Sodium in PDB 8e77: Rystal Structure of PCRYO_0616, the Aminotransferase Required to Synthesize Udp-N-Acetyl-3-Amino-D-Glucosaminuronic Acid (Udp- GLCNAC3NA), Incomplete with Its External Aldimine Reaction Intermediate

The structure of Rystal Structure of PCRYO_0616, the Aminotransferase Required to Synthesize Udp-N-Acetyl-3-Amino-D-Glucosaminuronic Acid (Udp- GLCNAC3NA), Incomplete with Its External Aldimine Reaction Intermediate, PDB code: 8e77 was solved by D.L.Hofmeister, C.A.Seltzner, N.J.Bockhaus, J.B.Thoden, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.27 / 1.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	57.708, 96.336, 139.467, 90, 90, 90
R / Rfree (%)	14.6 / 17.4

The binding sites of Sodium atom in the Rystal Structure of PCRYO_0616, the Aminotransferase Required to Synthesize Udp-N-Acetyl-3-Amino-D-Glucosaminuronic Acid (Udp- GLCNAC3NA), Incomplete with Its External Aldimine Reaction Intermediate (pdb code 8e77). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Rystal Structure of PCRYO_0616, the Aminotransferase Required to Synthesize Udp-N-Acetyl-3-Amino-D-Glucosaminuronic Acid (Udp- GLCNAC3NA), Incomplete with Its External Aldimine Reaction Intermediate, PDB code: 8e77:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Rystal Structure of PCRYO_0616, the Aminotransferase Required to Synthesize Udp-N-Acetyl-3-Amino-D-Glucosaminuronic Acid (Udp- GLCNAC3NA), Incomplete with Its External Aldimine Reaction Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rystal Structure of PCRYO_0616, the Aminotransferase Required to Synthesize Udp-N-Acetyl-3-Amino-D-Glucosaminuronic Acid (Udp- GLCNAC3NA), Incomplete with Its External Aldimine Reaction Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:6.6 occ:0.50 O A:HOH763 2.0 6.2 1.0 O A:HOH600 2.1 6.2 1.0 O A:HOH764 2.1 5.6 1.0 O A:HOH827 4.0 6.9 1.0 OD2 A:ASP231 4.1 6.3 1.0 O A:ASP192 4.2 5.7 1.0 OD1 A:ASP231 4.2 5.9 1.0 O A:HOH809 4.2 6.2 1.0 CG A:ASP231 4.4 5.9 1.0 O A:ALA57 4.7 6.0 1.0 CB A:ASP192 4.8 5.6 1.0 O A:ARG229 4.8 5.9 1.0 CB A:ALA57 4.9 6.5 1.0 C A:ASP192 4.9 5.8 1.0

Sodium binding site 2 out of 2 in the Rystal Structure of PCRYO_0616, the Aminotransferase Required to Synthesize Udp-N-Acetyl-3-Amino-D-Glucosaminuronic Acid (Udp- GLCNAC3NA), Incomplete with Its External Aldimine Reaction Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rystal Structure of PCRYO_0616, the Aminotransferase Required to Synthesize Udp-N-Acetyl-3-Amino-D-Glucosaminuronic Acid (Udp- GLCNAC3NA), Incomplete with Its External Aldimine Reaction Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:27.6 occ:1.00 O A:HOH916 2.3 35.8 1.0 O A:HOH1102 2.4 38.5 1.0 O A:HOH958 2.4 46.9 1.0 O A:ASP267 2.4 15.0 1.0 O A:HOH866 2.5 12.9 1.0 O A:HOH626 2.7 30.7 1.0 O A:HOH1146 3.4 41.0 1.0 O A:HOH1061 3.6 29.7 1.0 C A:ASP267 3.7 11.8 1.0 O A:HOH942 3.9 30.1 1.0 CA A:ILE268 4.2 10.2 0.5 CA A:ILE268 4.3 10.2 0.5 OG1 A:THR269 4.3 13.0 1.0 N A:THR269 4.4 8.0 1.0 N A:ILE268 4.4 11.1 0.5 N A:ILE268 4.4 10.9 0.5 O A:HOH655 4.4 16.1 1.0 O A:HOH1134 4.6 33.0 1.0 CB A:ASP267 4.7 14.6 1.0 CA A:ASP267 4.7 12.0 1.0 CD1 A:ILE268 4.8 15.9 0.5 C A:ILE268 4.8 10.7 0.5 C A:ILE268 4.8 9.6 0.5 O A:HOH891 4.8 49.4 1.0

D.L.Hofmeister, C.A.Seltzner, N.J.Bockhaus, J.B.Thoden, H.M.Holden. Investigation of the Enzymes Required For the Biosynthesis of 2,3-Diacetamido-2,3-Dideoxy-D-Glucuronic Acid in Psychrobacter Cryohalolentis K5 T. Protein Sci. E4502 2022.
ISSN: ESSN 1469-896X
PubMed: 36346293
DOI: 10.1002/PRO.4502