Sodium in PDB 4grx: Structure of An Omega-Aminotransferase From Paracoccus Denitrificans

The structure of Structure of An Omega-Aminotransferase From Paracoccus Denitrificans, PDB code: 4grx was solved by C.Rausch, A.Lerchner, A.Schiefner, A.Skerra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.83 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.790, 103.630, 145.430, 90.00, 98.88, 90.00
R / Rfree (%)	17.8 / 22.7

The binding sites of Sodium atom in the Structure of An Omega-Aminotransferase From Paracoccus Denitrificans (pdb code 4grx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of An Omega-Aminotransferase From Paracoccus Denitrificans, PDB code: 4grx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of An Omega-Aminotransferase From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of An Omega-Aminotransferase From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:28.2 occ:1.00 O A:HOH674 2.2 36.6 1.0 O A:PHE106 2.3 49.6 1.0 O A:VAL101 2.4 44.1 1.0 O A:SER104 2.5 44.0 1.0 O A:GLU102 2.8 45.8 1.0 C A:PHE106 3.4 50.1 1.0 C A:GLU102 3.4 45.2 1.0 C A:SER104 3.5 42.1 1.0 C A:VAL101 3.6 43.9 1.0 OG A:SER104 3.6 41.8 1.0 CA A:GLU102 3.7 46.3 1.0 N A:PHE106 3.8 45.4 1.0 N A:SER104 4.0 40.9 1.0 C A:PRO105 4.1 45.5 1.0 N A:GLU102 4.1 44.8 1.0 CA A:SER104 4.2 40.5 1.0 CA A:PHE106 4.2 47.5 1.0 CB A:SER104 4.4 40.4 1.0 N A:PRO105 4.4 42.1 1.0 N A:ASP107 4.4 44.4 1.0 N A:VAL103 4.5 43.0 1.0 O A:PRO105 4.5 47.5 1.0 CA A:PRO105 4.5 43.9 1.0 CA A:ASP107 4.6 48.0 1.0 C A:VAL103 4.7 40.9 1.0 CG1 A:VAL101 4.7 45.5 1.0 C A:ASP107 4.8 47.8 1.0 O A:ASP107 4.8 49.4 1.0 CA A:VAL101 4.8 42.7 1.0 CB A:PHE106 5.0 46.2 1.0

Sodium binding site 2 out of 4 in the Structure of An Omega-Aminotransferase From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of An Omega-Aminotransferase From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:29.9 occ:1.00 O B:GLU102 2.3 27.1 1.0 O B:HOH650 2.4 29.0 1.0 O B:PHE106 2.4 25.5 1.0 O B:HOH632 2.4 20.2 1.0 O B:SER104 2.6 25.3 1.0 O B:VAL101 2.6 24.8 1.0 C B:GLU102 3.2 26.7 1.0 CA B:GLU102 3.5 27.1 1.0 C B:PHE106 3.6 25.8 1.0 C B:VAL101 3.7 24.9 1.0 C B:SER104 3.7 24.7 1.0 OG B:SER104 4.1 23.1 1.0 N B:GLU102 4.1 25.7 1.0 N B:SER104 4.1 24.1 1.0 O B:ASP107 4.3 27.2 1.0 N B:VAL103 4.3 25.8 1.0 N B:PHE106 4.3 25.3 1.0 CA B:ASP107 4.3 27.4 1.0 C B:PRO105 4.4 26.1 1.0 N B:ASP107 4.4 26.6 1.0 CA B:SER104 4.4 23.8 1.0 CA B:PHE106 4.6 25.2 1.0 C B:ASP107 4.6 27.0 1.0 C B:VAL103 4.6 24.9 1.0 N B:PRO105 4.6 25.1 1.0 O B:PRO105 4.8 26.9 1.0 CA B:PRO105 4.8 25.9 1.0 CB B:SER104 4.9 23.1 1.0 CA B:VAL103 4.9 25.3 1.0 CB B:GLU102 4.9 28.4 1.0 CA B:VAL101 5.0 23.9 1.0

Sodium binding site 3 out of 4 in the Structure of An Omega-Aminotransferase From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of An Omega-Aminotransferase From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:48.3 occ:1.00 O C:HOH661 2.4 43.8 1.0 O C:HOH664 2.4 33.6 1.0 O C:SER104 2.5 44.7 1.0 O C:PHE106 2.6 48.3 1.0 O C:GLU102 2.6 46.1 1.0 O C:VAL101 3.3 44.3 1.0 C C:GLU102 3.6 44.9 1.0 C C:PHE106 3.7 49.2 1.0 C C:SER104 3.7 42.8 1.0 CA C:GLU102 4.1 45.8 1.0 N C:PHE106 4.1 46.0 1.0 C C:PRO105 4.2 46.6 1.0 C C:VAL101 4.3 43.7 1.0 N C:ASP107 4.5 47.4 1.0 O C:PRO105 4.5 48.6 1.0 CA C:PRO105 4.5 45.0 1.0 N C:SER104 4.5 40.4 1.0 CA C:PHE106 4.5 47.6 1.0 CA C:ASP107 4.5 50.0 1.0 N C:PRO105 4.6 43.0 1.0 OG C:SER104 4.6 41.4 1.0 CA C:SER104 4.7 40.5 1.0 N C:GLU102 4.7 44.3 1.0 N C:VAL103 4.7 42.5 1.0 C C:VAL103 4.7 40.8 1.0 OD1 C:ASP107 5.0 51.8 1.0

Sodium binding site 4 out of 4 in the Structure of An Omega-Aminotransferase From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of An Omega-Aminotransferase From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ D:Na501 b:26.2 occ:1.00 O D:PHE106 2.2 31.8 1.0 O D:HOH643 2.4 27.4 1.0 O D:SER104 2.5 32.3 1.0 O D:GLU102 2.5 34.5 1.0 O D:HOH629 2.6 21.5 1.0 O D:VAL101 2.7 31.9 1.0 C D:PHE106 3.4 31.8 1.0 C D:GLU102 3.4 33.9 1.0 C D:SER104 3.6 31.4 1.0 OG D:SER104 3.8 30.1 1.0 C D:VAL101 3.8 31.1 1.0 CA D:GLU102 3.8 34.0 1.0 N D:PHE106 3.9 31.1 1.0 N D:SER104 4.1 31.4 1.0 C D:PRO105 4.2 31.6 1.0 CA D:PHE106 4.2 31.0 1.0 N D:GLU102 4.3 32.2 1.0 N D:ASP107 4.3 32.3 1.0 CA D:SER104 4.4 30.6 1.0 N D:VAL103 4.4 33.0 1.0 CA D:ASP107 4.4 33.3 1.0 N D:PRO105 4.5 31.3 1.0 C D:VAL103 4.5 32.7 1.0 CA D:PRO105 4.6 31.8 1.0 O D:PRO105 4.6 32.5 1.0 O D:ASP107 4.6 33.3 1.0 CB D:SER104 4.6 30.1 1.0 C D:ASP107 4.7 32.8 1.0 CA D:VAL103 4.9 33.0 1.0

C.Rausch, A.Lerchner, A.Schiefner, A.Skerra. Crystal Structure of the Omega-Aminotransferase From Paracoccus Denitrificans and Its Phylogenetic Relationship with Other Class III Aminotransferases That Have Biotechnological Potential. Proteins V. 81 774 2013.
ISSN: ISSN 0887-3585
PubMed: 23239223
DOI: 10.1002/PROT.24233