Calcium in PDB 2fyc: Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose

The structure of Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose, PDB code: 2fyc 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)	32.56 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.374, 94.615, 99.603, 90.00, 101.78, 90.00
R / Rfree (%)	20 / 24.6

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose (pdb code 2fyc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose, PDB code: 2fyc:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca124 b:23.8 occ:1.00 O A:GLU84 2.2 22.2 1.0 O A:LYS79 2.3 21.8 1.0 OD1 A:ASP87 2.4 23.3 1.0 O A:HOH1005 2.5 26.1 1.0 OD2 A:ASP88 2.5 23.0 1.0 OD1 A:ASP82 2.5 28.9 1.0 O A:HOH1014 2.5 26.2 1.0 CG A:ASP87 3.3 25.1 1.0 CG A:ASP82 3.4 29.3 1.0 C A:GLU84 3.4 24.2 1.0 CG A:ASP88 3.6 23.4 1.0 C A:LYS79 3.6 24.1 1.0 OD2 A:ASP87 3.6 25.9 1.0 OD2 A:ASP82 3.6 30.2 1.0 OD1 A:ASP88 4.0 21.9 1.0 CA A:LEU80 4.2 24.1 1.0 N A:GLU84 4.3 24.4 1.0 CA A:GLU84 4.3 24.0 1.0 O A:ASP82 4.3 29.6 1.0 N A:LEU80 4.3 22.3 1.0 N A:LEU85 4.4 24.8 1.0 N A:ASP88 4.4 22.8 1.0 CB A:GLU84 4.4 22.7 1.0 CA A:LEU85 4.4 25.2 1.0 O A:HOH1184 4.5 35.8 1.0 N A:ASP82 4.5 25.3 1.0 CA A:LYS79 4.6 23.7 1.0 C A:ASP82 4.7 29.0 1.0 C A:LEU80 4.7 24.3 1.0 CB A:ASP82 4.7 27.1 1.0 CB A:ASP87 4.7 24.5 1.0 CB A:ASP88 4.8 21.0 1.0 N A:ASP87 4.8 25.6 1.0 CA A:ASP82 4.9 27.1 1.0 C A:LEU85 4.9 25.1 1.0 N A:LEU81 4.9 23.6 1.0 CD2 A:LEU80 5.0 23.4 1.0 O A:HOH1043 5.0 28.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:34.2 occ:1.00 O1A B:GDU403 2.2 28.8 1.0 O2B B:GDU403 2.3 28.8 1.0 O B:HOH1027 2.5 32.0 1.0 O B:HOH1158 2.5 45.0 1.0 NE2 B:HIS344 2.5 41.1 1.0 OD2 B:ASP254 2.6 34.0 1.0 NE2 B:HIS347 2.6 40.2 1.0 CE1 B:HIS344 3.4 40.0 1.0 CG B:ASP254 3.4 31.3 1.0 CE1 B:HIS347 3.5 43.9 1.0 PA B:GDU403 3.5 31.8 1.0 CD2 B:HIS344 3.5 40.5 1.0 CD2 B:HIS347 3.6 43.7 1.0 OD1 B:ASP254 3.6 33.5 1.0 PB B:GDU403 3.7 31.3 1.0 O3A B:GDU403 4.0 32.9 1.0 O3D B:GDU403 4.0 24.6 1.0 NZ B:LYS279 4.3 45.7 1.0 O3B B:GDU403 4.3 32.3 1.0 O2A B:GDU403 4.3 35.4 1.0 NH2 B:ARG191 4.4 31.7 1.0 O B:HOH1556 4.5 59.7 1.0 ND1 B:HIS344 4.5 38.1 1.0 O5D B:GDU403 4.6 30.9 1.0 CB B:ASP254 4.6 30.6 1.0 CG B:HIS344 4.6 39.9 1.0 ND1 B:HIS347 4.7 45.0 1.0 O1B B:GDU403 4.7 32.6 1.0 CG B:HIS347 4.7 45.2 1.0 C5D B:GDU403 4.7 28.2 1.0 OD2 B:ASP252 4.8 29.6 1.0 NH1 B:ARG191 4.8 32.5 1.0 C3D B:GDU403 4.8 26.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca526 b:33.0 occ:1.00 OD1 C:ASP87 2.1 32.6 1.0 O C:HOH1006 2.2 25.6 1.0 O C:LYS79 2.3 29.5 1.0 O C:GLU84 2.4 38.9 1.0 OD2 C:ASP88 2.4 27.2 1.0 O C:HOH1057 2.5 34.1 1.0 OD1 C:ASP82 2.5 41.6 1.0 CG C:ASP87 3.1 33.0 1.0 OD2 C:ASP87 3.4 33.5 1.0 C C:GLU84 3.5 39.6 1.0 C C:LYS79 3.5 31.1 1.0 CG C:ASP82 3.5 38.3 1.0 CG C:ASP88 3.6 30.1 1.0 OD2 C:ASP82 3.8 38.4 1.0 OD1 C:ASP88 4.1 26.2 1.0 CA C:LEU80 4.1 31.8 1.0 N C:LEU80 4.2 31.9 1.0 O C:HOH1368 4.3 42.1 1.0 N C:GLU84 4.3 41.4 1.0 CA C:GLU84 4.3 40.4 1.0 N C:LEU85 4.4 36.7 1.0 CB C:GLU84 4.4 43.3 1.0 N C:ASP88 4.4 28.2 1.0 CA C:LEU85 4.4 34.3 1.0 O C:ASP82 4.5 41.5 1.0 N C:ASP82 4.5 36.7 1.0 CB C:ASP87 4.6 29.9 1.0 C C:LEU80 4.6 33.1 1.0 CA C:LYS79 4.6 29.5 1.0 C C:ASP82 4.7 40.9 1.0 CB C:ASP82 4.8 39.7 1.0 N C:ASP87 4.8 30.2 1.0 CB C:ASP88 4.8 28.4 1.0 N C:LEU81 4.9 31.9 1.0 CA C:ASP82 4.9 39.9 1.0 C C:LEU85 4.9 33.8 1.0 CD2 C:LEU80 4.9 26.5 1.0 CD1 C:LEU85 5.0 31.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Catalytic Domain of Bovine BETA1,4- Galactosyltransferase-I in Complex with Alpha-Lactalbumin, Ca and Udp-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca527 b:29.4 occ:1.00 NE2 D:HIS347 2.3 35.4 1.0 O2B D:GDU528 2.3 26.1 1.0 O1A D:GDU528 2.3 26.8 1.0 OD2 D:ASP254 2.4 27.3 1.0 NE2 D:HIS344 2.4 31.1 1.0 O D:HOH1028 2.6 30.6 1.0 O D:HOH1093 2.8 42.8 1.0 CE1 D:HIS347 3.2 34.1 1.0 CE1 D:HIS344 3.2 32.9 1.0 CG D:ASP254 3.3 26.5 1.0 CD2 D:HIS347 3.3 34.3 1.0 CD2 D:HIS344 3.5 31.8 1.0 PA D:GDU528 3.6 30.4 1.0 PB D:GDU528 3.7 28.2 1.0 OD1 D:ASP254 3.7 27.0 1.0 O3A D:GDU528 4.0 26.6 1.0 O3D D:GDU528 4.1 25.2 1.0 O3B D:GDU528 4.3 28.4 1.0 O2A D:GDU528 4.3 30.2 1.0 ND1 D:HIS347 4.3 35.2 1.0 NH2 D:ARG191 4.4 27.5 1.0 ND1 D:HIS344 4.4 31.7 1.0 CG D:HIS347 4.5 36.6 1.0 NZ D:LYS279 4.5 43.0 1.0 NH1 D:ARG191 4.5 28.6 1.0 CB D:ASP254 4.5 26.0 1.0 CG D:HIS344 4.6 31.5 1.0 O5D D:GDU528 4.7 27.6 1.0 O D:HOH1555 4.7 67.7 1.0 O1B D:GDU528 4.7 30.9 1.0 C5D D:GDU528 4.9 26.1 1.0 OD2 D:ASP252 4.9 28.0 1.0 C3D D:GDU528 4.9 24.8 1.0 CZ D:ARG191 5.0 27.8 1.0 O D:HOH1253 5.0 54.1 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