Manganese in PDB 6eql: Crystal Structure of Human Glycogenin-1 (GYG1) TYR195PIPHE Mutant Complexed with Manganese and Udp

All present enzymatic activity of Crystal Structure of Human Glycogenin-1 (GYG1) TYR195PIPHE Mutant Complexed with Manganese and Udp:
2.4.1.186;

The structure of Crystal Structure of Human Glycogenin-1 (GYG1) TYR195PIPHE Mutant Complexed with Manganese and Udp, PDB code: 6eql was solved by H.J.Bailey, J.Kopec, M.K.Bilyard, G.A.Bezerra, S.Seo Lee, C.H.Arrowsmith, A.M.Edwards, C.Bountra, B.G.Davis, W.W.Yue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.55 / 2.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.170, 81.050, 111.200, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 28.1

The structure of Crystal Structure of Human Glycogenin-1 (GYG1) TYR195PIPHE Mutant Complexed with Manganese and Udp also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Human Glycogenin-1 (GYG1) TYR195PIPHE Mutant Complexed with Manganese and Udp (pdb code 6eql). 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) TYR195PIPHE Mutant Complexed with Manganese and Udp, PDB code: 6eql:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human Glycogenin-1 (GYG1) TYR195PIPHE Mutant Complexed with Manganese and Udp


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) TYR195PIPHE Mutant Complexed with Manganese and Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:38.7 occ:1.00 O2B A:UDP301 2.1 35.3 1.0 NE2 A:HIS212 2.1 37.6 1.0 OD1 A:ASP104 2.1 48.3 1.0 OD2 A:ASP102 2.2 41.4 1.0 OD2 A:ASP104 2.2 40.9 1.0 O2A A:UDP301 2.2 57.2 1.0 CG A:ASP104 2.5 45.6 1.0 CE1 A:HIS212 3.0 38.0 1.0 O5' A:UDP301 3.1 51.5 1.0 PA A:UDP301 3.1 44.0 1.0 CG A:ASP102 3.2 38.9 1.0 CD2 A:HIS212 3.2 38.1 1.0 PB A:UDP301 3.4 42.2 1.0 CB A:ASP102 3.5 43.6 1.0 O3A A:UDP301 3.6 48.2 1.0 O3' A:UDP301 3.8 42.2 1.0 CB A:ASP104 4.0 37.1 1.0 NZ A:LYS218 4.1 39.0 1.0 O3B A:UDP301 4.1 45.0 1.0 ND1 A:HIS212 4.2 34.9 1.0 OD1 A:ASP102 4.3 42.2 1.0 CG A:HIS212 4.3 38.3 1.0 C5' A:UDP301 4.5 42.7 1.0 O1B A:UDP301 4.6 43.0 1.0 O1A A:UDP301 4.6 45.8 1.0 C3' A:UDP301 4.7 45.2 1.0 N A:ASP104 4.7 37.0 1.0 CA A:LEU214 4.8 46.6 1.0 CA A:ASP104 4.8 43.7 1.0 C4' A:UDP301 4.9 35.9 1.0 CA A:ASP102 4.9 37.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human Glycogenin-1 (GYG1) TYR195PIPHE Mutant Complexed with Manganese and Udp


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) TYR195PIPHE Mutant Complexed with Manganese and Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:44.0 occ:1.00 OD1 B:ASP104 2.2 49.2 1.0 OD2 B:ASP102 2.2 40.8 1.0 OD2 B:ASP104 2.2 41.0 1.0 O1B B:UDP301 2.2 55.9 1.0 NE2 B:HIS212 2.2 45.7 1.0 O1A B:UDP301 2.5 53.9 1.0 CG B:ASP104 2.5 39.2 1.0 CG B:ASP102 3.1 39.0 1.0 CE1 B:HIS212 3.2 43.0 1.0 CD2 B:HIS212 3.2 42.5 1.0 O5' B:UDP301 3.3 47.3 1.0 PA B:UDP301 3.4 46.5 1.0 PB B:UDP301 3.4 45.0 1.0 CB B:ASP102 3.5 43.9 1.0 O2B B:UDP301 3.8 37.5 1.0 CD2 B:LEU214 3.8 56.2 1.0 O3' B:UDP301 3.8 43.5 1.0 O3A B:UDP301 3.9 45.1 1.0 CB B:ASP104 4.0 38.2 1.0 O B:HOH413 4.0 46.1 1.0 NZ B:LYS218 4.2 43.6 1.0 OD1 B:ASP102 4.3 36.9 1.0 ND1 B:HIS212 4.3 41.2 1.0 CG B:HIS212 4.4 46.6 1.0 C5' B:UDP301 4.6 47.3 1.0 O3B B:UDP301 4.7 50.0 1.0 N B:ASP104 4.7 43.2 1.0 C3' B:UDP301 4.7 53.7 1.0 O2A B:UDP301 4.8 50.8 1.0 CA B:ASP104 4.8 42.1 1.0 CA B:ASP102 4.9 48.4 1.0 O B:PHE213 4.9 48.3 1.0 CG B:LEU214 5.0 45.3 1.0

M.K.Bilyard, H.J.Bailey, L.Raich, M.A.Gafitescu, T.Machida, J.Iglesias-Fernandez, S.S.Lee, C.D.Spicer, C.Rovira, W.W.Yue, B.G.Davis. Palladium-Mediated Enzyme Activation Suggests Multiphase Initiation of Glycogenesis. Nature V. 563 235 2018.
ISSN: ESSN 1476-4687
PubMed: 30356213
DOI: 10.1038/S41586-018-0644-7