Sodium in PDB 5ggp: Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide

The structure of Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide, PDB code: 5ggp was solved by N.Kuwabara, T.Senda, R.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.55 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.113, 49.743, 61.716, 90.00, 105.89, 90.00
R / Rfree (%)	21.6 / 24.6

The binding sites of Sodium atom in the Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide (pdb code 5ggp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide, PDB code: 5ggp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide


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 N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:10.3 occ:1.00 OG A:SER232 3.0 13.1 1.0 O3 C:MAN101 3.2 14.3 1.0 NH2 A:ARG207 3.4 13.2 1.0 O4 C:MAN101 3.6 18.6 1.0 CB A:SER232 3.7 12.7 1.0 CA A:SER232 3.9 13.5 1.0 NH1 A:ARG207 4.3 12.7 1.0 CZ A:ARG207 4.3 11.8 1.0 C3 C:MAN101 4.3 15.2 1.0 C4 C:MAN101 4.3 18.2 1.0 O A:LEU231 4.5 11.9 1.0 N A:SER232 4.7 12.4 1.0 C A:LEU231 4.9 12.4 1.0 C A:SER232 5.0 15.1 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide


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 N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:18.1 occ:1.00 O A:HOH514 2.7 17.4 1.0 O A:GLY235 2.8 13.4 1.0 N A:ARG107 2.9 9.7 1.0 CG A:PRO237 3.5 12.1 1.0 CA A:SER106 3.5 12.8 1.0 CD A:PRO237 3.5 12.1 1.0 CB A:ARG107 3.6 10.5 1.0 C A:SER106 3.7 10.0 1.0 CB A:SER106 3.7 12.7 1.0 N A:PRO237 3.7 11.6 1.0 O A:HOH492 3.7 20.3 1.0 O A:HOH495 3.8 20.0 1.0 CA A:ARG107 3.8 14.0 1.0 CG2 A:THR209 3.8 11.0 1.0 CB A:TRP234 4.0 12.2 1.0 C A:GLY235 4.0 12.3 1.0 CA A:PRO237 4.1 10.6 1.0 C A:ASP236 4.2 12.9 1.0 CB A:PRO237 4.3 12.0 1.0 CA A:ASP236 4.6 13.6 1.0 O A:ASP236 4.7 12.2 1.0 OG A:SER106 4.7 11.7 1.0 CG A:TRP234 4.8 12.5 1.0 N A:ASP236 4.8 11.0 1.0 O A:SER106 4.9 9.4 1.0 N A:SER106 4.9 10.4 1.0 C A:TRP234 4.9 12.8 1.0 N A:GLY235 4.9 11.5 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:13.8 occ:1.00 N B:HIS155 3.2 16.4 1.0 NZ B:LYS186 3.3 18.2 1.0 CD2 B:HIS184 3.6 18.8 1.0 CA B:PRO154 3.7 14.6 1.0 CB B:HIS184 3.9 12.4 1.0 CD B:LYS186 3.9 20.0 1.0 ND1 B:HIS155 4.0 21.3 1.0 C B:PRO154 4.0 17.6 1.0 CE B:LYS186 4.0 20.8 1.0 CG B:HIS184 4.0 16.2 1.0 CA B:HIS155 4.1 14.6 1.0 CE1 B:HIS155 4.1 25.1 1.0 CB B:PRO154 4.2 17.6 1.0 CG B:HIS155 4.2 19.8 1.0 CG B:LYS186 4.2 18.2 1.0 O B:HIS184 4.3 14.6 1.0 OD1 B:ASP157 4.3 14.3 1.0 NE2 B:HIS155 4.4 24.2 1.0 CD2 B:HIS155 4.5 21.5 1.0 OE2 B:GLU158 4.6 21.2 1.0 CA B:HIS184 4.7 13.4 1.0 CB B:HIS155 4.8 16.8 1.0 NE2 B:HIS184 4.8 20.4 1.0 C B:HIS184 4.9 13.5 1.0 N B:PRO154 5.0 17.9 1.0 O B:HOH427 5.0 12.8 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:8.6 occ:1.00 OG B:SER232 3.0 12.2 1.0 O3 D:MAN101 3.2 14.9 1.0 NH2 B:ARG207 3.3 11.9 1.0 O4 D:MAN101 3.6 17.9 1.0 CB B:SER232 3.7 13.9 1.0 CA B:SER232 3.8 14.7 1.0 O D:HOH212 4.3 22.4 1.0 CZ B:ARG207 4.3 12.6 1.0 C4 D:MAN101 4.3 16.8 1.0 C3 D:MAN101 4.3 13.9 1.0 NH1 B:ARG207 4.3 13.0 1.0 O B:LEU231 4.5 14.1 1.0 O B:HOH467 4.5 23.8 1.0 N B:SER232 4.7 11.4 1.0 C B:LEU231 4.9 11.5 1.0 C B:SER232 4.9 14.4 1.0 O D:HOH220 5.0 33.7 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of N-Terminal Domain of Human Protein O-Mannose Beta-1,2-N-Acetylglucosaminyltransferase in Complex with Glcnac- BETA1,2-Man-Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:19.9 occ:1.00 NE B:ARG171 3.2 20.0 1.0 N B:ALA168 3.3 15.2 1.0 CG B:ARG171 3.6 16.6 1.0 O B:HOH519 3.7 52.9 1.0 CB B:ALA168 3.9 10.5 1.0 CA B:VAL167 3.9 12.4 1.0 CD B:ARG171 4.0 17.8 1.0 C B:VAL167 4.1 15.5 1.0 NH2 B:ARG171 4.1 16.7 1.0 CZ B:ARG171 4.1 20.2 1.0 CE B:MET144 4.2 19.2 1.0 CA B:ALA168 4.2 15.4 1.0 O B:MET166 4.2 18.0 1.0 CG1 B:VAL167 4.3 12.1 1.0 SD B:MET144 4.6 15.2 1.0 CB B:VAL167 4.6 13.8 1.0 CB B:ARG171 4.9 14.7 1.0 N B:VAL167 5.0 14.1 1.0

N.Kuwabara, H.Manya, T.Yamada, H.Tateno, M.Kanagawa, K.Kobayashi, K.Akasaka-Manya, Y.Hirose, M.Mizuno, M.Ikeguchi, T.Toda, J.Hirabayashi, T.Senda, T.Endo, R.Kato. Carbohydrate-Binding Domain of the POMGNT1 Stem Region Modulates O-Mannosylation Sites of Alpha-Dystroglycan Proc.Natl.Acad.Sci.Usa V. 113 9280 2016.
ISSN: ESSN 1091-6490
PubMed: 27493216
DOI: 10.1073/PNAS.1525545113