Sodium in PDB 4l1q: Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex

All present enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.99.3;

The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 4l1q was solved by E.Y.Yukl, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.35 / 1.92
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 / 20.7

The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex 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 the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex (pdb code 4l1q). 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 the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 4l1q:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex


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 the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:47.6 occ:1.00 O A:LEU250 2.2 38.6 1.0 O A:HOH674 2.2 50.3 1.0 O A:ARG252 2.5 39.9 1.0 O A:HOH724 2.5 42.6 1.0 O A:ILE255 2.5 45.9 1.0 O A:HOH511 2.7 53.1 1.0 C A:LEU250 3.4 37.7 1.0 C A:ARG252 3.4 37.5 1.0 C A:ILE255 3.6 42.2 1.0 C A:ALA251 3.8 39.7 1.0 N A:ILE255 3.9 42.6 1.0 O A:ALA251 4.0 37.5 1.0 CA A:PRO253 4.0 42.9 1.0 N A:ARG252 4.0 40.3 1.0 CA A:ALA251 4.1 40.2 1.0 N A:PRO253 4.1 40.5 1.0 N A:ALA251 4.1 38.6 1.0 CA A:ILE255 4.2 38.6 1.0 N A:GLY254 4.2 43.8 1.0 CB A:ILE255 4.3 39.7 1.0 OE2 A:GLU256 4.3 73.7 1.0 CA A:ARG252 4.3 38.8 1.0 C A:PRO253 4.4 42.8 1.0 CA A:LEU250 4.4 36.1 1.0 CD1 A:LEU250 4.6 42.1 1.0 CD A:GLU256 4.7 67.2 1.0 OE1 A:GLU256 4.7 74.9 1.0 N A:GLU256 4.8 43.8 1.0 C A:GLY254 4.8 42.2 1.0 CG A:LEU250 4.9 41.4 1.0 O A:LEU249 4.9 33.8 1.0 O A:HOH698 5.0 51.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex


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 the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:30.3 occ:1.00 OG1 B:THR233 2.2 33.2 1.0 OD1 B:ASN231 2.3 23.6 1.0 O B:HOH813 2.3 32.1 1.0 O B:HOH820 2.5 33.6 1.0 O B:HOH662 2.5 32.4 1.0 O B:HOH718 2.5 26.9 1.0 CG B:ASN231 3.1 25.9 1.0 ND2 B:ASN231 3.3 24.2 1.0 CB B:THR233 3.4 33.3 1.0 CG2 B:THR233 3.9 35.6 1.0 N B:THR233 3.9 27.4 1.0 O B:HOH733 4.0 38.5 1.0 O B:HOH801 4.1 42.7 1.0 CA B:THR233 4.1 30.0 1.0 N B:ALA234 4.3 26.9 1.0 O B:HOH752 4.3 33.0 1.0 CB B:ASN231 4.5 23.7 1.0 O B:HOH720 4.5 30.8 1.0 O B:HOH705 4.6 45.4 1.0 C B:THR233 4.7 28.4 1.0 C B:ASN231 4.7 22.9 1.0 N B:GLU232 4.7 25.9 1.0 O B:HOH805 4.7 50.4 1.0 CA B:ASN231 4.7 23.0 1.0 O B:HOH765 4.8 34.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex


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 the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:31.2 occ:1.00 O B:ILE255 2.1 30.2 1.0 O B:LEU250 2.3 26.1 1.0 O B:HOH830 2.3 36.3 1.0 O B:HOH681 2.6 42.0 1.0 O B:HOH777 2.6 39.7 1.0 O B:ARG252 2.8 25.4 1.0 C B:ILE255 3.2 31.9 1.0 C B:LEU250 3.4 25.2 1.0 N B:ILE255 3.7 31.6 1.0 C B:ARG252 3.7 27.4 1.0 CA B:ILE255 3.9 30.8 1.0 C B:ALA251 3.9 27.2 1.0 N B:GLY254 4.1 36.3 1.0 CB B:ILE255 4.1 28.9 1.0 N B:ARG252 4.1 25.4 1.0 O B:ALA251 4.2 27.3 1.0 CA B:ALA251 4.2 27.8 1.0 CA B:PRO253 4.3 33.8 1.0 OE2 B:GLU256 4.3 51.4 1.0 N B:ALA251 4.3 26.4 1.0 N B:GLU256 4.3 33.0 1.0 CD1 B:LEU250 4.4 28.6 1.0 CA B:LEU250 4.4 25.8 1.0 N B:PRO253 4.4 33.2 1.0 C B:PRO253 4.4 33.4 1.0 OE1 B:GLU256 4.4 57.4 1.0 CD B:GLU256 4.5 47.0 1.0 CA B:ARG252 4.6 23.4 1.0 C B:GLY254 4.6 34.3 1.0 CG B:LEU250 4.7 26.8 1.0 CA B:GLU256 4.8 36.0 1.0 CA B:GLY254 4.9 38.2 1.0 O B:LEU249 4.9 23.6 1.0

N.Abu Tarboush, E.T.Yukl, S.Shin, M.Feng, C.M.Wilmot, V.L.Davidson. Carboxyl Group of GLU113 Is Required For Stabilization of the Diferrous and Bis-Fe(IV) States of Maug. Biochemistry V. 52 6358 2013.
ISSN: ISSN 0006-2960
PubMed: 23952537
DOI: 10.1021/BI400905S