Manganese in PDB 4wlm: Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese

The structure of Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese, PDB code: 4wlm was solved by H.Yu, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.306, 89.306, 154.303, 90.00, 90.00, 120.00
R / Rfree (%)	23 / 28.7

The binding sites of Manganese atom in the Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese (pdb code 4wlm). 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 Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese, PDB code: 4wlm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese


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 Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:39.4 occ:1.00 NE2 A:HIS382 1.9 41.6 1.0 OD2 A:ASP225 2.1 42.3 1.0 OD2 A:ASP227 2.3 42.5 1.0 OD1 A:ASP227 2.5 42.5 1.0 O3 A:SO4402 2.6 80.2 1.0 CE1 A:HIS382 2.6 41.4 1.0 CG A:ASP227 2.7 42.6 1.0 CD2 A:HIS382 3.1 41.6 1.0 CG A:ASP225 3.2 42.0 1.0 CB A:ASP225 3.6 42.2 1.0 ND1 A:HIS382 3.9 41.2 1.0 S A:SO4402 3.9 80.5 1.0 O1 A:SO4402 4.0 79.2 1.0 CG A:HIS382 4.1 41.6 1.0 CB A:ASN384 4.2 42.8 1.0 OD1 A:ASP225 4.2 42.0 1.0 CB A:ASP227 4.2 43.0 1.0 CA A:ASN384 4.5 43.5 1.0 O4 A:SO4402 4.6 80.4 1.0 O2 A:SO4402 4.9 80.0 1.0 N A:ASP227 5.0 43.5 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese


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 Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn404 b:46.1 occ:1.00 OD1 B:ASP227 2.1 55.5 1.0 OD2 B:ASP227 2.1 55.4 1.0 CG B:ASP227 2.4 55.3 1.0 OD2 B:ASP225 2.4 51.5 1.0 NE2 B:HIS382 2.4 51.6 1.0 CG B:ASP225 3.2 51.6 1.0 O2 B:SO4402 3.2 56.7 1.0 CD2 B:HIS382 3.4 51.9 1.0 CB B:ASP225 3.4 51.9 1.0 CE1 B:HIS382 3.4 51.3 1.0 CB B:ASP227 3.9 55.5 1.0 OD1 B:ASP225 4.3 51.4 1.0 CB B:ASN384 4.3 51.4 1.0 S B:SO4402 4.6 56.8 1.0 ND1 B:HIS382 4.6 51.7 1.0 CG B:HIS382 4.6 52.1 1.0 CA B:ASN384 4.6 52.3 1.0 N B:ASP227 4.7 55.6 1.0 CA B:ASP227 4.7 55.4 1.0 CA B:ASP225 4.9 52.3 1.0 O4 B:SO4402 4.9 57.1 1.0

H.Yu, M.Takeuchi, J.Lebarron, J.Kantharia, E.London, H.Bakker, R.S.Haltiwanger, H.Li, H.Takeuchi. Notch-Modifying Xylosyltransferase Structures Support An Sni-Like Retaining Mechanism. Nat.Chem.Biol. V. 11 847 2015.
ISSN: ESSN 1552-4469
PubMed: 26414444
DOI: 10.1038/NCHEMBIO.1927