Calcium in PDB 5tsp: Crystal Structure of the Catalytic Domain of Clostridium Perfringens Neuraminidase (Nani) in Complex with A Ches

The structure of Crystal Structure of the Catalytic Domain of Clostridium Perfringens Neuraminidase (Nani) in Complex with A Ches, PDB code: 5tsp was solved by Y.Lee, H.-S.Youn, J.-G.Lee, J.Y.An, K.R.Park, J.Y.Kang, M.S.Jin, Y.B.Ryu, K.H.Park, S.H.Eom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.20 / 1.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.386, 98.007, 72.648, 90.00, 90.99, 90.00
R / Rfree (%)	14.4 / 15.8

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Clostridium Perfringens Neuraminidase (Nani) in Complex with A Ches (pdb code 5tsp). 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 the Catalytic Domain of Clostridium Perfringens Neuraminidase (Nani) in Complex with A Ches, PDB code: 5tsp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Clostridium Perfringens Neuraminidase (Nani) in Complex with A Ches


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 Clostridium Perfringens Neuraminidase (Nani) in Complex with A Ches within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:6.8 occ:1.00 OD2 A:ASP319 2.3 8.4 1.0 OD2 A:ASP296 2.3 8.0 1.0 O A:TYR320 2.4 7.6 1.0 OD2 A:ASP298 2.4 7.2 1.0 O A:HOH1172 2.4 9.8 1.0 O A:HOH1313 2.5 6.9 1.0 O A:HOH1303 2.5 8.7 1.0 CG A:ASP296 3.4 7.3 1.0 CG A:ASP319 3.4 9.2 1.0 CG A:ASP298 3.4 7.0 1.0 C A:TYR320 3.5 7.1 1.0 N A:TYR320 3.6 7.2 1.0 OD1 A:ASP296 3.7 7.8 1.0 OD1 A:ASP298 3.8 8.8 1.0 C A:ASP319 4.1 7.6 1.0 CA A:ASP319 4.1 8.3 1.0 CA A:TYR320 4.2 7.2 1.0 OD1 A:ASP319 4.2 12.2 1.0 O A:HOH1438 4.2 16.4 1.0 CB A:ASP319 4.3 8.9 1.0 O A:SER324 4.3 7.8 1.0 O A:HOH1286 4.3 25.5 1.0 O A:ILE297 4.5 5.9 1.0 N A:PRO321 4.5 7.7 1.0 CB A:ASP296 4.7 8.1 1.0 O A:HOH1869 4.7 29.4 1.0 CA A:PRO321 4.7 7.8 1.0 C A:ILE297 4.7 5.7 1.0 C A:ASP296 4.8 6.3 1.0 CB A:ASP298 4.8 7.8 1.0 N A:ILE297 4.8 6.3 1.0 O A:HOH1865 4.9 29.9 1.0 N A:ASP298 5.0 6.0 1.0 O A:ASP319 5.0 9.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Clostridium Perfringens Neuraminidase (Nani) in Complex with A Ches


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 Clostridium Perfringens Neuraminidase (Nani) in Complex with A Ches within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:6.7 occ:1.00 OD1 B:ASP319 2.3 8.4 1.0 OD2 B:ASP296 2.3 7.7 1.0 O B:TYR320 2.4 6.6 1.0 OD2 B:ASP298 2.4 6.9 1.0 O B:HOH1172 2.4 9.1 1.0 O B:HOH1328 2.4 6.3 1.0 O B:HOH1213 2.5 9.3 1.0 CG B:ASP296 3.4 7.1 1.0 CG B:ASP319 3.4 8.5 1.0 CG B:ASP298 3.4 6.7 1.0 C B:TYR320 3.5 6.6 1.0 N B:TYR320 3.6 7.0 1.0 OD1 B:ASP296 3.7 7.2 1.0 OD1 B:ASP298 3.8 8.0 1.0 C B:ASP319 4.1 7.5 1.0 CA B:ASP319 4.1 7.4 1.0 CA B:TYR320 4.2 6.3 1.0 OD2 B:ASP319 4.2 12.6 1.0 CB B:ASP319 4.3 8.5 1.0 O B:SER324 4.3 7.5 1.0 O B:HOH1544 4.3 18.0 1.0 O B:HOH1187 4.3 20.4 1.0 O B:ILE297 4.5 5.3 1.0 N B:PRO321 4.5 6.7 1.0 O B:HOH1830 4.6 27.7 1.0 CB B:ASP296 4.7 7.5 1.0 CA B:PRO321 4.7 6.6 1.0 C B:ILE297 4.7 5.5 1.0 CB B:ASP298 4.8 6.5 1.0 C B:ASP296 4.8 5.9 1.0 N B:ILE297 4.8 6.0 1.0 O B:HOH1912 4.9 31.1 1.0 N B:ASP298 5.0 5.1 1.0

Y.Lee, H.-S.Youn, J.-G.Lee, J.Y.An, K.R.Park, J.Y.Kang, Y.B.Ryu, M.S.Jin, K.H.Park, S.H.Eom. Crystal Structure of the Catalytic Domain of Clostridium Perfringens Neuraminidase in Complex with A Non-Carbohydrate-Based Inhibitor, 2-(Cyclohexylamino)Ethanesulfonic Acid Biochem. Biophys. Res. V. 486 470 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28315686
DOI: 10.1016/J.BBRC.2017.03.064