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Sodium in PDB 6g3s: Structure of Tellurium-Centred Anderson-Evans Polyoxotungstate (Tew) Bound to the Nucleotide Binding Domain of HSP70. Second Structure of Two Tew-HSP70 Structures Deposited.

Protein crystallography data

The structure of Structure of Tellurium-Centred Anderson-Evans Polyoxotungstate (Tew) Bound to the Nucleotide Binding Domain of HSP70. Second Structure of Two Tew-HSP70 Structures Deposited., PDB code: 6g3s was solved by A.Mac Sweeney, A.Chambovey, M.Wicki, M.Mueller, N.Artico, R.Lange, A.Bijelic, J.Breibeck, A.Rompel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.51 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.900, 70.967, 99.295, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 25

Other elements in 6g3s:

The structure of Structure of Tellurium-Centred Anderson-Evans Polyoxotungstate (Tew) Bound to the Nucleotide Binding Domain of HSP70. Second Structure of Two Tew-HSP70 Structures Deposited. also contains other interesting chemical elements:

Tungsten (W) 24 atoms
Tellurium (Te) 4 atoms
Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Tellurium-Centred Anderson-Evans Polyoxotungstate (Tew) Bound to the Nucleotide Binding Domain of HSP70. Second Structure of Two Tew-HSP70 Structures Deposited. (pdb code 6g3s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Tellurium-Centred Anderson-Evans Polyoxotungstate (Tew) Bound to the Nucleotide Binding Domain of HSP70. Second Structure of Two Tew-HSP70 Structures Deposited., PDB code: 6g3s:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6g3s

Go back to Sodium Binding Sites List in 6g3s
Sodium binding site 1 out of 3 in the Structure of Tellurium-Centred Anderson-Evans Polyoxotungstate (Tew) Bound to the Nucleotide Binding Domain of HSP70. Second Structure of Two Tew-HSP70 Structures Deposited.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Tellurium-Centred Anderson-Evans Polyoxotungstate (Tew) Bound to the Nucleotide Binding Domain of HSP70. Second Structure of Two Tew-HSP70 Structures Deposited. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:25.0
occ:1.00
OG1 A:THR204 2.6 31.8 1.0
O1 A:PO4403 2.7 30.6 1.0
O A:HOH505 2.8 24.9 1.0
OD1 A:ASP199 2.8 47.3 1.0
O A:THR204 2.8 28.6 1.0
NA A:NA406 3.3 44.2 1.0
CG A:ASP199 3.4 43.2 1.0
OD2 A:ASP206 3.5 56.8 1.0
P A:PO4403 3.6 29.6 1.0
O3 A:PO4403 3.6 24.2 1.0
N A:GLY201 3.6 30.1 1.0
C A:THR204 3.6 30.7 1.0
OD2 A:ASP199 3.7 47.7 1.0
O A:ASP199 3.8 33.8 1.0
CB A:THR204 3.9 30.2 1.0
CA A:GLY201 3.9 29.3 1.0
O4 A:PO4403 3.9 27.4 1.0
O A:HOH504 4.0 34.5 1.0
MG A:MG402 4.0 37.0 1.0
O1B A:ADP401 4.1 37.9 1.0
CA A:THR204 4.3 29.8 1.0
C A:ASP199 4.3 32.7 1.0
CB A:ASP199 4.4 34.8 1.0
C A:LEU200 4.5 28.7 1.0
N A:PHE205 4.5 33.9 1.0
N A:THR204 4.6 28.5 1.0
CG A:ASP206 4.6 54.1 1.0
O2B A:ADP401 4.7 31.8 1.0
N A:LEU200 4.7 31.1 1.0
CA A:PHE205 4.8 33.0 1.0
CA A:LEU200 4.8 30.7 1.0
N A:ASP206 4.8 33.5 1.0
C A:GLY201 4.9 29.0 1.0
O2 A:PO4403 4.9 33.8 1.0
CA A:ASP199 5.0 35.4 1.0

Sodium binding site 2 out of 3 in 6g3s

Go back to Sodium Binding Sites List in 6g3s
Sodium binding site 2 out of 3 in the Structure of Tellurium-Centred Anderson-Evans Polyoxotungstate (Tew) Bound to the Nucleotide Binding Domain of HSP70. Second Structure of Two Tew-HSP70 Structures Deposited.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Tellurium-Centred Anderson-Evans Polyoxotungstate (Tew) Bound to the Nucleotide Binding Domain of HSP70. Second Structure of Two Tew-HSP70 Structures Deposited. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:26.6
occ:1.00
O2B A:ADP401 2.4 31.8 1.0
O A:HOH508 2.4 33.6 1.0
O A:TYR15 2.4 31.5 1.0
OD2 A:ASP10 2.5 35.7 1.0
O A:HOH509 2.7 35.3 1.0
O3A A:ADP401 3.0 32.4 1.0
MG A:MG402 3.1 37.0 1.0
PB A:ADP401 3.2 30.1 1.0
CG A:ASP10 3.4 30.6 1.0
O A:HOH503 3.5 30.8 1.0
C A:TYR15 3.5 27.6 1.0
PA A:ADP401 3.7 30.1 1.0
O2A A:ADP401 3.8 32.3 1.0
OD1 A:ASP10 3.9 37.0 1.0
O3B A:ADP401 3.9 33.6 1.0
O1A A:ADP401 4.0 27.0 1.0
CA A:GLY12 4.1 27.9 1.0
CA A:TYR15 4.3 28.1 1.0
O1B A:ADP401 4.4 37.9 1.0
CB A:TYR15 4.4 28.4 1.0
N A:SER16 4.4 26.9 1.0
N A:TYR15 4.5 27.7 1.0
O A:ASP366 4.5 31.0 1.0
O A:HOH505 4.6 24.9 1.0
CA A:SER16 4.6 28.8 1.0
CB A:ASP10 4.6 30.4 1.0
N A:GLY12 4.7 26.2 1.0
O1 A:PO4403 4.9 30.6 1.0
O A:HOH504 4.9 34.5 1.0
O2 A:PO4403 5.0 33.8 1.0

Sodium binding site 3 out of 3 in 6g3s

Go back to Sodium Binding Sites List in 6g3s
Sodium binding site 3 out of 3 in the Structure of Tellurium-Centred Anderson-Evans Polyoxotungstate (Tew) Bound to the Nucleotide Binding Domain of HSP70. Second Structure of Two Tew-HSP70 Structures Deposited.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Tellurium-Centred Anderson-Evans Polyoxotungstate (Tew) Bound to the Nucleotide Binding Domain of HSP70. Second Structure of Two Tew-HSP70 Structures Deposited. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:44.2
occ:1.00
O3 A:PO4403 2.4 24.2 1.0
O1B A:ADP401 2.8 37.9 1.0
OG1 A:THR204 2.9 31.8 1.0
N A:THR204 3.2 28.5 1.0
N A:GLY203 3.2 25.0 1.0
O1 A:PO4403 3.2 30.6 1.0
NA A:NA404 3.3 25.0 1.0
P A:PO4403 3.4 29.6 1.0
N A:GLY202 3.5 30.1 1.0
O3B A:ADP401 3.5 33.6 1.0
PB A:ADP401 3.5 30.1 1.0
CB A:THR204 3.7 30.2 1.0
O A:THR204 3.8 28.6 1.0
CA A:THR204 3.9 29.8 1.0
CA A:GLY203 3.9 24.6 1.0
CA A:GLY201 3.9 29.3 1.0
CB A:THR13 4.0 27.9 1.0
C A:GLY201 4.0 29.0 1.0
C A:GLY203 4.0 25.5 1.0
CG2 A:THR204 4.0 30.4 1.0
O A:HOH505 4.0 24.9 1.0
O2B A:ADP401 4.1 31.8 1.0
C A:GLY202 4.2 25.6 1.0
O2 A:PO4403 4.2 33.8 1.0
OG1 A:THR13 4.2 29.9 1.0
CA A:GLY202 4.2 26.8 1.0
C A:THR204 4.3 30.7 1.0
OG1 A:THR14 4.5 29.6 1.0
N A:GLY201 4.5 30.1 1.0
O4 A:PO4403 4.6 27.4 1.0
CG2 A:THR13 4.7 28.1 1.0
MG A:MG402 4.7 37.0 1.0
N A:THR14 4.9 29.5 1.0
CG2 A:THR14 4.9 27.1 1.0
O A:GLY201 4.9 28.5 1.0
N A:THR13 5.0 27.6 1.0
O3A A:ADP401 5.0 32.4 1.0
CA A:THR13 5.0 28.8 1.0

Reference:

A.Mac Sweeney, A.Chambovey, M.Wicki, M.Muller, N.Artico, R.Lange, A.Bijelic, J.Breibeck, A.Rompel. The Crystallization Additive Hexatungstotellurate Promotes the Crystallization of the HSP70 Nucleotide Binding Domain Into Two Different Crystal Forms. Plos One V. 13 99639 2018.
ISSN: ESSN 1932-6203
PubMed: 29949628
DOI: 10.1371/JOURNAL.PONE.0199639
Page generated: Tue Dec 15 12:16:36 2020

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