Manganese in PDB 3u2w: Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Glucose or A Glucal Species

All present enzymatic activity of Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Glucose or A Glucal Species:
2.4.1.186;

The structure of Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Glucose or A Glucal Species, PDB code: 3u2w 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)	22.59 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.290, 80.180, 69.530, 90.00, 100.67, 90.00
R / Rfree (%)	15.7 / 19

The binding sites of Manganese atom in the Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Glucose or A Glucal Species (pdb code 3u2w). 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 Glucose or A Glucal Species, PDB code: 3u2w:
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 Glucose or A Glucal Species


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 Glucose or A Glucal Species within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn263 b:13.1 occ:1.00 O3B A:UDP264 2.0 15.4 1.0 O2A A:UDP264 2.0 13.7 1.0 OD2 A:ASP102 2.0 13.6 1.0 OD1 A:ASP104 2.1 13.4 1.0 NE2 A:HIS212 2.2 13.5 1.0 OD2 A:ASP104 2.5 14.1 1.0 CG A:ASP104 2.6 13.8 1.0 CG A:ASP102 3.1 11.8 1.0 CD2 A:HIS212 3.1 12.2 1.0 CE1 A:HIS212 3.2 14.6 1.0 PB A:UDP264 3.2 15.4 1.0 PA A:UDP264 3.3 15.1 1.0 O3A A:UDP264 3.5 12.8 1.0 CB A:ASP102 3.5 11.0 1.0 O3' A:UDP264 3.8 12.1 1.0 O2B A:UDP264 3.9 14.4 1.0 O2 A:GLC267 4.1 12.7 0.5 CB A:ASP104 4.1 15.6 1.0 NZ A:LYS218 4.2 12.8 1.0 C5' A:UDP264 4.2 15.3 1.0 O3 A:GLC267 4.2 11.8 0.5 OD1 A:ASP102 4.2 14.1 1.0 O5' A:UDP264 4.3 15.8 1.0 ND1 A:HIS212 4.3 12.9 1.0 CG A:HIS212 4.3 13.5 1.0 C3 A:GLC267 4.4 31.9 0.5 O1A A:UDP264 4.5 15.2 1.0 O1B A:UDP264 4.5 15.2 1.0 CA A:LEU214 4.6 13.9 1.0 C3' A:UDP264 4.6 13.8 1.0 C4' A:UDP264 4.8 15.0 1.0 C3 A:LCN268 4.8 46.2 0.4 O3 A:LCN268 4.8 62.1 0.4 N A:LEU214 4.9 14.9 1.0 C2 A:GLC267 4.9 27.9 0.5 N A:ASP104 5.0 11.8 1.0 CA A:ASP104 5.0 13.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Glucose or A Glucal Species


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 Glucose or A Glucal Species within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn263 b:14.7 occ:1.00 O1A B:UDP264 2.0 16.0 1.0 O1B B:UDP264 2.0 17.9 1.0 OD1 B:ASP104 2.1 13.3 1.0 OD2 B:ASP102 2.1 13.8 1.0 OD2 B:ASP104 2.1 15.8 1.0 NE2 B:HIS212 2.2 15.5 1.0 CG B:ASP104 2.5 14.1 1.0 CD2 B:HIS212 3.1 13.1 1.0 CE1 B:HIS212 3.2 14.8 1.0 CG B:ASP102 3.2 13.2 1.0 PB B:UDP264 3.2 17.6 1.0 PA B:UDP264 3.3 17.2 1.0 CB B:ASP102 3.5 12.9 1.0 O3A B:UDP264 3.5 16.4 1.0 O2B B:UDP264 3.8 18.1 1.0 O3' B:UDP264 3.9 13.5 1.0 CB B:ASP104 4.0 15.4 1.0 NZ B:LYS218 4.3 18.4 1.0 C5' B:UDP264 4.3 16.3 1.0 ND1 B:HIS212 4.3 15.5 1.0 O3 B:GLC266 4.3 15.5 0.8 CG B:HIS212 4.3 14.6 1.0 OD1 B:ASP102 4.3 13.9 1.0 O5' B:UDP264 4.3 14.0 1.0 O2 B:GLC266 4.4 35.2 0.8 CA B:LEU214 4.4 24.4 1.0 O2A B:UDP264 4.4 18.1 1.0 O3B B:UDP264 4.5 18.2 1.0 C3 B:GLC266 4.5 35.2 0.8 C3' B:UDP264 4.7 14.3 1.0 N B:LEU214 4.8 20.1 1.0 CB B:LEU214 4.9 31.9 1.0 CA B:ASP104 4.9 14.1 1.0 N B:ASP104 4.9 12.2 1.0 C4' B:UDP264 4.9 15.6 1.0 O B:ASP104 5.0 13.4 1.0 CA B:ASP102 5.0 12.2 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