Sodium in PDB 2ri0: Crystal Structure of Glucosamine 6-Phosphate Deaminase (Nagb) From S. Mutans

All present enzymatic activity of Crystal Structure of Glucosamine 6-Phosphate Deaminase (Nagb) From S. Mutans:
3.5.99.6;

The structure of Crystal Structure of Glucosamine 6-Phosphate Deaminase (Nagb) From S. Mutans, PDB code: 2ri0 was solved by D.Li, C.Liu, L.F.Li, X.D.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.13 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.000, 82.170, 134.910, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 19.9

The binding sites of Sodium atom in the Crystal Structure of Glucosamine 6-Phosphate Deaminase (Nagb) From S. Mutans (pdb code 2ri0). 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 Glucosamine 6-Phosphate Deaminase (Nagb) From S. Mutans, PDB code: 2ri0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Glucosamine 6-Phosphate Deaminase (Nagb) From S. Mutans


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 Glucosamine 6-Phosphate Deaminase (Nagb) From S. Mutans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na234 b:22.4 occ:1.00 O B:HOH589 2.7 23.8 1.0 O8 B:BTB236 2.8 21.3 1.0 O B:HOH498 2.9 14.7 1.0 N B:ALA100 3.0 5.1 1.0 C8 B:BTB236 3.5 19.1 1.0 CA B:ALA99 3.6 5.3 1.0 CB B:ALA100 3.6 5.7 1.0 O B:HOH436 3.7 12.9 1.0 C B:ALA99 3.8 5.6 1.0 CA B:ALA100 3.9 5.7 1.0 O B:HOH531 4.0 24.4 1.0 O B:HOH429 4.2 12.8 1.0 O B:LEU98 4.3 4.5 1.0 CB B:ALA99 4.4 6.0 1.0 ND2 B:ASN96 4.6 5.4 1.0 N B:ALA99 4.7 4.5 1.0 O1 B:BTB236 4.7 9.6 1.0 C3 B:BTB236 4.7 20.7 1.0 C7 B:BTB236 4.9 19.6 1.0 N B:ASP101 4.9 4.7 1.0 C B:LEU98 4.9 4.0 1.0 C B:ALA100 5.0 6.0 1.0 O B:ALA99 5.0 6.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Glucosamine 6-Phosphate Deaminase (Nagb) From S. Mutans


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 Glucosamine 6-Phosphate Deaminase (Nagb) From S. Mutans within 5.0Å range: probe atom residue distance (Å) B Occ B:Na235 b:16.8 occ:1.00 O B:HOH433 2.6 13.9 1.0 OE2 B:GLU105 2.8 4.4 1.0 O B:LEU94 2.8 3.5 1.0 CE2 B:TYR108 3.4 7.4 1.0 N B:ASN96 3.4 3.5 1.0 CB B:ASN96 3.8 3.7 1.0 CD B:GLU105 3.8 3.9 1.0 C B:LEU94 3.8 3.6 1.0 CA B:PRO95 3.9 3.3 1.0 C B:PRO95 3.9 3.6 1.0 O B:HOH432 4.0 12.0 1.0 CD2 B:TYR108 4.0 5.6 1.0 O B:HOH458 4.0 16.3 1.0 O6 B:BTB236 4.0 10.7 1.0 CE1 B:TYR109 4.1 2.0 1.0 C6 B:BTB236 4.1 15.1 1.0 CD1 B:TYR109 4.1 2.0 1.0 OE1 B:GLU105 4.1 5.5 1.0 CA B:ASN96 4.2 3.7 1.0 CZ B:TYR108 4.3 6.1 1.0 N B:PRO95 4.3 3.0 1.0 OH B:TYR108 4.4 6.7 1.0 O B:PRO95 4.7 3.6 1.0 O B:HOH617 4.8 27.8 1.0 O B:HOH554 4.8 18.3 1.0 N B:LEU94 4.9 4.5 1.0

C.Liu, D.Li, Y.H.Liang, L.F.Li, X.D.Su. Ring-Opening Mechanism Revealed By Crystal Structures of Nagb and Its Es Intermediate Complex J.Mol.Biol. V. 379 73 2008.
ISSN: ISSN 0022-2836
PubMed: 18436239
DOI: 10.1016/J.JMB.2008.03.031