Calcium in PDB 1nkh: Crystal Structure of Lactose Synthase Complex with Udp and Manganese

All present enzymatic activity of Crystal Structure of Lactose Synthase Complex with Udp and Manganese:
2.4.1.22; 2.4.1.38; 2.4.1.90;

The structure of Crystal Structure of Lactose Synthase Complex with Udp and Manganese, PDB code: 1nkh 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)	24.71 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.469, 99.145, 102.261, 90.00, 104.14, 90.00
R / Rfree (%)	19.6 / 25.1

The structure of Crystal Structure of Lactose Synthase Complex with Udp and Manganese also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Lactose Synthase Complex with Udp and Manganese (pdb code 1nkh). 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 Udp and Manganese, PDB code: 1nkh:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Lactose Synthase Complex with Udp and Manganese


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 Udp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca805 b:34.2 occ:1.00 O A:LYS79 2.2 38.0 1.0 O A:GLU84 2.2 35.5 1.0 OD2 A:ASP88 2.4 36.1 1.0 OD1 A:ASP87 2.4 36.1 1.0 O A:HOH909 2.6 30.0 1.0 O A:HOH945 2.6 34.9 1.0 OD1 A:ASP82 2.8 40.5 1.0 C A:LYS79 3.4 39.4 1.0 CG A:ASP87 3.4 37.3 1.0 C A:GLU84 3.4 36.3 1.0 CG A:ASP82 3.4 39.0 1.0 CG A:ASP88 3.5 34.9 1.0 OD2 A:ASP82 3.5 42.6 1.0 OD2 A:ASP87 3.6 34.4 1.0 OD1 A:ASP88 3.8 35.3 1.0 CA A:LEU80 3.9 38.3 1.0 O A:HOH1300 4.1 42.4 1.0 N A:LEU80 4.1 38.2 1.0 N A:GLU84 4.3 38.8 1.0 CA A:GLU84 4.3 37.4 1.0 N A:LEU85 4.4 36.3 1.0 O A:ASP82 4.4 39.4 1.0 CA A:LEU85 4.4 36.2 1.0 CB A:GLU84 4.5 37.2 1.0 CA A:LYS79 4.5 40.1 1.0 N A:ASP88 4.6 34.7 1.0 C A:LEU80 4.6 38.8 1.0 N A:ASP82 4.6 40.0 1.0 C A:ASP82 4.7 39.8 1.0 CB A:ASP82 4.7 39.3 1.0 CB A:ASP88 4.8 32.8 1.0 CB A:LYS79 4.8 44.1 1.0 CB A:ASP87 4.8 36.1 1.0 CD2 A:LEU80 4.9 29.0 1.0 C A:LEU85 4.9 37.6 1.0 N A:ASP87 4.9 36.5 1.0 N A:LEU81 4.9 38.7 1.0 CA A:ASP82 5.0 39.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Lactose Synthase Complex with Udp and Manganese


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 Udp and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca806 b:33.1 occ:1.00 O C:GLU84 2.2 40.9 1.0 OD1 C:ASP82 2.3 39.4 1.0 OD1 C:ASP87 2.3 31.4 1.0 O C:LYS79 2.3 33.3 1.0 O C:HOH922 2.4 28.0 1.0 OD2 C:ASP88 2.4 28.2 1.0 O C:HOH910 2.6 35.5 1.0 CG C:ASP82 3.2 37.0 1.0 CG C:ASP87 3.2 31.3 1.0 C C:GLU84 3.4 39.4 1.0 OD2 C:ASP82 3.5 37.8 1.0 OD2 C:ASP87 3.5 28.0 1.0 C C:LYS79 3.5 32.3 1.0 CG C:ASP88 3.6 27.1 1.0 OD1 C:ASP88 4.0 26.3 1.0 CA C:LEU80 4.2 28.9 1.0 N C:LEU85 4.3 38.8 1.0 CA C:GLU84 4.3 39.7 1.0 O C:ASP82 4.3 34.4 1.0 N C:LEU80 4.3 32.3 1.0 CA C:LEU85 4.4 36.2 1.0 N C:GLU84 4.4 38.3 1.0 N C:ASP88 4.4 27.5 1.0 CB C:GLU84 4.5 39.9 1.0 CA C:LYS79 4.6 33.0 1.0 CB C:ASP82 4.6 35.0 1.0 CB C:ASP87 4.6 30.3 1.0 N C:ASP82 4.7 30.2 1.0 C C:ASP82 4.7 33.9 1.0 CD1 C:LEU85 4.7 34.7 1.0 N C:ASP87 4.7 34.5 1.0 C C:LEU85 4.8 35.6 1.0 CB C:ASP88 4.8 28.5 1.0 C C:LEU80 4.8 29.1 1.0 CB C:LYS79 4.9 33.6 1.0 O C:HOH1035 4.9 36.4 1.0 CA C:ASP82 5.0 33.7 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