Sodium in PDB 4a3u: X-Structure of the Old Yellow Enzyme Homologue From Zymomonas Mobilis (Ncr)

The structure of X-Structure of the Old Yellow Enzyme Homologue From Zymomonas Mobilis (Ncr), PDB code: 4a3u was solved by H.W.Hoeffken, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.06 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.600, 90.500, 76.600, 90.00, 108.30, 90.00
R / Rfree (%)	23.9 / 30.3

The structure of X-Structure of the Old Yellow Enzyme Homologue From Zymomonas Mobilis (Ncr) also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Sodium atom in the X-Structure of the Old Yellow Enzyme Homologue From Zymomonas Mobilis (Ncr) (pdb code 4a3u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Structure of the Old Yellow Enzyme Homologue From Zymomonas Mobilis (Ncr), PDB code: 4a3u:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Structure of the Old Yellow Enzyme Homologue From Zymomonas Mobilis (Ncr)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Structure of the Old Yellow Enzyme Homologue From Zymomonas Mobilis (Ncr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1360 b:24.0 occ:1.00 OE2 B:GLU219 2.0 13.5 1.0 ND1 A:HIS89 2.6 11.0 1.0 CD B:GLU219 2.7 12.4 1.0 OE1 B:GLU219 2.9 14.8 1.0 O A:HOH2090 3.4 20.2 1.0 O B:GLY11 3.4 15.1 1.0 CG A:HIS89 3.6 10.9 1.0 CE1 A:HIS89 3.6 10.8 1.0 CA A:GLN86 3.7 12.2 1.0 CB A:HIS89 3.8 10.8 1.0 NE2 A:GLN86 3.8 13.8 1.0 NH2 B:ARG9 3.8 18.1 1.0 O A:THR85 3.9 12.6 1.0 CA B:ALA12 3.9 13.7 1.0 N A:GLN86 4.0 12.0 1.0 C B:GLY11 4.1 14.5 1.0 CD A:GLN86 4.1 15.2 1.0 C A:THR85 4.1 11.7 1.0 CG B:GLU219 4.1 11.5 1.0 OE1 A:GLN86 4.2 19.6 1.0 N B:ALA12 4.3 13.7 1.0 CB B:ALA12 4.5 12.7 1.0 OG1 A:THR85 4.6 11.0 1.0 O B:HOH2006 4.6 9.8 1.0 O A:HOH2094 4.6 9.7 1.0 CB A:GLN86 4.6 12.9 1.0 O A:GLY165 4.6 6.2 1.0 O A:GLN86 4.7 11.2 1.0 CB B:GLU219 4.7 10.4 1.0 C A:GLN86 4.7 11.8 1.0 NE2 A:HIS89 4.7 10.5 1.0 CD2 A:HIS89 4.7 11.0 1.0 CB A:THR85 4.8 11.3 1.0

Sodium binding site 2 out of 3 in the X-Structure of the Old Yellow Enzyme Homologue From Zymomonas Mobilis (Ncr)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Structure of the Old Yellow Enzyme Homologue From Zymomonas Mobilis (Ncr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1360 b:28.6 occ:1.00 O B:ALA141 2.3 13.3 1.0 O B:HOH2100 2.7 23.8 1.0 NH1 B:ARG140 3.3 15.4 1.0 C B:ALA141 3.4 13.8 1.0 CB B:ARG140 3.7 14.5 1.0 N B:ALA141 3.8 13.7 1.0 CG B:ARG140 3.9 14.5 1.0 CD B:ARG140 4.1 15.0 1.0 CA B:ALA141 4.1 13.3 1.0 C B:ARG140 4.2 13.3 1.0 CA B:ARG140 4.4 13.6 1.0 N B:LEU142 4.5 13.7 1.0 CZ B:ARG140 4.5 14.6 1.0 CB B:ALA141 4.6 13.7 1.0 NE B:ARG140 4.8 15.3 1.0 N B:ARG143 4.8 15.8 1.0 CG B:ARG143 4.8 19.0 1.0 CA B:LEU142 4.8 14.0 1.0 C B:LEU142 4.9 14.4 1.0

Sodium binding site 3 out of 3 in the X-Structure of the Old Yellow Enzyme Homologue From Zymomonas Mobilis (Ncr)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Structure of the Old Yellow Enzyme Homologue From Zymomonas Mobilis (Ncr) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1361 b:28.8 occ:1.00 O B:ALA120 2.4 12.2 1.0 ND1 B:HIS189 2.7 18.7 1.0 CE1 B:HIS189 3.3 19.7 1.0 CB B:SER119 3.4 13.1 1.0 C B:ALA120 3.5 12.2 1.0 CB B:SER121 3.9 12.2 1.0 CG B:HIS189 3.9 17.4 1.0 C B:SER119 4.1 13.0 1.0 N B:ALA120 4.3 12.8 1.0 O B:SER119 4.3 12.6 1.0 N B:SER121 4.4 12.5 1.0 CA B:SER119 4.4 12.8 1.0 CA B:SER121 4.4 12.7 1.0 CB B:HIS189 4.4 17.1 1.0 O B:THR187 4.5 10.8 1.0 OG B:SER119 4.5 12.1 1.0 CA B:ALA120 4.5 12.4 1.0 NE2 B:HIS189 4.6 19.9 1.0 OG B:SER121 4.7 11.1 1.0 O B:HOH2092 4.9 10.3 1.0 CD2 B:HIS189 4.9 19.2 1.0

S.Reich, H.W.Hoeffken, B.Rosche, B.M.Nestl, B.Hauer. Crystal Structure Determination and Mutagenesis Analysis of the Ene Reductase Ncr. Chembiochem V. 13 2400 2012.
ISSN: ISSN 1439-4227
PubMed: 23033175
DOI: 10.1002/CBIC.201200404