Manganese in PDB 1v84: Crystal Structure of Human Glcat-P in Complex with N- Acetyllactosamine, Udp, and MN2+

All present enzymatic activity of Crystal Structure of Human Glcat-P in Complex with N- Acetyllactosamine, Udp, and MN2+:
2.4.1.135;

The structure of Crystal Structure of Human Glcat-P in Complex with N- Acetyllactosamine, Udp, and MN2+, PDB code: 1v84 was solved by S.Kakuda, T.Shiba, M.Ishiguro, H.Tagawa, S.Oka, Y.Kajihara, T.Kawasaki, S.Wakatsuki, R.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.311, 85.782, 122.766, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.4

The binding sites of Manganese atom in the Crystal Structure of Human Glcat-P in Complex with N- Acetyllactosamine, Udp, and MN2+ (pdb code 1v84). 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 Human Glcat-P in Complex with N- Acetyllactosamine, Udp, and MN2+, PDB code: 1v84:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human Glcat-P in Complex with N- Acetyllactosamine, Udp, and MN2+


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 Human Glcat-P in Complex with N- Acetyllactosamine, Udp, and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:18.2 occ:1.00 O A:HOH507 2.2 18.9 1.0 O3B A:UDP503 2.3 25.7 1.0 OD2 A:ASP197 2.3 16.8 1.0 O A:HOH508 2.3 14.8 1.0 OD1 A:ASP197 2.4 15.5 1.0 O2A A:UDP503 2.4 37.7 1.0 CG A:ASP197 2.7 16.8 1.0 O3A A:UDP503 3.1 30.1 1.0 PB A:UDP503 3.2 25.1 1.0 PA A:UDP503 3.5 27.1 1.0 O5' A:UDP503 3.6 31.2 1.0 O1B A:UDP503 3.8 26.9 1.0 CE1 A:HIS311 4.1 17.6 1.0 NH1 A:ARG313 4.1 39.5 1.0 CD A:ARG313 4.1 31.8 1.0 NE2 A:HIS311 4.1 16.9 1.0 O A:HOH581 4.1 20.1 1.0 CB A:ASP197 4.2 15.6 1.0 ND2 A:ASN198 4.2 11.3 1.0 OD1 A:ASP195 4.3 15.7 1.0 O A:THR312 4.3 15.2 1.0 CB A:ASP195 4.5 12.7 1.0 O2B A:UDP503 4.5 28.9 1.0 O1A A:UDP503 4.7 40.8 1.0 O A:HOH582 4.7 14.8 1.0 ND1 A:HIS311 4.8 17.8 1.0 C5' A:UDP503 4.9 22.7 1.0 CG A:ASP195 4.9 13.9 1.0 CD2 A:HIS311 4.9 16.0 1.0 CZ A:ARG313 5.0 37.4 1.0 CG A:ASN198 5.0 16.9 1.0 NE A:ARG313 5.0 35.0 1.0 CA A:ASP197 5.0 15.4 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human Glcat-P in Complex with N- Acetyllactosamine, Udp, and MN2+


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 Human Glcat-P in Complex with N- Acetyllactosamine, Udp, and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:18.8 occ:1.00 O B:HOH510 2.2 17.6 1.0 O B:HOH509 2.2 16.7 1.0 O3B B:UDP504 2.2 26.7 1.0 OD1 B:ASP197 2.3 18.7 1.0 OD2 B:ASP197 2.3 15.8 1.0 O2A B:UDP504 2.4 41.8 1.0 CG B:ASP197 2.6 16.7 1.0 O3A B:UDP504 3.1 34.8 1.0 PB B:UDP504 3.2 28.9 1.0 PA B:UDP504 3.5 32.5 1.0 O5' B:UDP504 3.6 34.7 1.0 O1B B:UDP504 3.8 29.5 1.0 NE B:ARG313 3.9 38.4 1.0 CD B:ARG313 4.0 33.7 1.0 NE2 B:HIS311 4.1 18.4 1.0 O B:HOH550 4.1 18.7 1.0 ND2 B:ASN198 4.1 12.9 1.0 CE1 B:HIS311 4.1 17.8 1.0 CB B:ASP197 4.2 15.8 1.0 O B:THR312 4.3 18.3 1.0 OD1 B:ASP195 4.4 17.8 1.0 O2B B:UDP504 4.4 31.4 1.0 CB B:ASP195 4.5 14.1 1.0 O1A B:UDP504 4.7 42.7 1.0 O B:HOH541 4.7 18.8 1.0 ND1 B:HIS311 4.8 20.5 1.0 CD2 B:HIS311 4.8 19.3 1.0 C5' B:UDP504 4.8 24.1 1.0 CG B:ASN198 4.8 16.7 1.0 CZ B:ARG313 4.9 39.2 1.0 CG B:ASP195 4.9 15.2 1.0 CA B:ASP197 5.0 15.6 1.0

S.Kakuda, T.Shiba, M.Ishiguro, H.Tagawa, S.Oka, Y.Kajihara, T.Kawasaki, S.Wakatsuki, R.Kato. Structural Basis For Acceptor Substrate Recognition of A Human Glucuronyltransferase, Glcat-P, An Enzyme Critical in the Biosynthesis of the Carbohydrate Epitope Hnk-1 J.Biol.Chem. V. 279 22693 2004.
ISSN: ISSN 0021-9258
PubMed: 14993226
DOI: 10.1074/JBC.M400622200