Calcium in PDB 6p06: Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp

The structure of Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp, PDB code: 6p06 was solved by B.Selvaraj, M.J.Cuneo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.98 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.710, 97.950, 100.700, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 22.1

The binding sites of Calcium atom in the Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp (pdb code 6p06). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp, PDB code: 6p06:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:30.4 occ:1.00 OE2 B:GLU145 2.3 31.9 1.0 OD1 A:ASP52 2.4 36.1 1.0 O A:HOH408 2.4 30.8 1.0 O4 A:NMY301 2.4 28.7 1.0 O2A A:APC302 2.6 21.5 1.0 OD2 A:ASP50 2.6 28.6 1.0 OE1 B:GLU145 2.8 30.9 1.0 CD B:GLU145 2.9 27.8 1.0 OD1 A:ASP50 3.2 27.1 1.0 O3 A:NMY301 3.2 27.7 1.0 CG A:ASP50 3.3 31.1 1.0 CG A:ASP52 3.4 31.1 1.0 C4 A:NMY301 3.6 35.0 1.0 PA A:APC302 3.6 25.6 1.0 OD2 A:ASP52 3.7 28.1 1.0 C3 A:NMY301 3.7 30.9 1.0 O1A A:APC302 3.7 27.7 1.0 CA A:CA304 3.8 27.0 1.0 NZ A:LYS74 4.2 37.2 1.0 OE1 A:GLU76 4.4 31.4 1.0 O5' A:APC302 4.4 36.1 1.0 CG B:GLU145 4.4 27.2 1.0 O B:HOH426 4.6 33.3 1.0 C5' A:APC302 4.6 32.3 1.0 C5 A:NMY301 4.7 30.0 1.0 CB A:ASP52 4.7 23.6 1.0 CB A:ASP50 4.8 23.6 1.0

Calcium binding site 2 out of 4 in the Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:27.0 occ:1.00 O2A A:APC302 2.3 21.5 1.0 O1B A:APC302 2.3 26.6 1.0 O A:HOH409 2.3 28.4 1.0 OD2 A:ASP52 2.3 28.1 1.0 OD1 A:ASP50 2.4 27.1 1.0 O1G A:APC302 2.7 40.7 1.0 CG A:ASP52 3.4 31.1 1.0 PB A:APC302 3.5 26.6 1.0 PA A:APC302 3.5 25.6 1.0 CG A:ASP50 3.6 31.1 1.0 O A:ASP50 3.6 29.7 1.0 OD1 A:ASP52 3.7 36.1 1.0 CA A:CA303 3.8 30.4 1.0 C3A A:APC302 3.8 30.2 1.0 PG A:APC302 4.0 34.3 1.0 O B:HOH426 4.1 33.3 1.0 C A:ASP50 4.1 26.6 1.0 OE2 B:GLU145 4.1 31.9 1.0 N A:ASP50 4.2 28.1 1.0 O3B A:APC302 4.2 30.4 1.0 OD2 A:ASP50 4.2 28.6 1.0 OG A:SER39 4.2 30.1 1.0 O A:HOH420 4.3 30.1 1.0 C5' A:APC302 4.3 32.3 1.0 N A:SER39 4.4 26.6 1.0 O5' A:APC302 4.4 36.1 1.0 CA A:ASP50 4.5 24.5 1.0 O3G A:APC302 4.6 31.8 1.0 CB A:ASP50 4.6 23.6 1.0 O1A A:APC302 4.6 27.7 1.0 O2B A:APC302 4.7 30.8 1.0 CB A:ASP52 4.7 23.6 1.0 N A:ILE51 4.8 21.7 1.0 CA A:GLY38 4.8 29.5 1.0 N A:ASP52 5.0 26.8 1.0 CB A:SER39 5.0 25.3 1.0

Calcium binding site 3 out of 4 in the Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:22.2 occ:1.00 OD1 B:ASP52 2.3 17.1 1.0 O4 A:NMY305 2.3 21.9 1.0 OE2 A:GLU145 2.4 22.8 1.0 O B:HOH406 2.4 17.1 1.0 OD2 B:ASP50 2.4 24.1 1.0 O2A B:APC301 2.4 18.6 1.0 CD A:GLU145 3.0 26.3 1.0 OD1 B:ASP50 3.1 21.4 1.0 OE1 A:GLU145 3.1 25.7 1.0 CG B:ASP50 3.1 24.4 1.0 CG B:ASP52 3.3 20.4 1.0 O3 A:NMY305 3.5 21.2 1.0 C4 A:NMY305 3.6 30.4 1.0 PA B:APC301 3.6 21.2 1.0 CA B:CA302 3.7 21.2 1.0 OD2 B:ASP52 3.7 20.5 1.0 O1A B:APC301 3.7 25.9 1.0 C3 A:NMY305 3.9 26.1 1.0 O A:HOH433 4.2 25.7 1.0 O5' B:APC301 4.3 28.3 1.0 NZ B:LYS74 4.3 23.2 1.0 CG A:GLU145 4.4 27.8 1.0 OE2 B:GLU76 4.5 27.2 1.0 C5 A:NMY305 4.5 29.5 1.0 C5' B:APC301 4.5 23.9 1.0 O B:HOH401 4.6 19.0 1.0 CB B:ASP50 4.6 16.4 1.0 CB B:ASP52 4.6 19.0 1.0

Calcium binding site 4 out of 4 in the Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ternary Structure of the E52D Mutant of Ant-4 with Neomycin and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:21.2 occ:1.00 O B:HOH401 2.2 19.0 1.0 OD2 B:ASP52 2.3 20.5 1.0 O2A B:APC301 2.3 18.6 1.0 OD1 B:ASP50 2.4 21.4 1.0 O1B B:APC301 2.4 22.4 1.0 O B:HOH415 2.4 19.6 1.0 O3G B:APC301 3.2 32.0 1.0 CG B:ASP52 3.3 20.4 1.0 PA B:APC301 3.4 21.2 1.0 CG B:ASP50 3.5 24.4 1.0 PB B:APC301 3.6 18.8 1.0 OD1 B:ASP52 3.6 17.1 1.0 CA A:CA306 3.7 22.2 1.0 O B:ASP50 3.7 23.2 1.0 O A:HOH433 3.7 25.7 1.0 C3A B:APC301 3.8 21.0 1.0 C5' B:APC301 4.1 23.9 1.0 C B:ASP50 4.1 21.6 1.0 OD2 B:ASP50 4.1 24.1 1.0 OG B:SER39 4.2 23.6 1.0 O5' B:APC301 4.2 28.3 1.0 O B:HOH413 4.3 18.3 1.0 PG B:APC301 4.3 30.7 1.0 N B:ASP50 4.4 27.2 1.0 OE2 A:GLU145 4.4 22.8 1.0 O3B B:APC301 4.4 23.5 1.0 N B:SER39 4.5 22.5 1.0 CB B:ASP52 4.6 19.0 1.0 CA B:ASP50 4.6 22.4 1.0 O1A B:APC301 4.6 25.9 1.0 CB B:ASP50 4.7 16.4 1.0 CA B:GLY38 4.7 21.4 1.0 O2B B:APC301 4.7 24.1 1.0 O2G B:APC301 4.7 31.1 1.0 N B:ILE51 4.7 19.8 1.0 N B:ASP52 4.9 13.4 1.0

B.Selvaraj, M.J.Cuneo. Catch and Release: A Novel Variation of the Archetypal Nucleotidyl Transfer Reaction To Be Published.