Calcium in PDB 1nf5: Crystal Structure of Lactose Synthase, Complex with Glucose

All present enzymatic activity of Crystal Structure of Lactose Synthase, Complex with Glucose:
2.4.1.22; 2.4.1.38; 2.4.1.90;

The structure of Crystal Structure of Lactose Synthase, Complex with Glucose, PDB code: 1nf5 was solved by B.Ramakrishnan, P.K.Qasba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.73 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.223, 93.898, 99.968, 90.00, 101.50, 90.00
R / Rfree (%)	19 / 24.1

The binding sites of Calcium atom in the Crystal Structure of Lactose Synthase, Complex with Glucose (pdb code 1nf5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Lactose Synthase, Complex with Glucose, PDB code: 1nf5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Lactose Synthase, Complex with Glucose


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 Lactose Synthase, Complex with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca124 b:24.7 occ:1.00 O A:GLU84 2.1 19.3 1.0 O A:LYS79 2.3 22.1 1.0 OD1 A:ASP87 2.4 20.0 1.0 OD2 A:ASP88 2.4 19.0 1.0 OD1 A:ASP82 2.4 27.7 1.0 O A:HOH801 2.4 19.1 1.0 O A:HOH841 2.6 23.7 1.0 C A:GLU84 3.3 20.8 1.0 CG A:ASP82 3.3 28.5 1.0 CG A:ASP87 3.4 20.2 1.0 CG A:ASP88 3.5 20.9 1.0 C A:LYS79 3.6 22.8 1.0 OD2 A:ASP82 3.6 29.9 1.0 OD2 A:ASP87 3.7 18.1 1.0 OD1 A:ASP88 4.0 21.4 1.0 O A:HOH1120 4.1 37.6 1.0 CA A:GLU84 4.2 21.1 1.0 N A:GLU84 4.2 21.2 1.0 CA A:LEU80 4.2 25.3 1.0 N A:LEU85 4.3 21.7 1.0 O A:ASP82 4.3 26.8 1.0 N A:LEU80 4.3 24.0 1.0 CB A:GLU84 4.4 21.1 1.0 CA A:LEU85 4.4 22.5 1.0 N A:ASP88 4.5 20.4 1.0 N A:ASP82 4.5 28.1 1.0 C A:ASP82 4.6 27.6 1.0 CB A:ASP82 4.6 27.2 1.0 CA A:LYS79 4.7 22.2 1.0 C A:LEU80 4.7 26.9 1.0 CB A:ASP88 4.7 19.0 1.0 CB A:ASP87 4.8 19.7 1.0 CA A:ASP82 4.9 27.3 1.0 N A:ASP87 4.9 19.4 1.0 C A:LEU85 4.9 23.1 1.0 CB A:LYS79 5.0 24.0 1.0 N A:LEU81 5.0 25.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Lactose Synthase, Complex with Glucose


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 Lactose Synthase, Complex with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca526 b:24.3 occ:1.00 O C:GLU84 2.2 23.0 1.0 OD1 C:ASP82 2.3 26.6 1.0 OD1 C:ASP87 2.3 21.9 1.0 OD2 C:ASP88 2.4 16.3 1.0 O C:LYS79 2.4 19.5 1.0 O C:HOH803 2.5 18.3 1.0 O C:HOH805 2.5 21.7 1.0 CG C:ASP82 3.3 26.6 1.0 CG C:ASP87 3.3 20.5 1.0 C C:GLU84 3.4 23.1 1.0 CG C:ASP88 3.5 14.7 1.0 OD2 C:ASP82 3.6 26.5 1.0 OD2 C:ASP87 3.6 20.2 1.0 C C:LYS79 3.6 18.4 1.0 OD1 C:ASP88 3.9 17.5 1.0 CA C:LEU80 4.2 20.4 1.0 O C:HOH940 4.2 26.5 1.0 CA C:GLU84 4.3 24.7 1.0 O C:ASP82 4.3 25.7 1.0 N C:GLU84 4.3 24.8 1.0 N C:LEU85 4.3 23.3 1.0 N C:LEU80 4.3 20.0 1.0 CB C:GLU84 4.4 24.0 1.0 N C:ASP88 4.4 17.0 1.0 CA C:LEU85 4.4 22.6 1.0 N C:ASP82 4.5 24.1 1.0 CB C:ASP82 4.6 26.2 1.0 C C:ASP82 4.6 26.4 1.0 C C:LEU80 4.7 19.8 1.0 CA C:LYS79 4.7 19.9 1.0 CB C:ASP87 4.8 17.4 1.0 CB C:ASP88 4.8 12.1 1.0 CA C:ASP82 4.8 25.7 1.0 C C:LEU85 4.8 22.6 1.0 N C:ASP87 4.9 20.7 1.0 CD2 C:LEU80 4.9 19.1 1.0 CD1 C:LEU85 5.0 22.9 1.0

B.Ramakrishnan, P.K.Qasba. Crystal Structure of Lactose Synthase Reveals A Large Conformational Change in Its Catalytic Component, the Beta-1,4-Galactosyltransferase J.Mol.Biol. V. 310 205 2001.
ISSN: ISSN 0022-2836
PubMed: 11419947
DOI: 10.1006/JMBI.2001.4757