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Manganese in PDB 5ogl: Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog

Enzymatic activity of Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog

All present enzymatic activity of Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog:
2.4.99.19;

Protein crystallography data

The structure of Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog, PDB code: 5ogl was solved by M.Napiorkowska, J.Boilevin, T.Sovdat, T.Darbre, J.-L.Reymond, M.Aebi, K.P.Locher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.77 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.940, 116.180, 172.020, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.4

Other elements in 5ogl:

The structure of Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog (pdb code 5ogl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog, PDB code: 5ogl:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5ogl

Go back to Manganese Binding Sites List in 5ogl
Manganese binding site 1 out of 2 in the Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:48.9
occ:1.00
O A:HOH903 2.2 44.3 1.0
O A:HOH910 2.2 58.5 1.0
OD1 A:ASP154 2.2 55.8 1.0
O A:HOH902 2.4 56.8 1.0
OD2 A:ASP56 2.6 57.4 1.0
CG A:ASP56 3.3 57.9 1.0
CG A:ASP154 3.3 56.3 1.0
CB A:ASP56 3.6 57.9 1.0
OE2 A:GLU319 3.6 58.7 1.0
OD2 A:ASP154 3.7 56.5 1.0
OD1 A:ASP56 4.2 58.6 1.0
OD1 A:ASP156 4.3 57.9 1.0
CD A:GLU319 4.5 58.3 1.0
OE1 A:GLU319 4.5 58.3 1.0
CB A:ASP154 4.7 57.2 1.0
NH1 A:ARG147 4.7 57.9 1.0
CB B:ASN13 4.8 57.3 1.0
O27 A:9UB803 4.8 73.7 1.0

Manganese binding site 2 out of 2 in 5ogl

Go back to Manganese Binding Sites List in 5ogl
Manganese binding site 2 out of 2 in the Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Acceptor Peptide and An Lipid-Linked Oligosaccharide Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn802

b:70.0
occ:0.74
O A:HOH906 2.2 62.7 1.0
OD1 A:ASP475 2.3 70.2 1.0
OD2 A:ASP76 2.4 70.7 1.0
OE1 A:GLN73 2.6 72.0 1.0
CG A:ASP475 3.4 69.3 1.0
CG A:ASP76 3.5 71.5 1.0
NH2 A:ARG65 3.5 66.4 1.0
OD2 A:ASP475 3.8 68.9 1.0
CD A:GLN73 3.8 72.8 1.0
OE2 A:GLU62 4.0 66.2 1.0
OD2 A:ASP66 4.0 71.0 1.0
N A:GLN73 4.2 71.7 1.0
CB A:ASP76 4.2 72.7 1.0
OD1 A:ASP66 4.4 70.3 1.0
OD1 A:ASP76 4.4 71.3 1.0
CB A:GLN73 4.5 74.7 1.0
CB A:ASP475 4.6 68.9 1.0
CG A:ASP66 4.6 70.5 1.0
CG A:GLN73 4.7 74.5 1.0
NE2 A:GLN73 4.7 72.2 1.0
CA A:ASP475 4.7 66.2 1.0
CB A:HIS72 4.7 71.2 1.0
C A:ASP475 4.7 68.0 1.0
CZ A:ARG65 4.8 65.4 1.0
CA A:HIS72 4.8 74.3 1.0
O A:ASP475 4.8 68.7 1.0
CG A:ARG456 4.9 72.3 1.0
C A:HIS72 5.0 75.5 1.0

Reference:

M.Napiorkowska, J.Boilevin, T.Sovdat, T.Darbre, J.L.Reymond, M.Aebi, K.P.Locher. Molecular Basis of Lipid-Linked Oligosaccharide Recognition and Processing By Bacterial Oligosaccharyltransferase. Nat. Struct. Mol. Biol. V. 24 1100 2017.
ISSN: ESSN 1545-9985
PubMed: 29058712
DOI: 10.1038/NSMB.3491
Page generated: Tue Dec 15 04:45:34 2020

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