Manganese in PDB 3cu0: Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex with Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser

All present enzymatic activity of Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex with Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser:
2.4.1.135;

The structure of Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex with Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser, PDB code: 3cu0 was solved by Y.Tone, L.C.Pedersen, T.Yamamoto, H.Kitagawa, J.Nishihara-Shimizu, J.Tamura, M.Negishi, K.Sugahara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.57 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.047, 48.399, 103.708, 90.00, 92.40, 90.00
R / Rfree (%)	21 / 23.4

The binding sites of Manganese atom in the Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex with Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser (pdb code 3cu0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex with Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser, PDB code: 3cu0:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex with Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex with Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:24.9 occ:1.00 OD2 A:ASP196 2.2 23.6 1.0 O A:HOH504 2.2 23.1 1.0 OD1 A:ASP196 2.3 22.7 1.0 O2A A:UDP501 2.3 25.1 1.0 O3B A:UDP501 2.3 31.0 1.0 O A:HOH505 2.3 20.7 1.0 CG A:ASP196 2.5 20.8 1.0 PB A:UDP501 3.1 32.2 1.0 PA A:UDP501 3.3 27.2 1.0 O3A A:UDP501 3.4 30.5 1.0 O1B A:UDP501 3.7 32.5 1.0 CB A:ASP196 4.0 21.8 1.0 O A:HOH547 4.1 28.8 1.0 O1A A:UDP501 4.1 26.6 1.0 CG A:ARG310 4.2 31.2 1.0 NE2 A:HIS308 4.3 23.5 1.0 OD1 A:ASN197 4.3 17.5 1.0 CE1 A:HIS308 4.3 25.4 1.0 O A:THR309 4.3 22.5 1.0 NH1 A:ARG310 4.4 45.1 1.0 OD1 A:ASP194 4.4 20.8 1.0 O2B A:UDP501 4.5 33.7 1.0 CB A:ASP194 4.5 14.8 1.0 O5' A:UDP501 4.6 26.5 1.0 O A:HOH522 4.8 22.4 1.0 C5' A:UDP501 4.9 23.8 1.0 CA A:ASP196 4.9 19.6 1.0 CD A:ARG310 4.9 34.0 1.0 N A:ASP196 4.9 18.6 1.0 CG A:ASP194 5.0 16.1 1.0 CG A:ASN197 5.0 18.1 1.0 CD2 A:HIS308 5.0 23.2 1.0

Manganese binding site 2 out of 2 in the Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex with Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Beta 1,3-Glucuronyltransferase I (Glcat-I) in Complex with Udp and Gal-Gal(6-SO4)-Xyl(2-PO4)-O-Ser within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn504 b:25.2 occ:1.00 O3B A:UDP503 2.1 27.5 1.0 OD1 B:ASP196 2.2 21.0 1.0 O B:HOH505 2.2 20.8 1.0 O B:HOH506 2.3 25.3 1.0 O2A A:UDP503 2.3 24.4 1.0 OD2 B:ASP196 2.3 20.7 1.0 CG B:ASP196 2.6 19.6 1.0 PB A:UDP503 3.1 31.7 1.0 PA A:UDP503 3.4 26.8 1.0 O3A A:UDP503 3.4 29.9 1.0 NH1 B:ARG310 4.0 48.5 1.0 O1B A:UDP503 4.0 33.9 1.0 O A:HOH514 4.0 25.9 1.0 CB B:ASP196 4.1 21.0 1.0 CE1 B:HIS308 4.2 23.7 1.0 CG B:ARG310 4.2 33.5 1.0 O1A A:UDP503 4.2 28.0 1.0 NE2 B:HIS308 4.2 22.9 1.0 OD1 B:ASN197 4.2 20.1 1.0 O2B A:UDP503 4.3 31.4 1.0 O B:THR309 4.3 20.9 1.0 OD1 B:ASP194 4.5 21.3 1.0 CB B:ASP194 4.6 17.8 1.0 O5' A:UDP503 4.6 27.0 1.0 O B:HOH542 4.8 23.3 1.0 C5' A:UDP503 4.9 25.9 1.0 ND1 B:HIS308 4.9 24.7 1.0 CG B:ASN197 4.9 18.6 1.0 CA B:ASP196 4.9 21.9 1.0 CD B:ARG310 4.9 38.7 1.0 N B:ASP196 5.0 21.2 1.0 CD2 B:HIS308 5.0 21.9 1.0

Y.Tone, L.C.Pedersen, T.Yamamoto, T.Izumikawa, H.Kitagawa, J.Nishihara, J.Tamura, M.Negishi, K.Sugahara. 2-O-Phosphorylation of Xylose and 6-O-Sulfation of Galactose in the Protein Linkage Region of Glycosaminoglycans Influence the Glucuronyltransferase-I Activity Involved in the Linkage Region Synthesis. J.Biol.Chem. V. 283 16801 2008.
ISSN: ISSN 0021-9258
PubMed: 18400750
DOI: 10.1074/JBC.M709556200