Calcium in PDB 9bgf: Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac

All present enzymatic activity of Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac:
2.7.8.17;

The structure of Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac (pdb code 9bgf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac, PDB code: 9bgf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1301 b:30.9 occ:1.00 OD1 A:ASP1018 2.3 15.5 1.0 O A:VAL1024 2.3 24.9 1.0 OE1 A:GLU1029 2.4 17.5 1.0 OE2 A:GLU1029 2.7 10.1 1.0 OG A:SER1022 2.8 25.2 1.0 CD A:GLU1029 2.9 10.9 1.0 CB A:ASP1020 3.0 17.7 1.0 CG A:ASP1018 3.4 15.7 1.0 C A:VAL1024 3.5 22.2 1.0 OG A:SER1026 3.8 16.7 1.0 OD1 A:ASP1020 3.9 23.6 1.0 CG A:ASP1020 4.0 30.6 1.0 N A:SER1026 4.1 13.8 1.0 OD2 A:ASP1018 4.1 17.3 1.0 CA A:ASP1020 4.1 18.1 1.0 CB A:SER1022 4.2 23.1 1.0 N A:ASP1020 4.2 19.7 1.0 CA A:LEU1025 4.2 14.2 1.0 N A:LEU1025 4.3 16.3 1.0 CG A:GLU1029 4.4 8.4 1.0 N A:VAL1024 4.4 17.5 1.0 CB A:ASP1018 4.5 11.5 1.0 C A:LEU1025 4.5 17.0 1.0 CA A:VAL1024 4.5 19.6 1.0 CA A:ASP1018 4.6 9.8 1.0 N A:SER1022 4.6 20.0 1.0 CB A:SER1026 4.7 12.1 1.0 C A:ASP1020 4.8 21.5 1.0 C A:ASP1018 4.9 10.1 1.0 CA A:SER1022 4.9 20.8 1.0 N A:GLN1021 4.9 21.8 1.0 N A:GLY1023 5.0 36.5 1.0

Calcium binding site 2 out of 2 in the Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Human Glcnac-1-Phosphotransferase Complexed with the Donor Substrate Udp-Glcnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1305 b:28.5 occ:1.00 OD1 B:ASP1020 2.1 21.2 1.0 OG B:SER1022 2.3 24.4 1.0 O B:VAL1024 2.3 19.7 1.0 OD1 B:ASP1018 2.4 16.2 1.0 OD2 B:ASP1020 2.5 29.7 1.0 OE1 B:GLU1029 2.5 11.6 1.0 CG B:ASP1020 2.6 21.2 1.0 OE2 B:GLU1029 2.9 11.7 1.0 CD B:GLU1029 3.1 7.1 1.0 C B:VAL1024 3.5 15.7 1.0 CG B:ASP1018 3.6 16.1 1.0 CB B:SER1022 3.6 24.5 1.0 OG B:SER1026 3.9 10.4 1.0 CB B:ASP1020 4.1 14.3 1.0 N B:SER1026 4.2 12.9 1.0 OD2 B:ASP1018 4.3 17.1 1.0 N B:VAL1024 4.3 16.9 1.0 CA B:LEU1025 4.4 9.9 1.0 N B:LEU1025 4.4 11.9 1.0 N B:SER1022 4.5 22.5 1.0 CA B:VAL1024 4.5 18.6 1.0 CG B:GLU1029 4.6 4.4 1.0 CA B:SER1022 4.6 23.8 1.0 CB B:ASP1018 4.6 9.6 1.0 N B:ASP1020 4.6 14.0 1.0 C B:LEU1025 4.7 13.3 1.0 CA B:ASP1018 4.7 10.2 1.0 CB B:SER1026 4.8 8.1 1.0 CA B:ASP1020 4.8 16.8 1.0 N B:GLY1023 4.9 30.4 1.0 C B:SER1022 5.0 28.0 1.0

H.Li, B.Doray, B.C.Jennings, W.S.Lee, L.Liu, S.Kornfeld, H.Li. Structure of A Truncated Human Glcnac-1-Phosphotransferase Variant Reveals the Basis For Its Hyperactivity. J.Biol.Chem. V. 300 07706 2024.
ISSN: ESSN 1083-351X
PubMed: 39178950
DOI: 10.1016/J.JBC.2024.107706