Sodium in PDB 6wb7: Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp

All present enzymatic activity of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp:
2.7.1.187;

The structure of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp, PDB code: 6wb7 was solved by P.D.Jeffrey, J.N.Balaich, M.A.Estrella, M.S.Donia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.53 / 2.44
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.545, 50.268, 127.794, 89.06, 80.18, 71.81
R / Rfree (%)	18.7 / 25

The structure of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp also contains other interesting chemical elements:

Manganese

(Mn)

5 atoms

The binding sites of Sodium atom in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp (pdb code 6wb7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp, PDB code: 6wb7:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:29.9 occ:1.00 O A:HOH432 2.5 29.4 1.0 O A:ASN244 2.5 37.6 1.0 O A:ASP242 2.5 32.3 1.0 O A:ALA278 2.8 30.3 1.0 O A:ILE281 3.3 40.6 1.0 C A:ASP242 3.4 33.4 1.0 C A:ASN244 3.5 36.0 1.0 CB A:ASP242 3.7 40.2 1.0 N A:ASN244 3.7 25.8 1.0 CG A:ASP242 3.8 38.4 1.0 C A:ALA278 3.9 28.9 1.0 CA A:ASN244 4.0 29.8 1.0 OD2 A:ASP242 4.1 44.5 1.0 CA A:ASP242 4.1 37.0 1.0 CB A:ASN244 4.1 32.8 1.0 O A:HOH500 4.2 16.3 1.0 OD1 A:ASP242 4.3 37.1 1.0 C A:ILE281 4.3 44.3 1.0 C A:SER243 4.4 30.9 1.0 N A:SER243 4.4 30.0 1.0 CB A:ILE281 4.5 35.4 1.0 CA A:CYS279 4.7 25.9 1.0 CA A:SER243 4.7 37.5 1.0 N A:ILE281 4.7 36.1 1.0 N A:CYS279 4.7 26.5 1.0 CA A:ILE281 4.7 34.3 1.0 N A:GLY245 4.7 26.1 1.0 N A:ASP242 4.8 30.8 1.0 CA A:ALA278 4.8 30.1 1.0 C A:CYS279 4.9 27.2 1.0 CB A:ALA278 4.9 27.0 1.0

Sodium binding site 2 out of 4 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:27.6 occ:1.00 O B:ASP242 2.5 31.3 1.0 O B:ASN244 2.5 32.9 1.0 O B:ALA278 2.9 26.0 1.0 O B:ILE281 3.1 40.4 1.0 C B:ASP242 3.5 27.4 1.0 C B:ASN244 3.6 32.3 1.0 CB B:ASP242 3.8 35.6 1.0 N B:ASN244 4.0 29.8 1.0 C B:ALA278 4.0 27.6 1.0 CG B:ASP242 4.0 31.3 1.0 OD2 B:ASP242 4.2 40.4 1.0 C B:ILE281 4.2 36.3 1.0 CA B:ASN244 4.2 29.6 0.5 CA B:ASN244 4.2 30.2 0.5 CA B:ASP242 4.2 32.3 1.0 CB B:ILE281 4.4 30.1 1.0 CB B:ASN244 4.4 29.9 0.5 CB B:ASN244 4.4 29.2 0.5 C B:SER243 4.5 30.7 1.0 O B:HOH407 4.5 29.1 1.0 N B:SER243 4.5 23.7 1.0 O B:HOH433 4.6 31.8 1.0 OD1 B:ASP242 4.7 30.8 1.0 CA B:ILE281 4.7 31.6 1.0 N B:ILE281 4.7 32.5 1.0 CA B:CYS279 4.7 32.5 1.0 N B:GLY245 4.8 25.3 1.0 CA B:SER243 4.8 31.7 1.0 N B:CYS279 4.8 31.0 1.0 N B:ASP242 4.9 26.8 1.0 CA B:ALA278 4.9 31.0 1.0

Sodium binding site 3 out of 4 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Na304 b:52.6 occ:1.00 O C:ASN244 2.5 46.1 1.0 O C:ASP242 3.4 36.6 1.0 O C:ALA278 3.5 34.8 1.0 O C:ILE281 3.5 40.0 1.0 OD2 C:ASP242 3.7 56.2 1.0 C C:ASN244 3.7 38.5 1.0 CB C:ASP242 4.0 48.5 1.0 CG C:ASP242 4.1 51.2 1.0 C C:ASP242 4.2 35.8 1.0 C C:ALA278 4.4 31.5 1.0 C C:ILE281 4.5 43.4 1.0 CA C:ASN244 4.6 37.3 1.0 N C:ASN244 4.6 36.4 1.0 O C:PRO282 4.6 57.5 1.0 CB C:ILE281 4.7 36.9 1.0 N C:GLY245 4.7 24.6 1.0 CA C:ASP242 4.7 33.5 1.0 CA C:GLY245 4.7 27.0 1.0 CB C:ASN244 4.8 32.0 1.0 CA C:ALA283 4.9 60.2 1.0 C C:PRO282 4.9 52.1 1.0

Sodium binding site 4 out of 4 in the Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Acarbose Kinase Acbk As A Complex with Acarbose and Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Na304 b:31.1 occ:1.00 O D:ASP242 2.4 41.4 1.0 O D:ASN244 2.4 39.3 1.0 O D:ALA278 2.6 40.9 1.0 O D:ILE281 2.7 37.9 1.0 OD2 D:ASP242 3.5 61.6 1.0 C D:ASP242 3.5 44.4 1.0 C D:ASN244 3.5 38.3 1.0 CG D:ASP242 3.7 52.1 1.0 N D:ASN244 3.7 48.0 1.0 C D:ALA278 3.7 35.7 1.0 CB D:ASP242 3.8 49.3 1.0 C D:ILE281 3.8 36.5 1.0 CA D:ASN244 4.0 43.5 1.0 CA D:ASP242 4.2 49.6 1.0 CB D:ASN244 4.3 48.0 1.0 CB D:ILE281 4.3 41.0 1.0 CA D:ILE281 4.4 42.1 1.0 OD1 D:ASP242 4.4 50.6 1.0 C D:SER243 4.4 46.5 1.0 N D:ILE281 4.5 39.8 1.0 N D:SER243 4.5 42.7 1.0 CA D:CYS279 4.5 34.3 1.0 N D:CYS279 4.5 37.0 1.0 N D:GLY245 4.6 40.0 1.0 CA D:ALA278 4.7 34.4 1.0 CA D:SER243 4.7 42.6 1.0 C D:PRO282 4.8 51.1 1.0 O D:PRO282 4.8 55.7 1.0 C D:CYS279 4.8 32.0 1.0 CB D:ALA278 4.8 32.6 1.0 N D:ASP242 4.8 45.5 1.0 N D:PRO282 4.9 46.2 1.0

J.N.Balaich, M.A.Estrella, P.D.Jeffrey, A.Biswas, A.Korennykh, M.S.Donia. Acarbose Sugar Kinases Encoded By the Human Microbiome Mediates Microbial Competition For Complex Carbohydrates To Be Published.