Sodium in PDB 3otk: Structure and Mechanisim of Core 2 BETA1,6-N- Acetylglucosaminyltransferase: A Metal-Ion Independent Gt-A Glycosyltransferase

All present enzymatic activity of Structure and Mechanisim of Core 2 BETA1,6-N- Acetylglucosaminyltransferase: A Metal-Ion Independent Gt-A Glycosyltransferase:
2.4.1.102;

The structure of Structure and Mechanisim of Core 2 BETA1,6-N- Acetylglucosaminyltransferase: A Metal-Ion Independent Gt-A Glycosyltransferase, PDB code: 3otk was solved by J.E.Pak, J.M.Rini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.874, 101.020, 136.612, 90.00, 93.42, 90.00
R / Rfree (%)	16.5 / 21.9

The binding sites of Sodium atom in the Structure and Mechanisim of Core 2 BETA1,6-N- Acetylglucosaminyltransferase: A Metal-Ion Independent Gt-A Glycosyltransferase (pdb code 3otk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure and Mechanisim of Core 2 BETA1,6-N- Acetylglucosaminyltransferase: A Metal-Ion Independent Gt-A Glycosyltransferase, PDB code: 3otk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure and Mechanisim of Core 2 BETA1,6-N- Acetylglucosaminyltransferase: A Metal-Ion Independent Gt-A Glycosyltransferase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure and Mechanisim of Core 2 BETA1,6-N- Acetylglucosaminyltransferase: A Metal-Ion Independent Gt-A Glycosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na586 b:43.4 occ:1.00 O A:HOH484 2.3 51.8 1.0 O A:HOH438 2.4 41.3 1.0 O A:VAL176 2.4 31.2 1.0 O A:ALA170 2.4 29.8 1.0 O A:PHE173 2.4 33.4 1.0 C A:ALA170 3.3 30.1 1.0 C A:VAL176 3.6 30.2 1.0 C A:PHE173 3.6 33.8 1.0 CA A:SER171 4.0 30.6 1.0 N A:SER171 4.0 30.4 1.0 CA A:ALA170 4.3 29.1 1.0 CA A:PHE177 4.3 32.5 1.0 CB A:ALA170 4.4 28.1 1.0 N A:PHE173 4.4 31.5 1.0 C A:SER171 4.4 31.1 1.0 CB A:PHE177 4.4 31.8 1.0 N A:PHE177 4.4 31.4 1.0 N A:VAL176 4.5 29.5 1.0 CA A:ASP174 4.5 35.7 1.0 N A:ASP174 4.5 34.3 1.0 C A:ASP174 4.6 33.8 1.0 CA A:PHE173 4.6 32.6 1.0 CA A:VAL176 4.6 28.7 1.0 O A:HOH501 4.6 36.5 1.0 O A:ASP174 4.7 33.9 1.0 O A:SER171 4.7 32.5 1.0 N A:CYS172 5.0 30.7 1.0

Sodium binding site 2 out of 2 in the Structure and Mechanisim of Core 2 BETA1,6-N- Acetylglucosaminyltransferase: A Metal-Ion Independent Gt-A Glycosyltransferase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure and Mechanisim of Core 2 BETA1,6-N- Acetylglucosaminyltransferase: A Metal-Ion Independent Gt-A Glycosyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na587 b:39.0 occ:1.00 O C:HOH29 2.2 44.2 1.0 O C:ALA170 2.4 27.3 1.0 O C:VAL176 2.4 30.6 1.0 O C:PHE173 2.4 31.9 1.0 C C:ALA170 3.4 28.9 1.0 C C:VAL176 3.6 29.0 1.0 C C:PHE173 3.6 31.5 1.0 N C:SER171 4.2 29.7 1.0 CA C:SER171 4.2 30.1 1.0 CA C:ALA170 4.3 28.7 1.0 N C:PHE173 4.4 30.8 1.0 N C:VAL176 4.4 27.2 1.0 CA C:PHE177 4.4 32.1 1.0 CB C:ALA170 4.4 28.4 1.0 C C:ASP174 4.5 31.1 1.0 O C:ASP174 4.5 32.2 1.0 CB C:PHE177 4.5 33.0 1.0 N C:PHE177 4.5 30.1 1.0 C C:SER171 4.5 30.5 1.0 N C:ASP174 4.5 32.4 1.0 CA C:VAL176 4.5 26.7 1.0 CA C:PHE173 4.6 30.4 1.0 CA C:ASP174 4.6 33.3 1.0 O C:HOH468 4.8 35.4 1.0 O C:SER171 4.8 30.1 1.0 CB C:VAL176 5.0 26.6 1.0 N C:ASN175 5.0 29.1 1.0 N C:CYS172 5.0 30.3 1.0

J.E.Pak, M.Satkunarajah, J.Seetharaman, J.M.Rini. Structural and Mechanistic Characterization of Leukocyte-Type Core 2 Beta 1,6-N-Acetylglucosaminyltransferase: A Metal-Ion-Independent Gt-A Glycosyltransferase. J.Mol.Biol. V. 414 798 2011.
ISSN: ISSN 0022-2836
PubMed: 22056345
DOI: 10.1016/J.JMB.2011.10.039