Manganese in PDB 3t7m: Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Udp, in A Triclinic Closed Form

All present enzymatic activity of Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Udp, in A Triclinic Closed Form:
2.4.1.186;

The structure of Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Udp, in A Triclinic Closed Form, PDB code: 3t7m 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)	38.26 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.006, 47.081, 70.020, 87.89, 78.88, 76.65
R / Rfree (%)	18.9 / 24.3

The binding sites of Manganese atom in the Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Udp, in A Triclinic Closed Form (pdb code 3t7m). 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 and Udp, in A Triclinic Closed Form, PDB code: 3t7m:
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 and Udp, in A Triclinic Closed Form


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 and Udp, in A Triclinic Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn263 b:13.3 occ:1.00 OD2 A:ASP102 2.0 14.2 1.0 O3B A:UDP264 2.0 17.6 1.0 O1A A:UDP264 2.0 16.4 1.0 OD1 A:ASP104 2.0 14.5 1.0 NE2 A:HIS212 2.1 13.6 1.0 OD2 A:ASP104 2.4 14.9 1.0 CG A:ASP104 2.6 14.1 1.0 CG A:ASP102 3.1 12.9 1.0 CE1 A:HIS212 3.1 13.8 1.0 CD2 A:HIS212 3.1 13.4 1.0 PB A:UDP264 3.3 18.0 1.0 PA A:UDP264 3.3 16.7 1.0 CB A:ASP102 3.4 12.6 1.0 O3A A:UDP264 3.5 17.4 1.0 O1B A:UDP264 3.9 15.4 1.0 O3' A:UDP264 4.0 14.3 1.0 CB A:ASP104 4.1 13.9 1.0 OD1 A:ASP102 4.2 13.4 1.0 ND1 A:HIS212 4.2 13.3 1.0 C5' A:UDP264 4.2 15.0 1.0 NZ A:LYS218 4.2 21.4 1.0 CG A:HIS212 4.3 12.9 1.0 O A:HOH406 4.3 25.8 1.0 O5' A:UDP264 4.3 15.6 1.0 O2A A:UDP264 4.4 16.6 1.0 CA A:LEU214 4.5 24.4 1.0 O2B A:UDP264 4.5 16.3 1.0 O A:HOH407 4.6 30.0 1.0 CB A:LEU214 4.6 26.0 1.0 C3' A:UDP264 4.7 14.7 1.0 C4' A:UDP264 4.9 14.3 1.0 CA A:ASP102 4.9 12.3 1.0 CA A:ASP104 4.9 13.1 1.0 N A:LEU214 5.0 22.4 1.0 N A:ASP104 5.0 12.2 1.0

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


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 and Udp, in A Triclinic Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn263 b:13.6 occ:1.00 OD2 B:ASP102 2.0 15.0 1.0 O2A B:UDP264 2.0 17.1 1.0 O2B B:UDP264 2.0 17.6 1.0 OD2 B:ASP104 2.0 16.6 1.0 OD1 B:ASP104 2.0 15.2 1.0 NE2 B:HIS212 2.1 14.2 1.0 CG B:ASP104 2.4 15.3 1.0 CG B:ASP102 3.1 13.8 1.0 CE1 B:HIS212 3.1 14.1 1.0 CD2 B:HIS212 3.1 14.4 1.0 PB B:UDP264 3.3 17.0 1.0 PA B:UDP264 3.3 17.1 1.0 CB B:ASP102 3.5 12.9 1.0 O3A B:UDP264 3.5 17.1 1.0 O3' B:UDP264 3.8 12.9 1.0 O B:HOH422 3.9 27.0 1.0 O1B B:UDP264 4.0 17.0 1.0 CB B:ASP104 4.0 15.4 1.0 C5' B:UDP264 4.2 15.5 1.0 ND1 B:HIS212 4.2 14.4 1.0 OD1 B:ASP102 4.2 15.3 1.0 CG B:HIS212 4.3 14.2 1.0 NZ B:LYS218 4.3 16.9 1.0 O5' B:UDP264 4.3 16.0 1.0 O1A B:UDP264 4.4 16.8 1.0 O3B B:UDP264 4.5 18.3 1.0 O B:HOH423 4.5 25.5 1.0 CA B:LEU214 4.6 22.2 1.0 CB B:LEU214 4.6 23.5 1.0 C3' B:UDP264 4.6 13.9 1.0 C4' B:UDP264 4.8 13.9 1.0 CA B:ASP104 4.9 13.9 1.0 N B:ASP104 4.9 12.9 1.0 CA B:ASP102 4.9 12.7 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