Manganese in PDB 5ggi: Crystal Structure of Human Protein O-Mannose Beta-1,2-N- Acetylglucosaminyltransferase in Complex with Mn, Udp and Mannosyl- Peptide

The structure of Crystal Structure of Human Protein O-Mannose Beta-1,2-N- Acetylglucosaminyltransferase in Complex with Mn, Udp and Mannosyl- Peptide, PDB code: 5ggi was solved by N.Kuwabara, T.Senda, R.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.37 / 2.60
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.162, 126.539, 172.865, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.9

The binding sites of Manganese atom in the Crystal Structure of Human Protein O-Mannose Beta-1,2-N- Acetylglucosaminyltransferase in Complex with Mn, Udp and Mannosyl- Peptide (pdb code 5ggi). 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 Protein O-Mannose Beta-1,2-N- Acetylglucosaminyltransferase in Complex with Mn, Udp and Mannosyl- Peptide, PDB code: 5ggi:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human Protein O-Mannose Beta-1,2-N- Acetylglucosaminyltransferase in Complex with Mn, Udp and Mannosyl- Peptide


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 Protein O-Mannose Beta-1,2-N- Acetylglucosaminyltransferase in Complex with Mn, Udp and Mannosyl- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:0.4 occ:1.00 O2A A:UDP701 1.9 0.1 1.0 OD2 A:ASP395 2.1 62.4 1.0 NE2 A:HIS500 2.4 54.8 1.0 O1B A:UDP701 2.9 0.1 1.0 CG A:ASP395 3.1 53.2 1.0 PA A:UDP701 3.3 0.3 1.0 CE1 A:HIS500 3.3 51.9 1.0 CD2 A:HIS500 3.4 49.4 1.0 OD1 A:ASP395 3.5 51.1 1.0 O2B A:UDP701 3.5 0.8 1.0 PB A:UDP701 3.6 0.1 1.0 OE1 A:GLU393 3.6 96.3 1.0 O3A A:UDP701 3.8 0.9 1.0 O5' A:UDP701 3.9 0.3 1.0 NH1 A:ARG311 4.3 56.3 1.0 NH2 A:ARG311 4.3 42.6 1.0 O1A A:UDP701 4.4 0.5 1.0 ND1 A:HIS500 4.4 53.9 1.0 CB A:ASP395 4.4 51.4 1.0 CG A:HIS500 4.5 47.6 1.0 C5' A:UDP701 4.5 0.4 1.0 CD A:GLU393 4.7 92.3 1.0 CZ A:ARG311 4.8 49.6 1.0 O A:GLY502 4.9 77.6 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human Protein O-Mannose Beta-1,2-N- Acetylglucosaminyltransferase in Complex with Mn, Udp and Mannosyl- Peptide


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 Protein O-Mannose Beta-1,2-N- Acetylglucosaminyltransferase in Complex with Mn, Udp and Mannosyl- Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn702 b:0.5 occ:1.00 OD2 B:ASP395 1.9 0.4 1.0 O2A B:UDP701 2.1 0.4 1.0 NE2 B:HIS500 2.6 65.6 1.0 O2B B:UDP701 2.7 0.8 1.0 CG B:ASP395 2.8 0.5 1.0 OD1 B:ASP395 3.1 0.6 1.0 PA B:UDP701 3.2 0.5 1.0 O5' B:UDP701 3.3 0.8 1.0 CD2 B:HIS500 3.5 55.6 1.0 CE1 B:HIS500 3.6 66.7 1.0 PB B:UDP701 3.9 0.1 1.0 O3A B:UDP701 3.9 0.9 1.0 OE2 B:GLU393 4.1 83.4 1.0 CB B:ASP395 4.2 81.6 1.0 NH2 B:ARG311 4.3 44.3 1.0 O1A B:UDP701 4.4 0.2 1.0 O1B B:UDP701 4.5 0.9 1.0 NH1 B:ARG311 4.6 56.2 1.0 C5' B:UDP701 4.6 0.3 1.0 CG B:HIS500 4.6 52.3 1.0 ND1 B:HIS500 4.6 62.8 1.0 CD B:GLU393 4.9 74.5 1.0 CZ B:ARG311 5.0 53.9 1.0

N.Kuwabara, H.Manya, T.Yamada, H.Tateno, M.Kanagawa, K.Kobayashi, K.Akasaka-Manya, Y.Hirose, M.Mizuno, M.Ikeguchi, T.Toda, J.Hirabayashi, T.Senda, T.Endo, R.Kato. Carbohydrate-Binding Domain of the POMGNT1 Stem Region Modulates O-Mannosylation Sites of Alpha-Dystroglycan Proc.Natl.Acad.Sci.Usa V. 113 9280 2016.
ISSN: ESSN 1091-6490
PubMed: 27493216
DOI: 10.1073/PNAS.1525545113