Calcium 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:

Manganese

(Mn)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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 A:Ca124 b:23.5 occ:1.00 O A:GLU84 2.3 21.6 1.0 O A:LYS79 2.4 19.9 1.0 OD1 A:ASP87 2.4 23.2 1.0 OD2 A:ASP88 2.4 23.6 1.0 OD1 A:ASP82 2.5 28.3 1.0 O A:HOH910 2.5 27.3 1.0 O A:HOH901 2.6 21.9 1.0 C A:GLU84 3.4 24.2 1.0 CG A:ASP82 3.4 26.6 1.0 CG A:ASP87 3.4 25.5 1.0 CG A:ASP88 3.6 24.1 1.0 C A:LYS79 3.6 23.6 1.0 OD2 A:ASP82 3.6 26.1 1.0 OD2 A:ASP87 3.7 23.9 1.0 OD1 A:ASP88 4.0 24.3 1.0 CA A:LEU80 4.2 22.4 1.0 CA A:GLU84 4.3 23.2 1.0 O A:HOH1015 4.3 26.1 1.0 N A:GLU84 4.3 24.0 1.0 N A:LEU85 4.3 24.0 1.0 O A:ASP82 4.4 29.6 1.0 N A:LEU80 4.4 23.2 1.0 CB A:GLU84 4.5 22.2 1.0 N A:ASP88 4.5 20.3 1.0 CA A:LEU85 4.5 25.2 1.0 N A:ASP82 4.6 26.6 1.0 C A:LEU80 4.7 24.4 1.0 CB A:ASP82 4.7 26.0 1.0 C A:ASP82 4.7 28.9 1.0 CA A:LYS79 4.7 23.0 1.0 CB A:ASP88 4.8 21.4 1.0 CB A:ASP87 4.8 20.9 1.0 N A:ASP87 4.9 24.9 1.0 CA A:ASP82 4.9 27.5 1.0 CD2 A:LEU80 5.0 17.1 1.0 C A:LEU85 5.0 24.0 1.0 CD1 A:LEU85 5.0 25.4 1.0

Calcium 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 Calcium with other atoms in the Ca 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 C:Ca526 b:27.5 occ:1.00 O C:GLU84 2.2 34.6 1.0 OD1 C:ASP87 2.3 27.0 1.0 O C:HOH919 2.4 27.5 1.0 O C:LYS79 2.4 21.7 1.0 OD2 C:ASP88 2.4 24.5 1.0 OD1 C:ASP82 2.4 32.6 1.0 O C:HOH924 2.5 33.9 1.0 CG C:ASP87 3.3 26.3 1.0 C C:GLU84 3.4 34.1 1.0 CG C:ASP82 3.4 33.6 1.0 CG C:ASP88 3.5 22.9 1.0 C C:LYS79 3.6 24.9 1.0 OD2 C:ASP87 3.6 28.9 1.0 OD2 C:ASP82 3.7 31.8 1.0 OD1 C:ASP88 4.0 26.1 1.0 CA C:LEU80 4.1 23.3 1.0 CB C:GLU84 4.2 38.5 1.0 CA C:GLU84 4.2 35.4 1.0 O C:HOH1068 4.2 30.3 1.0 N C:LEU80 4.3 23.9 1.0 N C:GLU84 4.3 35.2 1.0 N C:LEU85 4.3 31.4 1.0 CA C:LEU85 4.4 30.2 1.0 O C:ASP82 4.4 33.1 1.0 N C:ASP88 4.5 23.2 1.0 N C:ASP82 4.6 32.4 1.0 C C:LEU80 4.6 24.9 1.0 CA C:LYS79 4.7 26.9 1.0 CB C:ASP87 4.7 25.7 1.0 CB C:ASP82 4.7 33.1 1.0 C C:ASP82 4.8 35.4 1.0 CB C:ASP88 4.8 19.8 1.0 N C:ASP87 4.9 25.5 1.0 C C:LEU85 4.9 29.3 1.0 CD2 C:LEU80 4.9 17.9 1.0 N C:LEU81 4.9 23.8 1.0 CA C:ASP82 5.0 34.4 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