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Sodium in PDB 2yj7: Crystal Structure of A Hyperstable Protein From the Precambrian Period

Protein crystallography data

The structure of Crystal Structure of A Hyperstable Protein From the Precambrian Period, PDB code: 2yj7 was solved by J.A.Gavira, A.Ingles, B.Ibarra, J.M.Sanchez-Ruiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.449 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.072, 30.189, 59.004, 90.00, 116.81, 90.00
R / Rfree (%) 18.19 / 21.98

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Hyperstable Protein From the Precambrian Period (pdb code 2yj7). 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 A Hyperstable Protein From the Precambrian Period, PDB code: 2yj7:

Sodium binding site 1 out of 1 in 2yj7

Go back to Sodium Binding Sites List in 2yj7
Sodium binding site 1 out of 1 in the Crystal Structure of A Hyperstable Protein From the Precambrian Period


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 A Hyperstable Protein From the Precambrian Period within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1107

b:24.8
occ:1.00
OG A:SER73 2.9 12.6 1.0
O A:PRO75 3.0 9.5 1.0
C A:ILE74 3.4 8.3 1.0
O A:ILE74 3.4 10.1 1.0
CB A:SER73 3.5 10.8 1.0
CG1 A:VAL90 3.5 18.2 1.0
N A:GLY91 3.5 11.3 1.0
N A:ILE74 3.5 6.5 1.0
C A:SER73 3.7 8.8 1.0
N A:PRO75 3.7 8.7 1.0
CA A:ILE74 3.7 8.6 1.0
CA A:GLY91 3.8 13.3 1.0
C A:PRO75 3.8 7.2 1.0
O A:SER73 3.9 10.5 1.0
CD A:PRO75 4.2 12.1 1.0
CA A:SER73 4.2 10.7 1.0
OG1 A:THR76 4.2 8.7 1.0
O A:HOH2042 4.3 26.7 1.0
CA A:PRO75 4.4 6.8 1.0
C A:VAL90 4.4 16.6 1.0
CB A:VAL90 4.7 16.9 1.0
CA A:VAL90 4.8 18.5 1.0
N A:THR76 4.8 6.6 1.0
CG A:PRO75 4.8 10.3 1.0

Reference:

A.Ingles-Prieto, B.Ibarra-Molero, A.Delgado-Delgado, R.Perez-Jimenez, J.M.Fernandez, E.A.Gaucher, J.M.Sanchez-Ruiz, J.A.Gavira. Conservation of Protein Structure Over Four Billion Years Structure V. 21 1690 2013.
ISSN: ISSN 0969-2126
PubMed: 23932589
DOI: 10.1016/J.STR.2013.06.020
Page generated: Tue Dec 15 06:00:40 2020

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