Manganese in PDB 3t7n: Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Udp, in A Monoclinic Closed Form

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

The structure of Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Udp, in A Monoclinic Closed Form, PDB code: 3t7n 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)	29.16 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.020, 80.720, 69.850, 90.00, 100.92, 90.00
R / Rfree (%)	20.3 / 26.5

The binding sites of Manganese atom in the Crystal Structure of Human Glycogenin-1 (GYG1) Complexed with Manganese and Udp, in A Monoclinic Closed Form (pdb code 3t7n). 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 Monoclinic Closed Form, PDB code: 3t7n:
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 Monoclinic 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 Monoclinic Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn263 b:20.6 occ:1.00 OD2 A:ASP104 1.9 25.8 1.0 OD2 A:ASP102 2.0 21.9 1.0 O1A A:UDP264 2.0 24.4 1.0 OD1 A:ASP104 2.0 19.0 1.0 NE2 A:HIS212 2.1 24.1 1.0 CG A:ASP104 2.1 22.4 1.0 O3B A:UDP264 2.3 26.2 1.0 CG A:ASP102 3.0 17.6 1.0 CD2 A:HIS212 3.0 22.7 1.0 CE1 A:HIS212 3.1 23.6 1.0 PA A:UDP264 3.3 27.5 1.0 CB A:ASP102 3.4 18.1 1.0 PB A:UDP264 3.4 29.5 1.0 O3A A:UDP264 3.6 30.2 1.0 O3' A:UDP264 3.7 23.8 1.0 CB A:ASP104 3.8 19.8 1.0 O1B A:UDP264 3.9 28.3 1.0 OD1 A:ASP102 4.1 19.3 1.0 ND1 A:HIS212 4.2 21.7 1.0 NZ A:LYS218 4.2 20.7 1.0 CG A:HIS212 4.2 23.0 1.0 C5' A:UDP264 4.3 26.8 1.0 O5' A:UDP264 4.3 26.7 1.0 O2A A:UDP264 4.5 26.9 1.0 O A:HOH277 4.5 62.8 1.0 C3' A:UDP264 4.5 27.2 1.0 O2B A:UDP264 4.7 27.8 1.0 C4' A:UDP264 4.7 27.5 1.0 CA A:ASP104 4.7 19.3 1.0 CA A:LEU214 4.7 31.1 1.0 N A:ASP104 4.9 18.0 1.0 CA A:ASP102 4.9 16.5 1.0 C A:ASP104 5.0 19.1 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 Monoclinic 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 Monoclinic Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn263 b:16.1 occ:1.00 O2A B:UDP264 1.9 21.5 1.0 O1B B:UDP264 2.0 23.0 1.0 OD2 B:ASP102 2.0 11.3 1.0 OD1 B:ASP104 2.0 18.0 1.0 OD2 B:ASP104 2.1 18.6 1.0 NE2 B:HIS212 2.1 28.3 1.0 CG B:ASP104 2.4 17.5 1.0 CE1 B:HIS212 3.0 30.5 1.0 CG B:ASP102 3.0 18.7 1.0 CD2 B:HIS212 3.1 29.6 1.0 PB B:UDP264 3.2 27.1 1.0 PA B:UDP264 3.3 26.0 1.0 CB B:ASP102 3.5 17.0 1.0 O3A B:UDP264 3.6 26.9 1.0 O3' B:UDP264 3.8 24.1 1.0 O3B B:UDP264 3.8 24.2 1.0 CB B:ASP104 3.9 19.1 1.0 ND1 B:HIS212 4.2 30.4 1.0 OD1 B:ASP102 4.2 17.9 1.0 O1A B:UDP264 4.2 25.6 1.0 CG B:HIS212 4.2 31.0 1.0 C5' B:UDP264 4.2 25.5 1.0 O B:HOH269 4.2 28.4 1.0 O B:HOH368 4.3 28.2 1.0 O5' B:UDP264 4.3 25.8 1.0 NZ B:LYS218 4.4 28.6 1.0 O2B B:UDP264 4.4 30.5 1.0 CA B:LEU214 4.6 39.4 1.0 C3' B:UDP264 4.7 25.5 1.0 CA B:ASP104 4.8 19.1 1.0 N B:ASP104 4.9 18.4 1.0 C4' B:UDP264 4.9 24.8 1.0 CA B:ASP102 4.9 17.1 1.0 O B:ASP104 5.0 21.3 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