Atomistry » Sodium » PDB 6qtk-6r7j » 6qxa
Atomistry »
  Sodium »
    PDB 6qtk-6r7j »
      6qxa »

Sodium in PDB 6qxa: Structure of Membrane Bound Pyrophosphatase From Thermotoga Maritima in Complex with Imidodiphosphate and N-[(2-Amino-6-Benzothiazolyl) Methyl]-1H-Indole-2-Carboxamide (Atc)

Protein crystallography data

The structure of Structure of Membrane Bound Pyrophosphatase From Thermotoga Maritima in Complex with Imidodiphosphate and N-[(2-Amino-6-Benzothiazolyl) Methyl]-1H-Indole-2-Carboxamide (Atc), PDB code: 6qxa was solved by K.Vidilaseris, A.Goldman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.48 / 3.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.101, 141.594, 251.980, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 28.4

Other elements in 6qxa:

The structure of Structure of Membrane Bound Pyrophosphatase From Thermotoga Maritima in Complex with Imidodiphosphate and N-[(2-Amino-6-Benzothiazolyl) Methyl]-1H-Indole-2-Carboxamide (Atc) also contains other interesting chemical elements:

Magnesium (Mg) 20 atoms
Potassium (K) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Membrane Bound Pyrophosphatase From Thermotoga Maritima in Complex with Imidodiphosphate and N-[(2-Amino-6-Benzothiazolyl) Methyl]-1H-Indole-2-Carboxamide (Atc) (pdb code 6qxa). 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 Membrane Bound Pyrophosphatase From Thermotoga Maritima in Complex with Imidodiphosphate and N-[(2-Amino-6-Benzothiazolyl) Methyl]-1H-Indole-2-Carboxamide (Atc), PDB code: 6qxa:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6qxa

Go back to Sodium Binding Sites List in 6qxa
Sodium binding site 1 out of 3 in the Structure of Membrane Bound Pyrophosphatase From Thermotoga Maritima in Complex with Imidodiphosphate and N-[(2-Amino-6-Benzothiazolyl) Methyl]-1H-Indole-2-Carboxamide (Atc)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Membrane Bound Pyrophosphatase From Thermotoga Maritima in Complex with Imidodiphosphate and N-[(2-Amino-6-Benzothiazolyl) Methyl]-1H-Indole-2-Carboxamide (Atc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na807

b:70.6
occ:1.00
OG A:SER247 2.4 73.1 1.0
CG A:ASP703 2.7 82.2 1.0
OD1 A:ASP703 2.8 85.0 1.0
OD2 A:ASP703 2.9 83.3 1.0
OD1 A:ASP243 3.0 70.0 1.0
OE1 A:GLU246 3.0 77.8 1.0
NZ A:LYS707 3.3 83.1 1.0
CB A:ASP703 3.4 73.6 1.0
CE A:LYS707 3.4 79.1 1.0
CB A:SER247 3.6 79.0 1.0
C A:ASP703 4.0 69.2 1.0
N A:ILE704 4.0 70.6 1.0
O A:ASP243 4.1 67.0 1.0
CD A:GLU246 4.1 76.2 1.0
CG A:ASP243 4.1 75.7 1.0
CA A:SER247 4.1 74.6 1.0
O A:ASP703 4.3 66.3 1.0
CA A:ASP703 4.3 64.5 1.0
CB A:ALA502 4.3 61.9 1.0
O A:ALA502 4.4 70.8 1.0
N A:SER247 4.4 71.5 1.0
CG1 A:ILE704 4.4 64.0 1.0
OE2 A:GLU246 4.5 82.5 1.0
OD2 A:ASP243 4.5 62.0 1.0
CA A:ILE704 4.6 65.6 1.0
CB A:ALA506 4.7 73.5 1.0
C A:ALA502 4.8 68.5 1.0
CA A:ALA502 4.9 68.1 1.0
CD A:LYS707 4.9 74.0 1.0
C A:ASP243 5.0 71.9 1.0

Sodium binding site 2 out of 3 in 6qxa

Go back to Sodium Binding Sites List in 6qxa
Sodium binding site 2 out of 3 in the Structure of Membrane Bound Pyrophosphatase From Thermotoga Maritima in Complex with Imidodiphosphate and N-[(2-Amino-6-Benzothiazolyl) Methyl]-1H-Indole-2-Carboxamide (Atc)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Membrane Bound Pyrophosphatase From Thermotoga Maritima in Complex with Imidodiphosphate and N-[(2-Amino-6-Benzothiazolyl) Methyl]-1H-Indole-2-Carboxamide (Atc) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na807

b:68.8
occ:1.00
OG B:SER247 2.3 79.1 1.0
OD1 B:ASP243 2.4 74.7 1.0
OE1 B:GLU246 2.6 82.1 1.0
OD1 B:ASP703 2.7 80.5 1.0
CG B:ASP703 2.9 76.5 1.0
OD2 B:ASP703 3.0 78.5 1.0
NZ B:LYS707 3.5 78.5 1.0
CE B:LYS707 3.5 80.9 1.0
CG B:ASP243 3.6 77.0 1.0
O B:ASP243 3.6 78.0 1.0
CB B:SER247 3.7 77.9 1.0
CD B:GLU246 3.7 82.8 1.0
CB B:ASP703 3.8 75.1 1.0
CG1 B:ILE704 3.8 71.9 1.0
N B:ILE704 4.0 69.6 1.0
OD2 B:ASP243 4.1 66.9 1.0
C B:ASP703 4.2 68.7 1.0
OE2 B:GLU246 4.2 80.2 1.0
CA B:SER247 4.2 76.0 1.0
N B:SER247 4.2 81.7 1.0
CA B:ILE704 4.4 67.2 1.0
CB B:ALA502 4.4 84.3 1.0
C B:ASP243 4.5 77.6 1.0
O B:ASP703 4.6 70.6 1.0
CA B:ASP703 4.6 67.9 1.0
CD1 B:ILE704 4.7 80.5 1.0
CB B:ILE704 4.7 61.4 1.0
CB B:ASP243 4.8 77.9 1.0
CA B:ASP243 4.8 76.6 1.0
O B:ALA502 4.9 75.1 1.0
CG B:GLU246 4.9 84.3 1.0
O B:PRO700 4.9 75.2 1.0

Sodium binding site 3 out of 3 in 6qxa

Go back to Sodium Binding Sites List in 6qxa
Sodium binding site 3 out of 3 in the Structure of Membrane Bound Pyrophosphatase From Thermotoga Maritima in Complex with Imidodiphosphate and N-[(2-Amino-6-Benzothiazolyl) Methyl]-1H-Indole-2-Carboxamide (Atc)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Membrane Bound Pyrophosphatase From Thermotoga Maritima in Complex with Imidodiphosphate and N-[(2-Amino-6-Benzothiazolyl) Methyl]-1H-Indole-2-Carboxamide (Atc) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na807

b:74.6
occ:1.00
OG D:SER247 2.3 83.8 1.0
NZ D:LYS707 2.8 78.7 1.0
OD2 D:ASP703 2.9 84.4 1.0
CG D:ASP703 3.0 84.2 1.0
CB D:ALA502 3.3 77.1 1.0
O D:ALA502 3.4 74.7 1.0
CB D:SER247 3.4 84.5 1.0
CE D:LYS707 3.4 81.7 1.0
OD1 D:ASP243 3.5 72.8 1.0
OD1 D:ASP703 3.5 88.7 1.0
CB D:ASP703 3.6 74.6 1.0
C D:ALA502 3.7 75.0 1.0
CA D:ALA502 3.8 74.2 1.0
OE1 D:GLU246 3.9 90.6 1.0
CA D:SER247 4.3 87.6 1.0
CB D:ALA506 4.4 76.2 1.0
CG D:ASP243 4.4 75.2 1.0
OG D:SER505 4.4 88.3 1.0
O D:ASP243 4.5 78.2 1.0
OD2 D:ASP243 4.6 75.5 1.0
N D:ILE503 4.7 69.1 1.0
C D:ASP703 4.7 78.3 1.0
CA D:ASP703 4.8 71.0 1.0
N D:SER247 4.8 82.8 1.0
CD D:LYS707 4.9 77.4 1.0
N D:ILE704 4.9 77.9 1.0
O D:ASP703 5.0 82.3 1.0

Reference:

K.Vidilaseris, A.Kiriazis, A.Turku, A.Khattab, N.G.Johansson, T.O.Leino, P.S.Kiuru, G.Boije Af Gennas, S.Meri, J.Yli-Kauhaluoma, H.Xhaard, A.Goldman. Asymmetry in Catalysis Bythermotoga Maritimamembrane-Bound Pyrophosphatase Demonstrated By A Nonphosphorus Allosteric Inhibitor. Sci Adv V. 5 V7574 2019.
ISSN: ESSN 2375-2548
PubMed: 31131322
DOI: 10.1126/SCIADV.AAV7574
Page generated: Tue Dec 15 12:51:19 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy