Calcium in PDB 5i0d: Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan

The structure of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan, PDB code: 5i0d was solved by S.H.Light, G.Minasov, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.77
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.753, 101.233, 166.391, 90.00, 101.02, 90.00
R / Rfree (%)	14.4 / 17.1

The structure of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Chlorine	(Cl)	7 atoms

The binding sites of Calcium atom in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan (pdb code 5i0d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan, PDB code: 5i0d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1106 b:14.6 occ:1.00 OE1 A:GLU972 2.2 19.9 1.0 O A:GLY992 2.3 20.9 1.0 OE2 A:GLU972 2.3 20.2 1.0 OE1 A:GLU970 2.3 18.6 1.0 OD1 A:ASP1085 2.3 20.0 1.0 O A:THR989 2.4 19.9 1.0 O A:ASP1085 2.4 18.3 1.0 CD A:GLU972 2.4 20.4 1.0 C A:ASP1085 3.4 17.6 1.0 CD A:GLU970 3.4 17.6 1.0 C A:THR989 3.5 19.1 1.0 C A:GLY992 3.5 21.0 1.0 CG A:ASP1085 3.5 19.0 1.0 CA A:ASP1085 3.9 18.2 1.0 CG A:GLU972 4.0 19.9 1.0 OG1 A:THR989 4.1 18.7 1.0 CB A:GLU970 4.2 16.8 1.0 N A:GLY992 4.2 20.8 1.0 CG A:GLU970 4.2 16.9 1.0 N A:THR989 4.3 19.4 1.0 OE2 A:GLU970 4.3 18.1 1.0 N A:PHE993 4.3 21.3 1.0 N A:GLY990 4.3 18.9 1.0 CA A:PHE993 4.3 20.6 1.0 CB A:ASP1085 4.3 18.7 1.0 CA A:GLY990 4.4 18.9 1.0 CA A:THR989 4.4 19.4 1.0 CA A:GLY992 4.4 21.5 1.0 OD2 A:ASP1085 4.4 19.0 1.0 CB A:TYR988 4.5 20.6 1.0 CA A:GLU970 4.6 16.4 1.0 N A:HIS1086 4.6 17.0 1.0 N A:ALA971 4.6 17.2 1.0 CB A:HIS1086 4.7 16.6 1.0 C A:GLY990 4.8 19.6 1.0 N A:THR991 4.8 19.9 1.0 CB A:PHE993 4.9 21.0 1.0 CB A:THR989 4.9 18.9 1.0 CB A:GLU972 4.9 20.2 1.0 N A:GLU972 5.0 18.8 1.0 CD1 A:TYR988 5.0 21.3 1.0

Calcium binding site 2 out of 2 in the Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cycloalternan-Forming Enzyme From Listeria Monocytogenes in Complex with Cycloalternan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1104 b:11.6 occ:1.00 OE1 B:GLU970 2.3 14.8 1.0 O B:GLY992 2.3 14.0 1.0 OD1 B:ASP1085 2.3 14.1 1.0 O B:THR989 2.3 15.3 1.0 OE1 B:GLU972 2.3 15.9 1.0 OE2 B:GLU972 2.4 15.7 1.0 O B:ASP1085 2.4 13.1 1.0 CD B:GLU972 2.7 15.7 1.0 C B:ASP1085 3.4 12.3 1.0 C B:THR989 3.4 15.1 1.0 CD B:GLU970 3.4 14.1 1.0 C B:GLY992 3.5 14.3 1.0 CG B:ASP1085 3.5 13.3 1.0 CA B:ASP1085 3.9 12.3 1.0 OG1 B:THR989 4.1 14.0 1.0 CB B:GLU970 4.2 13.4 1.0 N B:GLY992 4.2 15.4 1.0 N B:GLY990 4.3 16.0 1.0 CG B:GLU972 4.3 15.7 1.0 N B:THR989 4.3 14.3 1.0 CG B:GLU970 4.3 13.7 1.0 OE2 B:GLU970 4.3 14.3 1.0 CB B:ASP1085 4.3 12.7 1.0 N B:PHE993 4.3 14.3 1.0 CA B:GLY990 4.4 16.2 1.0 OD2 B:ASP1085 4.4 13.9 1.0 CA B:THR989 4.4 14.9 1.0 CA B:PHE993 4.4 13.7 1.0 CA B:GLY992 4.5 15.1 1.0 CB B:TYR988 4.5 14.0 1.0 N B:HIS1086 4.5 12.3 1.0 N B:ALA971 4.5 13.5 1.0 CA B:GLU970 4.6 13.2 1.0 CB B:HIS1086 4.7 12.9 1.0 C B:GLY990 4.7 16.6 1.0 N B:THR991 4.8 16.8 1.0 CB B:THR989 4.9 14.7 1.0 CB B:PHE993 4.9 13.3 1.0 CD1 B:TYR988 5.0 15.2 1.0 N B:GLU972 5.0 14.5 1.0 C B:GLU970 5.0 13.2 1.0

S.H.Light, L.A.Cahoon, K.V.Mahasenan, M.Lee, B.Boggess, A.S.Halavaty, S.Mobashery, N.E.Freitag, W.F.Anderson. Transferase Versus Hydrolase: the Role of Conformational Flexibility in Reaction Specificity. Structure V. 25 295 2017.
ISSN: ISSN 1878-4186
PubMed: 28089449
DOI: 10.1016/J.STR.2016.12.007