Sodium in PDB 4ud8: ATBBE15

The structure of ATBBE15, PDB code: 4ud8 was solved by B.Daniel, B.Steiner, T.Pavkov-Keller, A.Dordic, A.Gutmann, C.W.Sensen, B.Nidetzky, E.Van Der Graaff, S.Wallner, K.Gruber, P.Macheroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.371 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.596, 94.742, 188.298, 90.00, 90.00, 90.00
R / Rfree (%)	18.35 / 22.09

The structure of ATBBE15 also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Sodium atom in the ATBBE15 (pdb code 4ud8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the ATBBE15, PDB code: 4ud8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the ATBBE15


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of ATBBE15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na906 b:26.3 occ:1.00 O A:HOH2311 2.4 40.9 1.0 O A:HOH2313 2.4 42.3 1.0 O A:THR491 2.5 45.7 1.0 O A:ASN487 2.6 35.1 1.0 O A:GLY489 2.7 52.9 1.0 O A:THR486 3.0 33.8 1.0 C A:ASN487 3.3 33.2 1.0 O A:HOH2310 3.4 51.6 1.0 C A:THR491 3.5 45.0 1.0 C A:GLY489 3.7 50.7 1.0 CA A:ASN487 3.9 30.0 1.0 C A:THR486 4.0 30.1 1.0 N A:GLY489 4.1 43.2 1.0 N A:THR491 4.2 49.4 1.0 CA A:ASP492 4.2 38.7 1.0 N A:ASP492 4.2 41.6 1.0 N A:GLU488 4.3 34.7 1.0 C A:GLU488 4.3 41.6 1.0 N A:ALA493 4.4 33.9 1.0 C A:GLU490 4.4 51.7 1.0 N A:ASN487 4.4 29.4 1.0 CA A:GLY489 4.5 46.2 1.0 CA A:THR491 4.5 47.2 1.0 C A:ASP492 4.5 35.7 1.0 N A:GLU490 4.6 51.8 1.0 O A:HOH2312 4.7 35.0 1.0 O A:GLU488 4.7 40.5 1.0 CA A:GLU488 4.7 41.7 1.0 CA A:GLU490 4.8 54.3 1.0 O A:GLU490 4.8 51.2 1.0

Sodium binding site 2 out of 3 in the ATBBE15


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of ATBBE15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na906 b:26.7 occ:1.00 O B:THR491 2.4 42.2 1.0 O B:HOH2256 2.4 46.0 1.0 O B:HOH2254 2.4 53.0 1.0 O B:THR486 2.5 28.7 1.0 O B:ASN487 2.5 41.4 1.0 O B:GLY489 2.6 52.7 1.0 C B:ASN487 3.3 40.0 1.0 C B:THR491 3.4 42.7 1.0 C B:GLY489 3.6 53.1 1.0 C B:THR486 3.6 27.9 1.0 CA B:ASN487 3.7 32.5 1.0 N B:GLY489 3.8 51.3 1.0 N B:ASN487 4.2 26.0 1.0 CA B:GLY489 4.2 52.0 1.0 N B:THR491 4.2 51.7 1.0 CA B:ASP492 4.2 41.6 1.0 N B:ASP492 4.2 40.5 1.0 N B:GLU488 4.3 44.7 1.0 N B:ALA493 4.3 37.8 1.0 C B:GLU490 4.4 54.9 1.0 CA B:THR491 4.4 47.2 1.0 C B:GLU488 4.4 52.9 1.0 C B:ASP492 4.5 37.9 1.0 O B:HOH2253 4.6 36.7 1.0 N B:GLU490 4.6 54.6 1.0 O B:GLU490 4.6 55.7 1.0 CA B:GLU488 4.7 51.5 1.0 CA B:THR486 4.9 26.6 1.0 CA B:GLU490 5.0 57.0 1.0 NE1 B:TRP496 5.0 33.6 1.0

Sodium binding site 3 out of 3 in the ATBBE15


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of ATBBE15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na907 b:34.6 occ:1.00 O B:HOH2147 2.4 41.8 1.0 O B:HOH2167 2.4 41.3 1.0 O B:HOH2162 2.4 44.1 1.0 O B:CYS342 2.4 34.1 1.0 O B:HOH2164 2.5 37.5 1.0 O B:LYS339 2.6 30.6 1.0 C B:CYS342 3.4 33.4 1.0 O B:HOH2166 3.7 36.9 1.0 C B:LYS339 3.7 31.5 1.0 O B:LYS340 4.1 34.6 1.0 CA B:CYS342 4.2 32.5 1.0 O B:HOH2168 4.2 34.7 1.0 N B:CYS342 4.2 32.3 1.0 CB B:CYS342 4.2 31.5 1.0 CA B:LYS340 4.3 33.3 1.0 C B:LYS340 4.3 33.3 1.0 CG B:LYS339 4.3 39.8 1.0 CD B:LYS339 4.4 41.7 1.0 N B:LYS340 4.4 32.2 1.0 N B:THR343 4.4 30.4 1.0 CA B:THR343 4.6 29.0 1.0 CA B:LYS339 4.8 32.8 1.0 CE B:LYS339 4.8 44.6 1.0

B.Daniel, T.Pavkov-Keller, B.Steiner, A.Dordic, A.Gutmann, B.Nidetzky, C.W.Sensen, E.Van Der Graaff, S.Wallner, K.Gruber, P.Macheroux. Oxidation of Monolignols By Members of the Berberine Bridge Enzyme Family Suggests A Role in Cell Wall Metabolism. J.Biol.Chem. V. 290 18770 2015.
ISSN: ISSN 0021-9258
PubMed: 26037923
DOI: 10.1074/JBC.M115.659631