Calcium in PDB 4n96: E. Coli Sliding Clamp in Complex with 6-Nitroindazole

All present enzymatic activity of E. Coli Sliding Clamp in Complex with 6-Nitroindazole:
2.7.7.7;

The structure of E. Coli Sliding Clamp in Complex with 6-Nitroindazole, PDB code: 4n96 was solved by Z.Yin, A.J.Oakley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.72 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.880, 64.670, 72.020, 73.97, 83.55, 84.36
R / Rfree (%)	22.7 / 27.5

The structure of E. Coli Sliding Clamp in Complex with 6-Nitroindazole also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the E. Coli Sliding Clamp in Complex with 6-Nitroindazole (pdb code 4n96). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the E. Coli Sliding Clamp in Complex with 6-Nitroindazole, PDB code: 4n96:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the E. Coli Sliding Clamp in Complex with 6-Nitroindazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E. Coli Sliding Clamp in Complex with 6-Nitroindazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:36.6 occ:1.00 O A:GLY46 3.4 17.4 1.0 C A:GLY46 3.5 16.9 1.0 OE1 A:GLU202 3.6 21.4 1.0 OE2 A:GLU202 3.6 19.8 1.0 N A:THR47 3.7 17.8 1.0 CA A:THR47 3.7 19.4 1.0 O A:MET51 4.0 15.5 1.0 CD A:GLU202 4.0 19.3 1.0 N A:MET53 4.1 16.1 1.0 C A:THR47 4.1 20.1 1.0 CA A:GLU52 4.2 17.6 1.0 N A:ASP48 4.3 20.6 1.0 CG A:MET51 4.3 16.8 1.0 CA A:GLY46 4.4 16.4 1.0 C A:GLU52 4.4 16.7 1.0 C A:MET51 4.4 16.7 1.0 N A:GLU52 4.5 16.7 1.0 O A:VAL17 4.6 19.3 1.0 CB A:MET53 4.7 16.7 1.0 O A:THR47 4.8 21.5 1.0 O A:HOH708 4.9 34.3 1.0

Calcium binding site 2 out of 3 in the E. Coli Sliding Clamp in Complex with 6-Nitroindazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E. Coli Sliding Clamp in Complex with 6-Nitroindazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:51.1 occ:1.00 O A:HOH587 2.4 17.2 1.0 OE1 A:GLU6 2.7 22.2 1.0 CD A:GLU6 3.4 21.7 1.0 CB A:GLU8 3.7 23.3 1.0 CA A:GLY85 3.8 21.7 1.0 CB A:GLU6 3.9 17.9 1.0 CG A:GLU6 4.0 19.5 1.0 O A:GLY85 4.1 20.5 1.0 C A:GLY85 4.1 21.1 1.0 O A:HOH543 4.2 19.0 1.0 O A:HOH526 4.2 16.7 1.0 OE2 A:GLU6 4.2 24.6 1.0 N A:GLY85 4.4 21.4 1.0 N A:GLU8 4.5 19.0 1.0 O A:ALA86 4.5 18.1 1.0 CG A:GLU8 4.6 26.4 1.0 CA A:GLU8 4.8 20.3 1.0 OE1 A:GLU8 4.8 31.2 1.0 N A:ALA86 4.9 20.1 1.0 CA A:GLU6 4.9 17.2 1.0

Calcium binding site 3 out of 3 in the E. Coli Sliding Clamp in Complex with 6-Nitroindazole


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of E. Coli Sliding Clamp in Complex with 6-Nitroindazole within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:27.4 occ:1.00 O B:GLY85 2.3 14.5 1.0 O B:HOH680 2.4 27.1 1.0 OE2 B:GLU87 2.4 19.8 1.0 OE2 B:GLU6 2.6 22.3 1.0 CD B:GLU87 3.4 17.9 1.0 C B:GLY85 3.4 14.4 1.0 CD B:GLU6 3.6 19.8 1.0 CG B:GLU87 3.8 16.9 1.0 CA B:GLY85 4.0 14.8 1.0 O B:HOH659 4.0 36.6 1.0 CG B:GLU6 4.1 17.6 1.0 OE1 B:GLU87 4.5 18.4 1.0 N B:ALA86 4.5 13.7 1.0 N B:GLU87 4.6 13.7 1.0 OE1 B:GLU6 4.6 21.2 1.0 C B:ALA86 4.7 13.4 1.0 CA B:ALA86 4.9 13.6 1.0

Z.Yin, L.R.Whittell, Y.Wang, S.Jergic, M.Liu, E.J.Harry, N.E.Dixon, J.L.Beck, M.J.Kelso, A.J.Oakley. Discovery of Lead Compounds Targeting the Bacterial Sliding Clamp Using A Fragment-Based Approach. J.Med.Chem. V. 57 2799 2014.
ISSN: ISSN 0022-2623
PubMed: 24592885
DOI: 10.1021/JM500122R