Manganese in PDB 6yv8: Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp and MN2+

The structure of Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp and MN2+, PDB code: 6yv8 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)	48.71 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.998, 107.644, 164.418, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 28

The binding sites of Manganese atom in the Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp and MN2+ (pdb code 6yv8). 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 and MN2+, PDB code: 6yv8:
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 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 and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:0.3 occ:1.00 O1B A:GDP401 2.1 0.1 1.0 O1A A:GDP401 2.2 78.6 1.0 OD2 A:ASP137 2.7 0.2 1.0 PB A:GDP401 3.2 0.2 1.0 CG A:ASP137 3.3 98.1 1.0 OD1 A:ASP137 3.4 97.1 1.0 PA A:GDP401 3.5 87.6 1.0 O3B A:GDP401 3.6 0.4 1.0 O3A A:GDP401 3.8 88.7 1.0 NH2 A:ARG261 4.4 87.1 1.0 NE1 A:TRP257 4.5 91.2 1.0 O2B A:GDP401 4.5 0.3 1.0 C5' A:GDP401 4.5 89.2 1.0 O2A A:GDP401 4.5 92.2 1.0 O5' A:GDP401 4.5 89.0 1.0 CB A:ASP137 4.5 94.2 1.0 OD2 A:ASP135 4.8 92.2 1.0 O A:ALA248 4.9 0.3 1.0

Manganese binding site 2 out of 2 in the Mannosyltransferase Pcmangt From Pyrobaculum Calidifontis in Complex with Gdp 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 and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:0.5 occ:1.00 O2A B:GDP401 2.0 0.6 1.0 O2B B:GDP401 2.2 0.6 1.0 OD2 B:ASP137 2.5 0.3 1.0 CG B:ASP137 3.2 1.0 1.0 OD1 B:ASP137 3.2 0.9 1.0 PA B:GDP401 3.3 0.1 1.0 PB B:GDP401 3.3 0.1 1.0 O3A B:GDP401 3.6 71.3 1.0 O1B B:GDP401 3.9 0.5 1.0 C5' B:GDP401 4.2 93.0 1.0 NH2 B:ARG261 4.2 77.2 1.0 O5' B:GDP401 4.2 96.0 1.0 O1A B:GDP401 4.3 0.5 1.0 NE1 B:TRP257 4.5 86.0 1.0 O3B B:GDP401 4.5 99.0 1.0 CB B:ASP137 4.6 96.3 1.0 OD2 B:ASP135 4.8 85.7 1.0 O B:ALA248 4.9 0.7 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