Sodium in PDB 6vlb: Crystal Structure of Ligand-Free Udp-Glcnac 2-Epimerase From Neisseria Meningitidis

All present enzymatic activity of Crystal Structure of Ligand-Free Udp-Glcnac 2-Epimerase From Neisseria Meningitidis:
5.1.3.14;

The structure of Crystal Structure of Ligand-Free Udp-Glcnac 2-Epimerase From Neisseria Meningitidis, PDB code: 6vlb was solved by A.J.Fisher, N.K.Hurlburt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.42 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	211.550, 49.510, 81.220, 90.00, 90.93, 90.00
R / Rfree (%)	18.2 / 21.6

The binding sites of Sodium atom in the Crystal Structure of Ligand-Free Udp-Glcnac 2-Epimerase From Neisseria Meningitidis (pdb code 6vlb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Ligand-Free Udp-Glcnac 2-Epimerase From Neisseria Meningitidis, PDB code: 6vlb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Ligand-Free Udp-Glcnac 2-Epimerase From Neisseria Meningitidis


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 Ligand-Free Udp-Glcnac 2-Epimerase From Neisseria Meningitidis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:33.6 occ:1.00 O A:HOH767 2.1 39.2 1.0 O A:ILE351 2.3 35.4 1.0 O A:HOH730 2.4 33.2 1.0 O A:ALA349 2.5 35.7 1.0 O A:PRO297 2.5 29.9 1.0 C A:ILE351 3.5 35.1 1.0 C A:ALA349 3.5 38.4 1.0 C A:PRO297 3.6 32.2 1.0 N A:ILE351 3.9 37.5 1.0 CA A:GLY300 4.1 32.4 1.0 C A:ASN350 4.1 38.0 1.0 CA A:PRO297 4.2 30.3 1.0 O A:HOH710 4.2 40.1 1.0 CA A:ILE351 4.2 38.5 1.0 N A:ASN350 4.3 40.7 1.0 O A:MET348 4.3 39.0 1.0 CB A:PRO297 4.3 30.0 1.0 CA A:ASN350 4.4 41.1 1.0 N A:GLY300 4.4 33.4 1.0 CA A:ALA349 4.4 39.6 1.0 N A:GLU352 4.5 34.5 1.0 O A:ASN350 4.6 40.1 1.0 N A:ASN353 4.6 33.2 1.0 CA A:GLU352 4.7 36.8 1.0 N A:SER298 4.7 29.4 1.0 CB A:ILE351 4.7 39.6 1.0 O A:HOH680 4.8 32.2 1.0 C A:GLU352 4.9 35.2 1.0 C A:GLY300 5.0 32.6 1.0 CG2 A:THR320 5.0 32.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Ligand-Free Udp-Glcnac 2-Epimerase From Neisseria Meningitidis


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 Ligand-Free Udp-Glcnac 2-Epimerase From Neisseria Meningitidis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:33.2 occ:1.00 O B:HOH746 2.1 35.0 1.0 O B:HOH730 2.1 31.8 1.0 O B:ILE351 2.2 37.6 1.0 O B:ALA349 2.6 39.1 1.0 O B:PRO297 2.6 27.8 1.0 C B:ILE351 3.4 41.0 1.0 C B:ALA349 3.5 44.5 1.0 C B:PRO297 3.7 27.7 1.0 N B:ILE351 3.8 37.3 1.0 C B:ASN350 4.0 37.8 1.0 CA B:GLY300 4.2 35.2 1.0 CA B:ILE351 4.2 35.5 1.0 CA B:PRO297 4.2 25.0 1.0 O B:HOH692 4.3 51.2 1.0 O B:HOH721 4.3 37.2 1.0 N B:ASN350 4.3 42.7 1.0 O B:MET348 4.3 42.4 1.0 CB B:PRO297 4.4 26.9 1.0 CA B:ASN350 4.4 45.3 1.0 N B:GLU352 4.4 37.6 1.0 N B:GLY300 4.4 37.0 1.0 CA B:ALA349 4.5 39.0 1.0 O B:ASN350 4.5 41.0 1.0 N B:ASN353 4.6 30.7 1.0 CA B:GLU352 4.6 39.0 1.0 N B:SER298 4.7 26.0 1.0 CB B:ILE351 4.8 36.3 1.0 C B:GLU352 4.8 31.2 1.0 CG2 B:THR320 4.9 27.0 1.0 O B:HOH644 4.9 30.8 1.0

N.K.Hurlburt, J.Guan, H.Ong, H.Yu, X.Chen, A.J.Fisher. Structural Characterization of A Nonhydrolyzing Udp-Glcnac 2-Epimerase From Neisseria Meningitidis Serogroup A. Acta Crystallogr.,Sect.F V. 76 557 2020.
ISSN: ESSN 2053-230X
PubMed: 33135674
DOI: 10.1107/S2053230X20013680