Calcium in PDB 2gxs: Hera N-Terminal Domain in Complex with Amp, Crystal Form 2

The structure of Hera N-Terminal Domain in Complex with Amp, Crystal Form 2, PDB code: 2gxs was solved by M.G.Rudolph, D.Klostermeier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.66
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.564, 42.838, 68.645, 90.00, 100.06, 90.00
R / Rfree (%)	18.9 / 23.9

The binding sites of Calcium atom in the Hera N-Terminal Domain in Complex with Amp, Crystal Form 2 (pdb code 2gxs). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Hera N-Terminal Domain in Complex with Amp, Crystal Form 2, PDB code: 2gxs:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Hera N-Terminal Domain in Complex with Amp, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hera N-Terminal Domain in Complex with Amp, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:26.6 occ:1.00 O A:GLY160 2.3 25.1 1.0 O A:HOH716 2.4 38.6 1.0 OE1 A:GLU163 2.5 25.4 1.0 OE1 A:GLU164 2.5 26.0 1.0 O A:HOH754 2.5 42.2 1.0 O A:HOH765 2.6 43.6 1.0 OE2 A:GLU164 2.6 32.9 1.0 CD A:GLU164 3.0 28.4 1.0 CD A:GLU163 3.5 30.9 1.0 C A:GLY160 3.5 22.8 1.0 OE2 A:GLU163 4.2 34.2 1.0 CA A:PHE161 4.2 22.8 1.0 OE1 A:GLU162 4.3 19.3 0.3 N A:PHE161 4.3 23.1 1.0 CB A:GLU163 4.4 25.5 1.0 CG A:GLU163 4.4 28.5 1.0 CG A:GLU164 4.5 24.9 1.0 CA A:GLY160 4.5 24.0 1.0 N A:GLU163 4.6 23.4 1.0 C A:PHE161 4.6 23.0 1.0 O A:HOH751 4.6 42.3 1.0 N A:GLU162 4.8 22.9 1.0 N A:GLU164 4.9 23.2 1.0

Calcium binding site 2 out of 5 in the Hera N-Terminal Domain in Complex with Amp, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hera N-Terminal Domain in Complex with Amp, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:48.3 occ:1.00 O B:HOH719 2.3 26.7 1.0 O B:HOH829 2.5 41.9 1.0 O A:HOH675 2.5 34.5 1.0 O A:HOH752 2.6 42.2 1.0 O B:HOH899 2.8 54.9 1.0 O B:HOH850 3.0 45.1 1.0 O A:HOH807 3.4 52.8 1.0 O A:HOH745 4.1 41.0 1.0 O A:ASP5 4.6 25.3 1.0 O A:HOH684 4.6 34.8 1.0 O B:ASP5 4.6 26.6 1.0 OD1 B:ASP5 4.7 24.1 1.0 CA A:ASP5 4.7 26.3 1.0 CA B:ASP5 4.8 25.8 1.0 O B:HOH881 4.9 49.2 1.0 O A:LYS4 4.9 26.0 1.0 OD1 A:ASP5 4.9 30.3 1.0

Calcium binding site 3 out of 5 in the Hera N-Terminal Domain in Complex with Amp, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Hera N-Terminal Domain in Complex with Amp, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:37.0 occ:1.00 OG1 A:THR127 3.0 23.0 1.0 N A:GLY129 3.1 21.0 1.0 N A:ARG130 3.3 21.9 1.0 O A:HOH616 3.3 24.7 1.0 CA A:GLY129 3.4 21.1 1.0 CB A:THR127 3.5 21.3 1.0 C A:GLY129 3.8 21.5 1.0 O A:HOH649 3.9 29.9 1.0 C A:THR127 3.9 20.7 1.0 N A:PRO128 4.1 20.7 1.0 CZ A:PHE161 4.1 28.9 1.0 CE1 A:PHE161 4.1 28.3 1.0 O A:THR127 4.2 20.5 1.0 CB A:ARG130 4.3 23.2 0.5 C A:PRO128 4.3 21.2 1.0 CA A:THR127 4.3 20.3 1.0 CA A:ARG130 4.4 22.8 0.5 CA A:ARG130 4.4 22.6 0.5 CB A:ARG130 4.4 22.5 0.5 CD A:PRO128 4.5 21.4 1.0 N A:GLY106 4.6 32.3 1.0 CA A:PRO128 4.8 20.8 1.0 CG2 A:THR127 4.8 23.0 1.0 CA A:GLY106 5.0 33.6 1.0

Calcium binding site 4 out of 5 in the Hera N-Terminal Domain in Complex with Amp, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Hera N-Terminal Domain in Complex with Amp, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca604 b:51.5 occ:1.00 O B:HOH706 2.1 24.3 1.0 O B:GLY160 2.5 32.7 1.0 O B:HOH882 2.5 50.0 1.0 OE1 B:GLU164 2.7 29.9 1.0 OE2 B:GLU164 2.9 33.3 1.0 CD B:GLU164 3.2 33.3 1.0 C B:GLY160 3.7 32.9 1.0 CA B:PHE161 4.3 29.8 1.0 N B:PHE161 4.5 30.8 1.0 OE1 B:GLU163 4.7 45.3 1.0 CG B:GLU164 4.7 29.5 1.0 C B:PHE161 4.7 29.6 1.0 CA B:GLY160 4.8 34.1 1.0 N B:GLU162 4.8 30.8 1.0 N B:GLU163 4.9 31.2 1.0 CB B:GLU163 4.9 32.0 1.0 O B:HOH902 5.0 55.6 1.0 OE1 B:GLU162 5.0 36.8 1.0

Calcium binding site 5 out of 5 in the Hera N-Terminal Domain in Complex with Amp, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Hera N-Terminal Domain in Complex with Amp, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca605 b:33.5 occ:1.00 OG1 B:THR127 3.0 20.9 1.0 O B:HOH754 3.0 32.7 1.0 N B:GLY129 3.3 25.8 1.0 N B:ARG130 3.3 26.9 1.0 CA B:GLY129 3.4 26.5 1.0 CB B:THR127 3.5 22.1 1.0 O B:HOH810 3.5 39.8 1.0 C B:GLY129 3.8 26.8 1.0 CZ B:PHE161 4.0 28.3 1.0 C B:THR127 4.1 20.9 1.0 CE1 B:PHE161 4.1 28.2 1.0 CB B:ARG130 4.2 27.0 1.0 O B:HOH711 4.2 25.8 1.0 N B:PRO128 4.2 23.0 1.0 O B:THR127 4.3 20.0 1.0 C B:PRO128 4.4 24.4 1.0 CA B:ARG130 4.4 26.9 1.0 CA B:THR127 4.4 21.2 1.0 C3 B:GOL701 4.6 35.9 1.0 CG2 B:THR127 4.6 22.4 1.0 CD B:PRO128 4.7 23.4 1.0 CA B:PRO128 4.9 24.3 1.0 O2 B:GOL701 5.0 36.9 1.0

M.G.Rudolph, R.Heissmann, J.G.Wittmann, D.Klostermeier. Crystal Structure and Nucleotide Binding of the Thermus Thermophilus Rna Helicase Hera N-Terminal Domain. J.Mol.Biol. V. 351 731 2006.
ISSN: ISSN 0022-2836
PubMed: 16890241
DOI: 10.1016/J.JMB.2006.06.065