Calcium in PDB 5dy1: Crystal of Selenomethionine Substituted Amtr From Corynebacterium Glutamicum

The structure of Crystal of Selenomethionine Substituted Amtr From Corynebacterium Glutamicum, PDB code: 5dy1 was solved by C.Palanca, V.Rubio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.11 / 2.65
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	160.464, 160.464, 52.435, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 22.1

The binding sites of Calcium atom in the Crystal of Selenomethionine Substituted Amtr From Corynebacterium Glutamicum (pdb code 5dy1). 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 of Selenomethionine Substituted Amtr From Corynebacterium Glutamicum, PDB code: 5dy1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal of Selenomethionine Substituted Amtr From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal of Selenomethionine Substituted Amtr From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:55.4 occ:0.71 O A:LYS111 2.5 36.8 1.0 O A:LYS175 2.6 39.5 1.0 NH2 A:ARG170 3.1 38.4 1.0 N A:ASP173 3.2 34.0 1.0 N A:GLY174 3.3 35.6 1.0 OD1 A:ASP173 3.5 48.5 1.0 CA A:ASN172 3.5 35.2 1.0 N A:LYS175 3.6 42.8 1.0 C A:LYS175 3.6 42.0 1.0 O A:ARG171 3.6 35.1 1.0 C A:LYS111 3.6 36.5 1.0 N A:ASN172 3.7 37.6 1.0 C A:ASN172 3.7 33.5 1.0 CG A:ARG171 3.8 36.9 1.0 C A:ARG171 3.8 34.9 1.0 C A:GLY174 3.9 38.5 1.0 CA A:GLY174 4.0 38.9 1.0 CD A:ARG171 4.0 37.6 1.0 C A:ASP173 4.1 39.1 1.0 CA A:ASP173 4.2 36.7 1.0 CA A:LYS175 4.2 45.6 1.0 CZ A:ARG170 4.3 32.1 1.0 CB A:ARG171 4.4 36.1 1.0 CA A:TRP112 4.4 36.4 1.0 N A:TRP112 4.5 37.8 1.0 CD A:PRO177 4.5 33.4 1.0 O A:THR110 4.5 38.5 1.0 CG A:ASP173 4.6 44.1 1.0 CA A:LYS111 4.6 35.5 1.0 OD1 A:ASN172 4.6 36.3 1.0 N A:ILE176 4.6 45.2 1.0 NE A:ARG171 4.7 46.5 1.0 O A:GLY174 4.7 59.0 1.0 CA A:ARG171 4.8 36.2 1.0 CB A:ASN172 4.8 31.1 1.0 NE A:ARG170 4.8 30.9 1.0 O A:ASN172 4.9 37.2 1.0 CE3 A:TRP112 4.9 32.0 1.0 CA A:ILE176 4.9 40.0 1.0 CB A:ASP173 5.0 39.9 1.0 C A:TRP112 5.0 34.0 1.0 CB A:LYS175 5.0 54.5 1.0

Calcium binding site 2 out of 2 in the Crystal of Selenomethionine Substituted Amtr From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal of Selenomethionine Substituted Amtr From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:28.3 occ:0.44 O B:LYS175 2.6 36.8 1.0 O B:LYS111 2.7 37.9 1.0 N B:ASP173 3.0 41.2 1.0 OD1 B:ASP173 3.2 50.7 1.0 NH2 B:ARG170 3.2 37.0 1.0 N B:GLY174 3.3 41.8 1.0 CA B:ASN172 3.4 36.5 1.0 N B:LYS175 3.5 38.8 1.0 O B:ARG171 3.6 33.6 1.0 CG B:ARG171 3.6 38.7 1.0 N B:ASN172 3.6 33.7 1.0 C B:LYS175 3.6 36.3 1.0 C B:ARG171 3.6 32.0 1.0 C B:ASN172 3.7 35.6 1.0 CD B:ARG171 3.8 41.5 1.0 C B:LYS111 3.9 34.3 1.0 C B:GLY174 3.9 44.2 1.0 C B:ASP173 4.0 44.3 1.0 CA B:GLY174 4.0 40.0 1.0 CA B:ASP173 4.0 42.8 1.0 CA B:LYS175 4.2 39.9 1.0 CB B:ARG171 4.2 36.4 1.0 CG B:ASP173 4.3 45.7 1.0 CZ B:ARG170 4.5 31.0 1.0 CD B:PRO177 4.5 38.2 1.0 CA B:ARG171 4.6 33.2 1.0 N B:ILE176 4.7 37.0 1.0 CA B:TRP112 4.7 30.6 1.0 N B:TRP112 4.7 32.3 1.0 O B:THR110 4.7 35.9 1.0 O B:GLY174 4.7 54.6 1.0 CB B:ASP173 4.8 43.8 1.0 OD1 B:ASN172 4.8 38.9 1.0 CB B:ASN172 4.8 34.3 1.0 CA B:LYS111 4.8 41.1 1.0 O B:ASN172 4.8 38.3 1.0 CB B:LYS175 4.8 47.4 1.0 NE B:ARG170 4.9 29.8 1.0 CA B:ILE176 5.0 35.0 1.0

C.Palanca, V.Rubio. Structure of Amtr, the Global Nitrogen Regulator of Corynebacterium Glutamicum, in Free and Dna-Bound Forms. Febs J. V. 283 1039 2016.
ISSN: ISSN 1742-464X
PubMed: 26744254
DOI: 10.1111/FEBS.13643