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

Enzymatic activity of 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;

Protein crystallography data

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

Manganese Binding Sites:

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 3t7m

Go back to Manganese Binding Sites List in 3t7m
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 3t7m

Go back to Manganese Binding Sites List in 3t7m
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

Reference:

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
Page generated: Sat Oct 5 17:59:28 2024

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