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Sodium in PDB 7c1x: Unliganded Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana

Protein crystallography data

The structure of Unliganded Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana, PDB code: 7c1x was solved by S.H.Kim, S.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.686, 48.352, 92.751, 90.00, 109.14, 90.00
R / Rfree (%) 20.8 / 24.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Unliganded Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana (pdb code 7c1x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Unliganded Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana, PDB code: 7c1x:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7c1x

Go back to Sodium Binding Sites List in 7c1x
Sodium binding site 1 out of 2 in the Unliganded Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Unliganded Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:67.4
occ:1.00
O A:ALA341 2.4 47.1 1.0
O A:ASP346 2.5 60.1 1.0
O A:LYS305 3.0 55.1 1.0
O A:SER344 3.1 67.2 1.0
O A:THR307 3.3 60.7 1.0
C A:ALA341 3.5 45.9 1.0
C A:ASP346 3.6 60.0 1.0
C A:SER344 3.8 65.3 1.0
CB A:LYS305 3.9 71.1 1.0
C A:LYS305 3.9 56.5 1.0
CE A:LYS305 4.0 83.0 1.0
CA A:VAL342 4.0 56.5 1.0
N A:VAL342 4.2 50.0 1.0
N A:SER344 4.2 60.0 1.0
CA A:ASN347 4.2 50.8 1.0
C A:VAL342 4.3 56.9 1.0
N A:ASN347 4.3 57.2 1.0
CA A:SER344 4.3 57.5 1.0
O A:ASN347 4.4 43.9 1.0
N A:ASP346 4.4 70.0 1.0
CA A:LYS305 4.4 66.4 1.0
CB A:SER344 4.4 48.3 1.0
O A:VAL342 4.4 55.5 1.0
C A:THR307 4.5 61.2 1.0
C A:ASN347 4.6 46.2 1.0
CA A:ALA341 4.6 47.2 1.0
N A:ASP345 4.6 64.4 1.0
CA A:ASP346 4.6 66.0 1.0
N A:LYS305 4.7 68.0 1.0
C A:ASP345 4.7 72.2 1.0
OG A:SER344 4.7 50.4 1.0
CA A:ASP345 4.7 71.0 1.0
NZ A:LYS305 4.8 85.2 1.0
CG A:LYS305 4.9 75.0 1.0
CB A:ALA341 4.9 42.4 1.0
N A:GLU343 5.0 54.8 1.0
N A:THR307 5.0 57.4 1.0
N A:LEU306 5.0 59.4 1.0

Sodium binding site 2 out of 2 in 7c1x

Go back to Sodium Binding Sites List in 7c1x
Sodium binding site 2 out of 2 in the Unliganded Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Unliganded Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:66.5
occ:1.00
O B:SER344 2.4 87.5 1.0
O B:ALA341 2.4 60.3 1.0
O B:ASP346 2.7 59.0 1.0
OG1 B:THR307 2.8 79.3 1.0
O B:THR307 3.0 66.5 1.0
O B:LYS305 3.0 74.0 1.0
C B:SER344 3.1 83.2 1.0
CA B:ASP345 3.4 86.1 1.0
N B:ASP345 3.6 81.9 1.0
C B:ALA341 3.6 61.2 1.0
C B:ASP345 3.8 84.5 1.0
C B:ASP346 3.8 65.9 1.0
N B:ASP346 3.8 92.3 1.0
CB B:THR307 3.9 75.8 1.0
C B:THR307 4.0 65.5 1.0
C B:LYS305 4.0 75.4 1.0
CA B:SER344 4.1 74.2 1.0
CA B:THR307 4.3 70.0 1.0
N B:THR307 4.3 68.5 1.0
CB B:SER344 4.3 73.1 1.0
N B:SER344 4.3 70.0 1.0
CA B:VAL342 4.3 67.4 1.0
OG B:SER344 4.4 75.5 1.0
OD1 B:ASP345 4.4 0.5 1.0
N B:VAL342 4.4 60.3 1.0
CB B:LYS305 4.5 84.8 1.0
CA B:ASP346 4.5 79.5 1.0
C B:VAL342 4.6 75.7 1.0
O B:ASN347 4.6 57.8 1.0
CA B:ALA341 4.6 61.8 1.0
CA B:LYS305 4.6 81.3 1.0
O B:ASP345 4.6 89.6 1.0
O B:VAL342 4.6 76.7 1.0
N B:ASN347 4.6 64.7 1.0
CA B:ASN347 4.6 58.6 1.0
CB B:ASP345 4.7 95.8 1.0
N B:LYS305 4.7 89.2 1.0
C B:ASN347 4.8 58.2 1.0
C B:LEU306 4.9 70.6 1.0
N B:LEU306 5.0 79.2 1.0

Reference:

S.H.Kim, S.Rhee. Unliganded Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana To Be Published.
Page generated: Tue Dec 15 17:32:53 2020

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