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Sodium in PDB 7c1z: Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana

Protein crystallography data

The structure of Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana, PDB code: 7c1z 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) 30.72 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.613, 47.917, 91.928, 90.00, 108.95, 90.00
R / Rfree (%) 18.6 / 23.7

Other elements in 7c1z:

The structure of Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana (pdb code 7c1z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana, PDB code: 7c1z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7c1z

Go back to Sodium Binding Sites List in 7c1z
Sodium binding site 1 out of 2 in the Atp Bound 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 Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:47.3
occ:1.00
O A:ALA341 2.2 34.7 1.0
O A:ASP346 2.5 36.3 1.0
O A:SER344 2.6 44.2 1.0
O A:LYS305 2.8 42.4 1.0
C A:ALA341 3.4 39.1 1.0
O A:THR307 3.5 44.9 1.0
C A:SER344 3.5 42.8 1.0
C A:ASP346 3.7 38.2 1.0
C A:LYS305 3.8 42.7 1.0
CB A:LYS305 4.0 49.8 1.0
N A:SER344 4.0 38.6 1.0
CA A:VAL342 4.1 39.0 1.0
CA A:SER344 4.1 39.0 1.0
N A:VAL342 4.2 36.4 1.0
CB A:SER344 4.2 42.5 1.0
CA A:ASN347 4.3 29.9 1.0
C A:ASP345 4.3 49.7 1.0
CA A:ALA341 4.3 31.0 1.0
C A:VAL342 4.3 43.0 1.0
O A:ASN347 4.3 34.5 1.0
CA A:LYS305 4.4 50.9 1.0
N A:ASN347 4.4 37.3 1.0
N A:ASP346 4.5 44.1 1.0
N A:ASP345 4.5 42.8 1.0
CG A:LYS305 4.5 54.1 1.0
O A:ASP345 4.5 54.0 1.0
C A:ASN347 4.5 29.4 1.0
O A:VAL342 4.5 37.8 1.0
CB A:ALA341 4.6 31.0 1.0
CD A:LYS305 4.6 61.4 1.0
C A:THR307 4.6 46.5 1.0
N A:LYS305 4.7 44.8 1.0
CA A:ASP345 4.7 50.8 1.0
OG A:SER344 4.7 45.5 1.0
CA A:ASP346 4.7 49.9 1.0
N A:GLU343 4.9 41.0 1.0
N A:LEU306 4.9 46.1 1.0
C A:LEU306 5.0 44.6 1.0

Sodium binding site 2 out of 2 in 7c1z

Go back to Sodium Binding Sites List in 7c1z
Sodium binding site 2 out of 2 in the Atp Bound 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 Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:48.0
occ:1.00
O B:ALA341 2.3 44.7 1.0
O B:ASP346 2.4 41.5 1.0
O B:THR307 2.5 40.7 1.0
O B:SER344 2.5 49.4 1.0
OG1 B:THR307 2.7 50.5 1.0
O B:LYS305 3.2 57.8 1.0
C B:SER344 3.4 50.2 1.0
C B:ALA341 3.4 39.4 1.0
C B:THR307 3.5 44.9 1.0
C B:ASP346 3.5 42.2 1.0
CB B:THR307 3.7 57.7 1.0
CA B:THR307 4.0 54.8 1.0
N B:THR307 4.0 62.5 1.0
CA B:SER344 4.1 50.6 1.0
C B:ASP345 4.1 50.0 1.0
N B:SER344 4.1 53.8 1.0
C B:LYS305 4.1 58.8 1.0
CB B:SER344 4.1 52.6 1.0
O B:ASP345 4.2 51.9 1.0
N B:ASP346 4.2 44.7 1.0
CA B:VAL342 4.3 43.0 1.0
N B:VAL342 4.3 38.9 1.0
CB B:LYS305 4.3 67.0 1.0
CA B:ALA341 4.3 37.5 1.0
N B:ASP345 4.3 50.5 1.0
CA B:ASN347 4.3 42.2 1.0
N B:ASN347 4.4 46.0 1.0
O B:ASN347 4.4 43.9 1.0
OG B:SER344 4.5 53.9 1.0
CA B:ASP346 4.5 45.5 1.0
CA B:ASP345 4.5 56.8 1.0
C B:ASN347 4.5 41.7 1.0
CB B:ALA341 4.6 36.8 1.0
C B:VAL342 4.6 49.7 1.0
N B:GLY308 4.6 42.8 1.0
C B:LEU306 4.7 62.1 1.0
CA B:LYS305 4.7 66.1 1.0
O B:VAL342 4.9 57.1 1.0
CA B:GLY308 5.0 41.5 1.0

Reference:

S.H.Kim, S.Rhee. Atp Bound Structure of Pseudouridine Kinase (Puki) From Arabidopsis Thaliana To Be Published.
Page generated: Tue Dec 15 17:33:44 2020

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