Calcium in PDB 7s05: Cryo-Em Structure of Human Glcnac-1-Phosphotransferase A2B2 Subcomplex

All present enzymatic activity of Cryo-Em Structure of Human Glcnac-1-Phosphotransferase A2B2 Subcomplex:
2.7.8.17;

The binding sites of Calcium atom in the Cryo-Em Structure of Human Glcnac-1-Phosphotransferase A2B2 Subcomplex (pdb code 7s05). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Human Glcnac-1-Phosphotransferase A2B2 Subcomplex, PDB code: 7s05:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Human Glcnac-1-Phosphotransferase A2B2 Subcomplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Human Glcnac-1-Phosphotransferase A2B2 Subcomplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1304 b:71.2 occ:1.00 O B:VAL1024 2.5 63.9 1.0 OD1 B:ASP1018 2.6 61.8 1.0 OD2 B:ASP1020 2.6 63.2 1.0 OE1 B:GLU1029 2.7 58.7 1.0 CB B:ASP1020 3.0 63.2 1.0 OE2 B:GLU1029 3.1 58.7 1.0 CG B:ASP1020 3.1 63.2 1.0 CD B:GLU1029 3.2 58.7 1.0 OG B:SER1022 3.4 65.5 1.0 C B:VAL1024 3.7 63.9 1.0 CG B:ASP1018 3.8 61.8 1.0 N B:ASP1020 4.0 63.2 1.0 CA B:ASP1020 4.1 63.2 1.0 CA B:LEU1025 4.1 62.5 1.0 OG B:SER1026 4.3 63.1 1.0 OD1 B:ASP1020 4.3 63.2 1.0 N B:LEU1025 4.4 62.5 1.0 OD2 B:ASP1018 4.4 61.8 1.0 CB B:SER1022 4.4 65.5 1.0 N B:SER1026 4.5 63.1 1.0 C B:LEU1025 4.6 62.5 1.0 N B:SER1022 4.7 65.5 1.0 CG B:GLU1029 4.7 58.7 1.0 C B:ASP1020 4.8 63.2 1.0 N B:GLN1021 4.8 64.9 1.0 N B:VAL1024 4.9 63.9 1.0 CA B:VAL1024 4.9 63.9 1.0 CB B:ASP1018 4.9 61.8 1.0 CA B:ASP1018 5.0 61.8 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Human Glcnac-1-Phosphotransferase A2B2 Subcomplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Human Glcnac-1-Phosphotransferase A2B2 Subcomplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1304 b:70.2 occ:1.00 O A:VAL1024 2.5 64.2 1.0 OD1 A:ASP1018 2.6 61.7 1.0 OD2 A:ASP1020 2.6 62.8 1.0 OE1 A:GLU1029 2.7 58.8 1.0 CB A:ASP1020 3.0 62.8 1.0 OE2 A:GLU1029 3.1 58.8 1.0 CG A:ASP1020 3.1 62.8 1.0 CD A:GLU1029 3.2 58.8 1.0 OG A:SER1022 3.4 65.2 1.0 C A:VAL1024 3.7 64.2 1.0 CG A:ASP1018 3.8 61.7 1.0 N A:ASP1020 4.0 62.8 1.0 CA A:ASP1020 4.1 62.8 1.0 CA A:LEU1025 4.1 62.5 1.0 OG A:SER1026 4.3 62.8 1.0 OD1 A:ASP1020 4.3 62.8 1.0 N A:LEU1025 4.4 62.5 1.0 OD2 A:ASP1018 4.4 61.7 1.0 CB A:SER1022 4.4 65.2 1.0 N A:SER1026 4.5 62.8 1.0 C A:LEU1025 4.6 62.5 1.0 N A:SER1022 4.7 65.2 1.0 CG A:GLU1029 4.7 58.8 1.0 C A:ASP1020 4.8 62.8 1.0 N A:GLN1021 4.8 64.7 1.0 N A:VAL1024 4.9 64.2 1.0 CA A:VAL1024 4.9 64.2 1.0 CB A:ASP1018 4.9 61.7 1.0 CA A:ASP1018 5.0 61.7 1.0

H.Li, W.S.Lee, X.Feng, L.Bai, B.C.Jennings, L.Liu, B.Doray, W.M.Canfield, S.Kornfeld, H.Li. Structure of the Human Glcnac-1-Phosphotransferase Alpha Beta Subunits Reveals Regulatory Mechanism For Lysosomal Enzyme Glycan Phosphorylation. Nat.Struct.Mol.Biol. V. 29 348 2022.
ISSN: ESSN 1545-9985
PubMed: 35332324
DOI: 10.1038/S41594-022-00748-0