Calcium in PDB 4rmo: Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale

The structure of Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale, PDB code: 4rmo was solved by F.Rao, J.E.Voss, F.L.Short, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.12 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.110, 185.891, 138.780, 90.00, 92.63, 90.00
R / Rfree (%)	19.9 / 23.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale (pdb code 4rmo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 48 binding sites of Calcium where determined in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale, PDB code: 4rmo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 48 in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale


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 Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:33.6 occ:1.00 OP2 F:A14 2.2 28.7 1.0 O F:HOH223 2.4 30.8 1.0 O A:HOH381 2.4 30.9 1.0 O F:HOH220 2.5 38.3 1.0 OD1 A:ASP80 2.5 27.4 1.0 O F:HOH222 2.5 27.5 1.0 CG A:ASP80 3.3 29.5 1.0 P F:A14 3.5 35.7 1.0 OP1 F:A14 3.9 33.5 1.0 CB A:ASP80 4.0 31.8 1.0 CA A:ASP80 4.1 32.6 1.0 OG1 A:THR114 4.1 27.6 1.0 OD2 A:ASP80 4.1 32.2 1.0 O A:HOH324 4.2 32.9 1.0 O F:HOH213 4.2 29.1 1.0 C3' F:G13 4.3 35.4 1.0 OP2 F:G36 4.3 38.8 1.0 O3' F:G13 4.4 32.8 1.0 OG A:SER115 4.4 31.4 1.0 O5' F:A14 4.6 28.4 1.0 N A:ASP80 4.7 29.1 1.0 O A:HOH336 5.0 29.5 1.0

Calcium binding site 2 out of 48 in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale


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 Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:50.7 occ:1.00 O B:HOH285 2.0 39.2 1.0 O B:HOH213 2.3 36.8 1.0 OP2 B:U19 2.3 35.3 1.0 O B:HOH245 2.4 25.4 1.0 P B:U19 3.8 38.0 1.0 O5' B:A18 4.3 37.6 1.0 O B:HOH286 4.3 38.5 1.0 OP2 B:A18 4.5 39.1 1.0 OP1 B:A18 4.6 38.5 1.0 O5' B:U19 4.6 33.2 1.0 O B:HOH214 4.6 25.4 1.0 P B:A18 4.6 37.9 1.0 O3' B:A18 4.6 31.8 1.0 C3' B:A18 4.6 32.9 1.0 OP1 B:U19 4.7 44.2 1.0 O B:HOH256 4.7 27.3 1.0 C5 B:U19 4.7 28.0 1.0

Calcium binding site 3 out of 48 in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:55.6 occ:1.00 O B:HOH203 2.3 39.3 1.0 O B:HOH277 2.5 40.4 1.0 O B:HOH233 2.7 29.1 1.0 O B:HOH281 2.7 47.1 1.0 O B:HOH244 2.8 41.2 1.0 O B:HOH260 3.0 43.8 1.0 OP1 B:G13 3.7 27.4 1.0 O B:HOH227 4.3 33.8 1.0 N7 B:G17 4.4 28.0 1.0 C8 B:G17 4.6 31.0 1.0 OP1 B:U12 4.6 25.1 1.0 O5' B:G13 4.7 26.9 1.0 O B:HOH214 4.7 25.4 1.0 OP2 B:G17 4.8 31.1 1.0 O B:HOH239 4.8 31.7 1.0 P B:G13 4.8 26.0 1.0

Calcium binding site 4 out of 48 in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca103 b:41.9 occ:1.00 O B:HOH201 2.2 33.0 1.0 O B:HOH276 2.3 39.3 1.0 O6 B:G41 2.4 30.2 1.0 O B:HOH223 2.6 32.4 1.0 O B:HOH272 2.6 38.5 1.0 O B:HOH237 3.1 46.0 1.0 C6 B:G41 3.5 31.9 1.0 OP2 B:G40 4.2 27.9 1.0 C5 B:G41 4.2 31.7 1.0 N7 B:G41 4.3 31.4 1.0 CB E:SER82 4.3 43.0 1.0 O B:HOH287 4.4 39.9 1.0 O4 B:U42 4.4 43.3 1.0 N7 B:G40 4.5 31.7 1.0 OG E:SER82 4.5 37.8 1.0 N1 B:G41 4.5 28.9 1.0 OP2 B:G39 4.6 36.2 1.0

Calcium binding site 5 out of 48 in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca104 b:61.6 occ:1.00 O B:HOH299 1.8 41.8 1.0 O B:HOH298 2.0 18.7 1.0 O B:HOH289 2.3 49.9 1.0 O B:HOH275 2.4 47.8 1.0 O B:HOH288 2.5 37.3 1.0 O B:HOH202 2.8 32.8 1.0 O B:HOH250 3.2 29.1 1.0 O6 B:G35 4.1 28.1 1.0 O4 B:U34 4.1 30.3 1.0 O B:HOH228 4.2 39.6 1.0 C5' B:U12 4.7 25.2 1.0 O B:HOH235 4.8 50.0 1.0 O B:HOH268 4.9 49.0 1.0 OP1 B:U12 5.0 25.1 1.0

Calcium binding site 6 out of 48 in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca105 b:69.5 occ:1.00 OP2 B:A32 2.0 46.7 1.0 O B:HOH294 2.2 58.2 1.0 O B:HOH293 2.4 61.7 1.0 O B:HOH236 2.5 39.0 1.0 OP1 B:A31 3.2 71.4 1.0 P B:A32 3.4 43.4 1.0 O5' B:A31 3.5 65.3 1.0 P B:A31 4.0 55.3 1.0 OP1 B:A32 4.1 45.1 1.0 O3' B:A31 4.2 47.8 1.0 C5' B:A31 4.4 57.8 1.0 O B:HOH252 4.5 46.0 1.0 O5' B:A32 4.5 38.0 1.0 C3' B:A31 4.5 49.4 1.0 O B:HOH235 4.7 50.0 1.0 OP2 B:A31 4.8 58.4 1.0

Calcium binding site 7 out of 48 in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca101 b:63.9 occ:1.00 O D:HOH270 2.5 42.1 1.0 O D:HOH288 2.5 40.8 1.0 O D:HOH283 2.5 43.1 1.0 O D:HOH214 2.8 49.4 1.0 O D:HOH268 3.0 37.0 1.0 OP2 D:A20 4.0 37.1 1.0 O D:HOH238 4.4 47.6 1.0 N4 D:C11 4.7 24.4 1.0 N7 D:A10 4.8 29.5 1.0 OP1 D:A20 4.9 42.2 1.0 P D:A20 4.9 43.5 1.0

Calcium binding site 8 out of 48 in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:40.1 occ:1.00 O H:HOH203 2.2 77.2 1.0 O H:HOH235 2.3 31.0 1.0 OP2 H:A14 2.4 30.7 1.0 O C:HOH387 2.4 35.3 1.0 OD1 C:ASP80 2.4 34.0 1.0 O H:HOH225 2.4 39.5 1.0 CG C:ASP80 3.2 32.5 1.0 P H:A14 3.6 36.2 1.0 CB C:ASP80 3.9 33.3 1.0 CA C:ASP80 3.9 35.0 1.0 OD2 C:ASP80 4.0 31.6 1.0 OP1 H:A14 4.1 33.0 1.0 OG1 C:THR114 4.1 38.5 1.0 O C:HOH331 4.2 49.3 1.0 OP2 H:G36 4.3 41.7 1.0 O H:HOH285 4.3 42.5 1.0 OG C:SER115 4.5 42.5 1.0 C3' H:G13 4.6 37.6 1.0 N C:ASP80 4.6 35.6 1.0 O3' H:G13 4.6 36.1 1.0 O5' H:A14 4.7 38.1 1.0 O C:HOH337 4.9 38.2 1.0 O H:HOH284 5.0 42.0 1.0

Calcium binding site 9 out of 48 in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca102 b:51.7 occ:1.00 O D:HOH267 2.4 46.2 1.0 O D:HOH291 2.5 42.9 1.0 O D:HOH237 2.5 36.4 1.0 O D:HOH201 2.6 34.7 1.0 O D:HOH285 2.6 41.7 1.0 O D:HOH220 2.7 21.8 1.0 O4' D:G13 4.4 29.1 1.0 OP1 D:U12 4.6 27.4 1.0 C5' D:U12 4.6 25.5 1.0 O6 D:G35 4.7 35.2 1.0 O4 D:U34 4.7 24.9 1.0 C1' D:G13 4.8 27.3 1.0 N7 D:G35 5.0 31.2 1.0

Calcium binding site 10 out of 48 in the Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of the Cptin Type III Toxin-Antitoxin System From Eubacterium Rectale within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca103 b:39.0 occ:1.00 O D:HOH211 2.3 37.4 1.0 N7 D:G24 2.4 23.3 1.0 O D:HOH210 2.4 34.0 1.0 O D:HOH202 2.5 28.9 1.0 O D:HOH209 2.5 34.2 1.0 O D:HOH203 2.7 36.1 1.0 C8 D:G24 3.1 24.2 1.0 C5 D:G24 3.6 25.1 1.0 O6 D:G24 4.1 25.3 1.0 C6 D:G24 4.2 25.5 1.0 O D:HOH233 4.2 31.2 1.0 N9 D:G24 4.3 25.2 1.0 OP2 D:G24 4.4 24.2 1.0 C5 D:U23 4.4 22.1 1.0 C4 D:G24 4.6 26.4 1.0 C4 D:U23 4.7 24.2 1.0 OP2 D:U23 4.8 33.4 1.0 C6 D:U23 4.8 21.6 1.0 O6 D:G25 4.8 34.1 1.0 O4 D:U23 5.0 23.5 1.0

F.Rao, F.L.Short, J.E.Voss, T.R.Blower, A.L.Orme, T.E.Whittaker, B.F.Luisi, G.P.Salmond. Co-Evolution of Quaternary Organization and Novel Rna Tertiary Interactions Revealed in the Crystal Structure of A Bacterial Protein-Rna Toxin-Antitoxin System. Nucleic Acids Res. V. 43 9529 2015.
ISSN: ISSN 0305-1048
PubMed: 26350213
DOI: 10.1093/NAR/GKV868