Manganese in PDB 6yv9: Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp-Man and MN2+

The structure of Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp-Man and MN2+, PDB code: 6yv9 was solved by C.Divne, R.Gandini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.41 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.465, 107.418, 163.845, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 26.5

The binding sites of Manganese atom in the Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp-Man and MN2+ (pdb code 6yv9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp-Man and MN2+, PDB code: 6yv9:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp-Man and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp-Man and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:0.0 occ:1.00 OD2 A:ASP137 2.4 0.2 1.0 O2B A:GDD400 2.5 0.2 1.0 CG A:ASP137 3.0 99.1 1.0 OD1 A:ASP137 3.1 89.4 1.0 O2A A:GDD400 3.2 0.3 1.0 PB A:GDD400 4.0 0.3 1.0 NH2 A:ARG261 4.2 0.7 1.0 C5' A:GDD400 4.2 85.6 1.0 NE1 A:TRP257 4.3 89.0 1.0 PA A:GDD400 4.3 0.5 1.0 CB A:ASP137 4.5 90.9 1.0 O3A A:GDD400 4.6 0.6 1.0 OD2 A:ASP135 4.6 71.4 1.0 O5' A:GDD400 4.7 0.1 1.0 O3B A:GDD400 4.8 0.4 1.0 O1B A:GDD400 4.8 0.8 1.0 CB A:ASP135 4.9 58.4 1.0

Manganese binding site 2 out of 2 in the Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp-Man and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp-Man and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:0.1 occ:1.00 OD2 B:ASP137 2.6 1.0 1.0 O2B B:GDD400 2.9 0.3 1.0 O2A B:GDD400 3.2 0.8 1.0 CG B:ASP137 3.5 87.0 1.0 OD1 B:ASP137 3.7 88.0 1.0 NE1 B:TRP257 4.0 86.1 1.0 NH2 B:ARG261 4.3 0.9 1.0 PB B:GDD400 4.4 0.0 1.0 PA B:GDD400 4.6 98.1 1.0 CE2 B:TRP257 4.8 82.8 1.0 CB B:ASP137 4.8 65.6 1.0 CZ2 B:TRP257 4.8 85.2 1.0 O3B B:GDD400 4.9 0.6 1.0 C5' B:GDD400 5.0 82.4 1.0 O B:ALA248 5.0 0.3 1.0 CD1 B:TRP257 5.0 79.6 1.0

R.Gandini, T.Reichenbach, O.Spadiut, T.C.Tan, D.C.Kalyani, C.Divne. A Transmembrane Crenarchaeal Mannosyltransferase Is Involved in N-Glycan Biosynthesis and Displays An Unexpected Minimal Cellulose-Synthase-Like Fold. J.Mol.Biol. V. 432 4658 2020.
ISSN: ESSN 1089-8638
PubMed: 32569746
DOI: 10.1016/J.JMB.2020.06.016