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Manganese in PDB 6gxc: Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog

Enzymatic activity of Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog

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

Protein crystallography data

The structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog, PDB code: 6gxc was solved by M.Napiorkowska, K.P.Locher, J.Boilevin, T.Darbre, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.09 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.810, 116.540, 173.890, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 28.3

Other elements in 6gxc:

The structure of Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive 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 Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog (pdb code 6gxc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog, PDB code: 6gxc:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6gxc

Go back to Manganese Binding Sites List in 6gxc
Manganese binding site 1 out of 2 in the Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive 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 Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:92.0
occ:1.00
 OD1 A:ASP154 2.1 85.4 1.0
OD2 A:ASP56 2.8 92.6 1.0
CG A:ASP154 3.2 85.9 1.0
OE2 A:GLU319 3.3 91.4 1.0
OD2 A:ASP154 3.6 86.1 1.0
CG A:ASP56 3.7 93.1 1.0
OD1 A:ASP156 3.8 84.4 1.0
CB A:ASP56 3.9 93.1 1.0
NH1 A:ARG375 4.0 95.2 1.0
O15 A:FFK806 4.1 0.3 0.7
C04 A:FFK806 4.4 0.3 0.7
CD A:GLU319 4.4 91.0 1.0
CB A:ASP154 4.5 86.8 1.0
NH1 A:ARG147 4.5 81.5 1.0
OD1 A:ASP56 4.7 93.8 1.0
N14 A:FFK806 4.7 0.3 0.7
O17 A:FFK806 4.7 0.3 0.7
O18 A:FFK806 4.8 0.3 0.7
OE1 A:GLU319 4.8 91.1 1.0
OH A:TYR152 4.8 82.3 1.0
P16 A:FFK806 4.9 0.3 0.7
ND B:DAB13 4.9 94.5 1.0
CG A:ASP156 4.9 85.2 1.0

Manganese binding site 2 out of 2 in 6gxc

Go back to Manganese Binding Sites List in 6gxc
Manganese binding site 2 out of 2 in the Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive 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 Bacterial Oligosaccharyltransferase Pglb in Complex with An Inhibitory Peptide and A Reactive Lipid-Linked Oligosaccharide Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn802

b:0.9
occ:0.82
 OD2 A:ASP76 2.2 0.3 1.0
OE1 A:GLN73 2.4 0.8 1.0
OD1 A:ASP475 2.6 0.4 1.0
CG A:ASP76 3.4 0.1 1.0
CD A:GLN73 3.6 0.6 1.0
CG A:ASP475 3.7 0.6 1.0
NH2 A:ARG65 3.8 0.2 1.0
N A:GLN73 4.1 1.0 1.0
OD2 A:ASP475 4.2 0.1 1.0
CB A:ASP76 4.3 0.3 1.0
OE2 A:GLU62 4.3 0.7 1.0
OD1 A:ASP76 4.3 0.9 1.0
OD2 A:ASP66 4.3 0.2 1.0
CB A:GLN73 4.4 0.4 1.0
CG A:GLN73 4.5 0.3 1.0
NE2 A:GLN73 4.5 1.0 1.0
CB A:HIS72 4.6 0.7 1.0
CA A:HIS72 4.7 0.8 1.0
OD1 A:ASP66 4.8 0.6 1.0
C A:ASP475 4.8 0.9 1.0
O A:ASP475 4.8 0.6 1.0
C A:HIS72 4.9 0.9 1.0
CA A:GLN73 4.9 0.4 1.0
CA A:ASP475 4.9 99.2 1.0
CB A:ASP475 4.9 0.1 1.0
CG A:ARG456 4.9 0.4 1.0
CG A:ASP66 4.9 0.7 1.0
O A:VAL476 4.9 0.4 1.0

Reference:

M.Napiorkowska, J.Boilevin, T.Darbre, J.L.Reymond, K.P.Locher. Structure of Bacterial Oligosaccharyltransferase Pglb Bound to A Reactive Llo and An Inhibitory Peptide. Sci Rep V. 8 16297 2018.
ISSN: ESSN 2045-2322
PubMed: 30389987
DOI: 10.1038/S41598-018-34534-0
Page generated: Sun Oct 6 04:46:23 2024

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