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Sodium in PDB 9gbt: De Novo Designed Retro-Aldolase 13 (RAD13)

Protein crystallography data

The structure of De Novo Designed Retro-Aldolase 13 (RAD13), PDB code: 9gbt was solved by A.Bijelic, D.Stoll, M.Chakatok, A.Tripp, M.Braun, G.Oberdorfer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.61 / 2.43
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.044, 76.936, 59.619, 90, 91.23, 90
R / Rfree (%) 22.3 / 26.7

Sodium Binding Sites:

The binding sites of Sodium atom in the De Novo Designed Retro-Aldolase 13 (RAD13) (pdb code 9gbt). 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 De Novo Designed Retro-Aldolase 13 (RAD13), PDB code: 9gbt:

Sodium binding site 1 out of 1 in 9gbt

Go back to Sodium Binding Sites List in 9gbt
Sodium binding site 1 out of 1 in the De Novo Designed Retro-Aldolase 13 (RAD13)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of De Novo Designed Retro-Aldolase 13 (RAD13) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:72.3
occ:1.00
O A:GLY38 2.3 67.9 1.0
O A:VAL34 2.6 44.8 1.0
O A:SER39 2.9 71.5 1.0
C A:SER39 3.0 56.7 1.0
C A:GLY38 3.2 64.3 1.0
N A:TYR40 3.3 54.6 1.0
CG2 A:VAL43 3.3 44.5 1.0
CA A:TYR40 3.5 53.9 1.0
O A:LYS35 3.6 47.8 1.0
C A:VAL34 3.6 48.4 1.0
CD1 A:TYR40 3.7 65.5 1.0
CA A:LYS35 3.7 47.3 1.0
CA A:SER39 3.8 56.8 1.0
CG A:TYR40 3.8 68.7 1.0
C A:LYS35 3.9 52.9 1.0
CB A:VAL43 3.9 45.2 1.0
N A:SER39 3.9 58.7 1.0
CE1 A:TYR40 4.0 72.0 1.0
N A:LYS35 4.1 42.0 1.0
N A:GLY38 4.1 46.0 1.0
CB A:TYR40 4.3 61.2 1.0
CA A:GLY38 4.3 48.4 1.0
CD2 A:TYR40 4.3 63.4 1.0
CG1 A:VAL34 4.3 30.1 1.0
CZ A:TYR40 4.5 84.1 1.0
CE2 A:TYR40 4.6 72.6 1.0
C A:TYR40 4.6 53.4 1.0
CG1 A:VAL43 4.7 37.8 1.0
CA A:VAL34 4.8 45.6 1.0
N A:GLU36 4.9 51.2 1.0
C A:ALA37 5.0 45.7 1.0
N A:ALA37 5.0 49.5 1.0
N A:VAL43 5.0 48.3 1.0

Reference:

M.Braun, A.Tripp, M.Chakatok, S.Kaltenbrunner, D.Stoll, A.Bijelic, E.Wael, M.G.Totaro, S.Y.Hoch, M.Hall, M.Aleotti, G.Oberdorfer. Computational Design of Highly Active De Novo Enzymes To Be Published.
Page generated: Mon Aug 18 17:08:09 2025

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