Manganese in PDB 3t7o: Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese, Udp-Glucose and Glucose

All present enzymatic activity of Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese, Udp-Glucose and Glucose:
2.4.1.186;

The structure of Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese, Udp-Glucose and Glucose, PDB code: 3t7o was solved by A.Chaikuad, D.S.Froese, E.Krysztofinska, F.Von Delft, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, C.Bountra, U.Oppermann, W.W.Yue, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.33 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.415, 46.590, 69.904, 79.54, 88.75, 75.83
R / Rfree (%)	19.5 / 25.5

The binding sites of Manganese atom in the Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese, Udp-Glucose and Glucose (pdb code 3t7o). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese, Udp-Glucose and Glucose, PDB code: 3t7o:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese, Udp-Glucose and Glucose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese, Udp-Glucose and Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn264 b:7.1 occ:0.70 O1A A:UPG265 2.0 17.6 1.0 O1B A:UPG265 2.0 19.0 1.0 OD1 A:ASP104 2.0 11.2 1.0 OD2 A:ASP102 2.0 13.4 1.0 OD2 A:ASP104 2.0 15.7 1.0 NE2 A:HIS212 2.1 11.2 1.0 CG A:ASP104 2.4 12.6 1.0 CG A:ASP102 3.0 12.7 1.0 CE1 A:HIS212 3.1 14.3 1.0 CD2 A:HIS212 3.1 12.0 1.0 PB A:UPG265 3.2 21.1 1.0 PA A:UPG265 3.3 18.9 1.0 CB A:ASP102 3.4 13.7 1.0 O3A A:UPG265 3.6 20.7 1.0 O3C A:UPG265 3.8 16.1 1.0 O2B A:UPG265 3.8 20.6 1.0 CB A:ASP104 3.9 15.8 1.0 OD1 A:ASP102 4.2 13.4 1.0 NZ A:LYS218 4.2 17.4 1.0 ND1 A:HIS212 4.2 15.5 1.0 O2' A:UPG265 4.2 32.0 1.0 CG A:HIS212 4.3 13.2 1.0 C5C A:UPG265 4.3 18.1 1.0 O5C A:UPG265 4.3 18.2 1.0 O2A A:UPG265 4.4 18.2 1.0 C3' A:UPG265 4.4 34.2 1.0 O3' A:UPG265 4.4 33.7 1.0 O3B A:UPG265 4.6 21.0 1.0 CA A:LEU214 4.6 27.9 1.0 C3C A:UPG265 4.7 17.8 1.0 CA A:ASP104 4.8 15.1 1.0 C2' A:UPG265 4.8 32.4 1.0 N A:ASP104 4.8 14.7 1.0 C4C A:UPG265 4.9 15.5 1.0 CA A:ASP102 4.9 13.6 1.0 CB A:LEU214 4.9 30.3 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese, Udp-Glucose and Glucose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese, Udp-Glucose and Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn263 b:8.6 occ:0.70 OD2 B:ASP102 2.0 15.2 1.0 O1B B:UPG264 2.0 20.1 1.0 O1A B:UPG264 2.0 19.3 1.0 OD1 B:ASP104 2.0 15.2 1.0 NE2 B:HIS212 2.1 17.1 1.0 OD2 B:ASP104 2.5 15.2 1.0 CG B:ASP104 2.6 14.4 1.0 CG B:ASP102 3.0 11.6 1.0 CE1 B:HIS212 3.1 16.0 1.0 CD2 B:HIS212 3.2 14.4 1.0 PB B:UPG264 3.2 19.7 1.0 PA B:UPG264 3.3 18.1 1.0 CB B:ASP102 3.4 12.4 1.0 O3A B:UPG264 3.5 16.4 1.0 O2B B:UPG264 3.9 17.5 1.0 O3C B:UPG264 3.9 16.4 1.0 CB B:ASP104 4.1 14.3 1.0 OD1 B:ASP102 4.2 14.6 1.0 NZ B:LYS218 4.2 14.7 1.0 O3' B:UPG264 4.2 35.0 1.0 ND1 B:HIS212 4.2 12.2 1.0 O2' B:UPG264 4.3 33.6 1.0 CG B:HIS212 4.3 15.0 1.0 O5C B:UPG264 4.3 14.7 1.0 C5C B:UPG264 4.3 18.9 1.0 C3' B:UPG264 4.4 35.1 1.0 O2A B:UPG264 4.4 13.8 1.0 O3B B:UPG264 4.5 22.9 1.0 CA B:LEU214 4.5 19.7 1.0 C3C B:UPG264 4.7 17.9 1.0 C2' B:UPG264 4.8 33.5 1.0 CB B:LEU214 4.9 20.1 1.0 C4C B:UPG264 4.9 17.1 1.0 CA B:ASP102 4.9 12.6 1.0 CA B:ASP104 4.9 14.2 1.0 N B:ASP104 4.9 14.2 1.0

A.Chaikuad, D.S.Froese, G.Berridge, F.Von Delft, U.Oppermann, W.W.Yue. Conformational Plasticity of Glycogenin and Its Maltosaccharide Substrate During Glycogen Biogenesis. Proc.Natl.Acad.Sci.Usa V. 108 21028 2011.
ISSN: ISSN 0027-8424
PubMed: 22160680
DOI: 10.1073/PNAS.1113921108