project Id PH0725 From Pyrococcus Horikoshii OT3 at 1.65 A Resolution

Enzymatic activity of Crystal Structure of Project Id PH0725 From Pyrococcus Horikoshii OT3 at 1.65 A Resolution

All present enzymatic activity of Crystal Structure of Project Id PH0725 From Pyrococcus Horikoshii OT3 at 1.65 A Resolution:
2.1.1.98;

Protein crystallography data

The structure of Crystal Structure of Project Id PH0725 From Pyrococcus Horikoshii OT3 at 1.65 A Resolution, PDB code: 2dek was solved by K.Shimizu, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.79 / 1.65
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.500, 104.500, 137.660, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 22.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Project Id PH0725 From Pyrococcus Horikoshii OT3 at 1.65 A Resolution (pdb code 2dek). 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 Crystal Structure of Project Id PH0725 From Pyrococcus Horikoshii OT3 at 1.65 A Resolution, PDB code: 2dek:

Sodium binding site 1 out of 1 in 2dek

Go back to Sodium Binding Sites List in 2dek
Sodium binding site 1 out of 1 in the Crystal Structure of Project Id PH0725 From Pyrococcus Horikoshii OT3 at 1.65 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Project Id PH0725 From Pyrococcus Horikoshii OT3 at 1.65 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1500

b:25.3
occ:1.00
 O A:HOH1502 2.3 24.7 1.0
O A:HOH1509 2.3 26.2 1.0
OH A:TYR117 2.3 25.7 1.0
O B:HOH268 2.4 25.7 1.0
O B:HOH266 2.5 24.3 1.0
CZ A:TYR117 3.3 24.9 1.0
CE2 A:TYR117 3.7 25.3 1.0
O B:GLY131 3.9 23.3 1.0
OG B:SER133 4.1 25.2 1.0
CD1 B:TYR117 4.1 24.4 1.0
O A:PHE130 4.2 26.1 1.0
CE1 B:TYR117 4.2 25.9 1.0
O A:ILE127 4.3 22.7 1.0
O B:HOH275 4.3 27.3 1.0
CB A:PHE130 4.3 23.1 1.0
O A:HOH1503 4.3 23.1 1.0
CE1 A:TYR117 4.4 23.9 1.0
CB B:PHE130 4.4 23.0 1.0
O A:HOH1506 4.5 28.9 1.0
O B:HOH270 4.7 24.1 1.0
C A:PHE130 4.8 24.9 1.0
O B:PHE130 4.8 24.6 1.0
O A:GLY131 4.8 25.8 1.0

Reference:

K.Shimizu, H.Mizutani, N.Kunishima. Crystal Structure of Project Id PH0725 From Pyrococcus Horikoshii OT3 at 1.65 A Resolution To Be Published.
Page generated: Mon Oct 7 02:14:06 2024

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