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)

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

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

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 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 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 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

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