Manganese in PDB 2fyd: Catalytic Domain of Bovine Beta 1, 4-Galactosyltransferase in Complex with Alpha-Lactalbumin, Glucose, Mn, and Udp-N- Acetylgalactosamine

The structure of Catalytic Domain of Bovine Beta 1, 4-Galactosyltransferase in Complex with Alpha-Lactalbumin, Glucose, Mn, and Udp-N- Acetylgalactosamine, PDB code: 2fyd was solved by B.Ramakrishnan, V.Ramasamy, P.K.Qasba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.08 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.068, 95.376, 100.389, 90.00, 101.33, 90.00
R / Rfree (%)	20.1 / 24.2

The structure of Catalytic Domain of Bovine Beta 1, 4-Galactosyltransferase in Complex with Alpha-Lactalbumin, Glucose, Mn, and Udp-N- Acetylgalactosamine also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Manganese atom in the Catalytic Domain of Bovine Beta 1, 4-Galactosyltransferase in Complex with Alpha-Lactalbumin, Glucose, Mn, and Udp-N- Acetylgalactosamine (pdb code 2fyd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Catalytic Domain of Bovine Beta 1, 4-Galactosyltransferase in Complex with Alpha-Lactalbumin, Glucose, Mn, and Udp-N- Acetylgalactosamine, PDB code: 2fyd:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Catalytic Domain of Bovine Beta 1, 4-Galactosyltransferase in Complex with Alpha-Lactalbumin, Glucose, Mn, and Udp-N- Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Catalytic Domain of Bovine Beta 1, 4-Galactosyltransferase in Complex with Alpha-Lactalbumin, Glucose, Mn, and Udp-N- Acetylgalactosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn405 b:28.4 occ:1.00 O1A B:UDP406 2.0 30.1 1.0 NE2 B:HIS347 2.2 30.5 1.0 OD2 B:ASP254 2.2 29.7 1.0 O B:HOH1008 2.4 28.9 1.0 O2B B:UDP406 2.4 35.4 1.0 SD B:MET344 2.8 33.7 1.0 CD2 B:HIS347 3.2 31.9 1.0 CE1 B:HIS347 3.2 31.4 1.0 CG B:ASP254 3.2 28.0 1.0 PA B:UDP406 3.3 32.6 1.0 PB B:UDP406 3.4 37.0 1.0 O3B B:UDP406 3.4 61.8 1.0 OD1 B:ASP254 3.5 27.7 1.0 O3A B:UDP406 3.7 35.8 1.0 CG B:MET344 3.8 31.7 1.0 CE B:MET344 3.8 35.4 1.0 O3' B:UDP406 4.0 28.6 1.0 O5' B:UDP406 4.0 36.2 1.0 O B:HOH985 4.0 41.6 1.0 O2A B:UDP406 4.2 33.4 1.0 ND1 B:HIS347 4.3 30.6 1.0 CG B:HIS347 4.3 33.9 1.0 NH2 B:ARG191 4.5 28.0 1.0 CB B:ASP254 4.5 27.4 1.0 NH1 B:ARG191 4.7 30.4 1.0 O1B B:UDP406 4.8 41.7 1.0 C3' B:UDP406 4.9 25.4 1.0

Manganese binding site 2 out of 2 in the Catalytic Domain of Bovine Beta 1, 4-Galactosyltransferase in Complex with Alpha-Lactalbumin, Glucose, Mn, and Udp-N- Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Catalytic Domain of Bovine Beta 1, 4-Galactosyltransferase in Complex with Alpha-Lactalbumin, Glucose, Mn, and Udp-N- Acetylgalactosamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn527 b:27.4 occ:1.00 O D:HOH911 2.0 27.2 1.0 O1A D:UDP528 2.1 27.0 1.0 NE2 D:HIS347 2.2 29.9 1.0 O2B D:UDP528 2.3 22.9 1.0 OD2 D:ASP254 2.3 19.0 1.0 SD D:MET344 2.8 30.4 1.0 CE1 D:HIS347 3.1 28.5 1.0 CG D:ASP254 3.3 22.6 1.0 CD2 D:HIS347 3.3 27.6 1.0 PA D:UDP528 3.4 28.4 1.0 PB D:UDP528 3.4 29.3 1.0 O3B D:UDP528 3.4 32.1 1.0 OD1 D:ASP254 3.5 20.7 1.0 CE D:MET344 3.6 29.5 1.0 O3A D:UDP528 3.7 29.9 1.0 CG D:MET344 3.8 27.6 1.0 O D:HOH926 3.8 34.3 1.0 O5' D:UDP528 4.1 30.8 1.0 O3' D:UDP528 4.1 22.3 1.0 O2A D:UDP528 4.2 27.2 1.0 ND1 D:HIS347 4.3 27.7 1.0 CG D:HIS347 4.4 30.3 1.0 NH2 D:ARG191 4.4 22.5 1.0 NH1 D:ARG191 4.6 22.7 1.0 CB D:ASP254 4.6 20.9 1.0 C8 D:NGA529 4.8 53.4 1.0 O1B D:UDP528 4.8 32.0 1.0 O D:HOH1370 4.9 58.7 1.0 C3' D:UDP528 4.9 22.7 1.0 O D:ILE345 5.0 25.9 1.0 CZ D:ARG191 5.0 24.7 1.0

B.Ramakrishnan, V.Ramasamy, P.K.Qasba. Structural Snapshots of Beta-1,4-Galactosyltransferase-I Along the Kinetic Pathway. J.Mol.Biol. V. 357 1619 2006.
ISSN: ISSN 0022-2836
PubMed: 16497331
DOI: 10.1016/J.JMB.2006.01.088