Sodium in PDB 6cbk: X-Ray Structure of Neob From Streptomyces Fradiae in Complex with Pmp

All present enzymatic activity of X-Ray Structure of Neob From Streptomyces Fradiae in Complex with Pmp:
2.6.1.93; 2.6.1.95;

The structure of X-Ray Structure of Neob From Streptomyces Fradiae in Complex with Pmp, PDB code: 6cbk was solved by J.B.Thoden, G.T.Dow, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.46 / 1.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.726, 82.705, 100.860, 75.59, 88.85, 70.60
R / Rfree (%)	17.5 / 20.8

The binding sites of Sodium atom in the X-Ray Structure of Neob From Streptomyces Fradiae in Complex with Pmp (pdb code 6cbk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of Neob From Streptomyces Fradiae in Complex with Pmp, PDB code: 6cbk:

Sodium binding site 1 out of 1 in the X-Ray Structure of Neob From Streptomyces Fradiae in Complex with Pmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Neob From Streptomyces Fradiae in Complex with Pmp within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:20.8 occ:1.00 O C:THR69 2.3 17.5 1.0 O B:HOH775 2.4 18.4 1.0 O D:ALA28 2.4 16.2 1.0 OG D:SER29 2.4 8.4 0.5 O D:HOH793 2.5 16.1 1.0 O D:HOH832 2.6 15.9 1.0 OG D:SER29 3.3 26.1 0.5 CB D:SER29 3.3 12.8 0.5 C D:ALA28 3.4 14.7 1.0 CB D:SER29 3.4 20.8 0.5 CA D:SER29 3.5 13.9 0.5 CA D:SER29 3.5 17.7 0.5 C C:THR69 3.5 15.3 1.0 NH2 B:ARG40 3.8 17.9 1.0 N D:SER29 3.9 15.2 1.0 CA C:GLY70 4.0 16.1 1.0 O D:HOH638 4.1 23.3 1.0 N C:GLY70 4.2 16.4 1.0 C C:GLY70 4.4 17.4 1.0 O D:HOH831 4.4 24.5 1.0 O D:HOH826 4.5 25.0 1.0 CA C:THR69 4.6 16.8 1.0 O D:HIS55 4.6 16.1 1.0 CA D:ALA28 4.7 15.6 1.0 N C:ALA71 4.7 17.4 1.0 CB C:THR69 4.7 18.0 1.0 N D:ALA28 4.7 16.9 1.0 CA D:GLY56 4.8 16.1 1.0 O C:GLY70 4.9 18.8 1.0 C D:SER29 4.9 14.8 1.0 OG1 C:THR69 4.9 18.6 1.0

G.T.Dow, J.B.Thoden, H.M.Holden. The Three-Dimensional Structure of Neob: An Aminotransferase Involved in the Biosynthesis of Neomycin. Protein Sci. V. 27 945 2018.
ISSN: ESSN 1469-896X
PubMed: 29516565
DOI: 10.1002/PRO.3400