Sodium in PDB 4fb1: Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days

All present enzymatic activity of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days:
1.4.9.1; 1.4.99.3;

The structure of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days, PDB code: 4fb1 was solved by E.T.Yukl, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.49 / 2.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.530, 83.520, 107.780, 109.94, 91.54, 105.78
R / Rfree (%)	16.2 / 22.2

The structure of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days (pdb code 4fb1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days, PDB code: 4fb1:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:60.1 occ:1.00 O A:LEU250 2.3 51.8 1.0 O A:ILE255 2.4 58.7 1.0 O A:ARG252 2.8 51.0 1.0 C A:ILE255 3.5 58.0 1.0 C A:LEU250 3.5 50.6 1.0 C A:ARG252 3.7 50.8 1.0 N A:ILE255 3.8 55.4 1.0 OE2 A:GLU256 3.9 75.7 1.0 N A:GLY254 3.9 54.1 1.0 CA A:ILE255 4.0 55.7 1.0 C A:ALA251 4.1 51.6 1.0 CB A:ILE255 4.2 54.6 1.0 CA A:PRO253 4.2 53.3 1.0 N A:PRO253 4.3 51.6 1.0 O A:ALA251 4.3 52.2 1.0 CD1 A:LEU250 4.3 50.6 1.0 C A:PRO253 4.3 53.5 1.0 CA A:ALA251 4.4 51.4 1.0 N A:ARG252 4.4 50.2 1.0 N A:ALA251 4.4 50.1 1.0 C A:GLY254 4.5 55.3 1.0 CA A:LEU250 4.5 49.2 1.0 N A:GLU256 4.6 59.7 1.0 CA A:ARG252 4.7 49.9 1.0 CA A:GLY254 4.8 55.4 1.0 CD A:GLU256 4.8 76.0 1.0 CG A:LEU250 4.9 52.5 1.0 CA A:GLU256 4.9 62.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:44.8 occ:1.00 O B:LEU250 2.2 38.0 1.0 O B:ILE255 2.3 41.0 1.0 O B:ARG252 2.7 36.6 1.0 C B:LEU250 3.3 37.2 1.0 C B:ILE255 3.4 41.9 1.0 C B:ARG252 3.7 37.9 1.0 N B:ILE255 3.8 41.8 1.0 C B:ALA251 3.9 38.5 1.0 CA B:ILE255 4.0 41.0 1.0 N B:ARG252 4.0 37.3 1.0 CB B:ILE255 4.1 39.8 1.0 CA B:ALA251 4.2 38.5 1.0 CD1 B:LEU250 4.2 34.6 1.0 N B:ALA251 4.2 37.7 1.0 O B:ALA251 4.3 39.3 1.0 N B:GLY254 4.3 43.2 1.0 CA B:LEU250 4.3 36.2 1.0 CA B:PRO253 4.3 41.4 1.0 OE2 B:GLU256 4.4 58.7 1.0 N B:PRO253 4.4 40.1 1.0 CA B:ARG252 4.5 37.0 1.0 CG B:LEU250 4.6 37.8 1.0 N B:GLU256 4.6 42.8 1.0 C B:PRO253 4.6 41.8 1.0 CD B:GLU256 4.7 55.8 1.0 C B:GLY254 4.7 43.3 1.0 OE1 B:GLU256 4.8 59.6 1.0 CA B:GLU256 4.9 45.2 1.0 O B:LEU249 4.9 33.5 1.0 CB B:LEU250 5.0 35.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 60 Days within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:48.2 occ:1.00 OG1 B:THR233 2.3 39.0 1.0 OD1 B:ASN231 2.4 37.1 1.0 O B:HOH609 2.5 26.4 1.0 CG B:ASN231 3.3 36.9 1.0 CB B:THR233 3.6 41.4 1.0 ND2 B:ASN231 3.6 26.4 1.0 CG2 B:THR233 3.9 38.9 1.0 N B:THR233 4.1 39.6 1.0 CA B:THR233 4.3 39.3 1.0 N B:ALA234 4.5 35.5 1.0 CB B:ASN231 4.8 34.1 1.0 C B:THR233 4.9 37.8 1.0 N B:GLU232 5.0 36.4 1.0

E.T.Yukl, F.Liu, J.Krzystek, S.Shin, L.M.Jensen, V.L.Davidson, C.M.Wilmot, A.Liu. Diradical Intermediate Within the Context of Tryptophan Tryptophylquinone Biosynthesis. Proc.Natl.Acad.Sci.Usa V. 110 4569 2013.
ISSN: ISSN 0027-8424
PubMed: 23487750
DOI: 10.1073/PNAS.1215011110