Manganese in PDB 4wlz: Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese and Udp

The structure of Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese and Udp, PDB code: 4wlz 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)	50.00 / 3.03
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.662, 89.662, 154.987, 90.00, 90.00, 120.00
R / Rfree (%)	23 / 28.8

The binding sites of Manganese atom in the Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese and Udp (pdb code 4wlz). 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 and Udp, PDB code: 4wlz:
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 and Udp


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 and Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:38.0 occ:1.00 OD2 A:ASP225 2.0 41.4 1.0 O1B A:UDP402 2.1 53.0 1.0 NE2 A:HIS382 2.2 41.4 1.0 O1A A:UDP402 2.3 51.8 1.0 OD1 A:ASP227 2.4 42.1 1.0 OD2 A:ASP227 2.4 42.4 1.0 CG A:ASP227 2.7 42.5 1.0 CE1 A:HIS382 3.1 41.1 1.0 CG A:ASP225 3.1 41.3 1.0 O3A A:UDP402 3.2 52.7 1.0 PB A:UDP402 3.2 53.1 1.0 CD2 A:HIS382 3.3 41.5 1.0 PA A:UDP402 3.3 52.2 1.0 CB A:ASP225 3.6 41.2 1.0 O2B A:UDP402 3.9 52.7 1.0 O3' A:UDP402 4.0 53.3 1.0 OD1 A:ASP225 4.2 41.3 1.0 CB A:ASP227 4.2 42.9 1.0 CB A:ASN384 4.2 44.1 1.0 C5' A:UDP402 4.2 53.5 1.0 O5' A:UDP402 4.3 52.6 1.0 ND1 A:HIS382 4.3 41.2 1.0 CG A:HIS382 4.4 41.5 1.0 O3B A:UDP402 4.4 53.2 1.0 CA A:ASN384 4.5 44.6 1.0 O2A A:UDP402 4.5 52.2 1.0 C3' A:UDP402 4.7 54.2 1.0 C4' A:UDP402 4.9 54.3 1.0 N A:ASP227 4.9 43.2 1.0

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


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 and Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:54.5 occ:1.00 OD2 B:ASP225 2.2 62.4 1.0 NE2 B:HIS382 2.2 62.6 1.0 O3B B:UDP402 2.3 98.0 1.0 O2A B:UDP402 2.3 100.0 1.0 OD1 B:ASP227 2.4 67.0 1.0 OD2 B:ASP227 2.4 66.2 1.0 CG B:ASP227 2.8 66.7 1.0 CE1 B:HIS382 3.0 62.4 1.0 CG B:ASP225 3.2 62.9 1.0 CD2 B:HIS382 3.3 62.8 1.0 PB B:UDP402 3.7 99.1 1.0 PA B:UDP402 3.7 0.5 1.0 CB B:ASP225 3.7 63.2 1.0 CB B:ASN384 3.9 61.8 1.0 O3A B:UDP402 4.1 0.3 1.0 OD1 B:ASP225 4.2 62.3 1.0 ND1 B:HIS382 4.2 62.9 1.0 CB B:ASP227 4.3 66.5 1.0 CA B:ASN384 4.3 62.0 1.0 C5' B:UDP402 4.3 0.0 1.0 O3' B:UDP402 4.3 0.5 1.0 O2B B:UDP402 4.3 98.2 1.0 CG B:HIS382 4.4 63.1 1.0 O5' B:UDP402 4.5 0.5 1.0 O1B B:UDP402 4.8 97.5 1.0 N B:ASN384 4.8 62.1 1.0 O1A B:UDP402 4.8 0.3 1.0 C3' B:UDP402 4.9 0.3 1.0 N B:ASP227 5.0 66.6 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