Calcium in PDB 7ri3: Crystal Structure of Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli

The structure of Crystal Structure of Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli, PDB code: 7ri3 was solved by S.N.Sugiman-Marangos, S.K.Gill, R.A.Melnyk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.80 / 2.69
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.95, 137.08, 203.51, 90, 90, 90
R / Rfree (%)	20.3 / 24.8

The binding sites of Calcium atom in the Crystal Structure of Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli (pdb code 7ri3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli, PDB code: 7ri3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli


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 Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:48.0 occ:1.00 OE1 A:GLU393 2.3 51.5 1.0 O A:HOH725 2.4 54.2 1.0 O A:ILE233 2.4 61.6 1.0 O A:GLU393 2.5 50.3 1.0 O A:HOH786 2.6 28.8 1.0 OH A:TYR481 2.8 45.1 1.0 O A:HOH750 3.0 52.9 1.0 CD A:GLU393 3.5 53.4 1.0 C A:GLU393 3.5 51.7 1.0 C A:ILE233 3.6 62.5 1.0 CZ A:TYR481 3.8 44.1 1.0 CE2 A:TYR481 3.8 43.8 1.0 CA A:GLU393 3.9 52.8 1.0 CG A:GLU393 4.1 54.8 1.0 O A:GLY232 4.2 60.1 1.0 O A:CYS231 4.2 62.7 1.0 CA A:ASN234 4.3 63.2 1.0 O A:LEU395 4.4 41.0 1.0 N A:ASN234 4.4 64.3 1.0 N A:VAL235 4.4 47.0 1.0 C A:GLY232 4.4 60.7 1.0 OE2 A:GLU393 4.5 54.4 1.0 N A:ILE233 4.6 64.2 1.0 CB A:GLU393 4.6 54.9 1.0 CG2 A:VAL235 4.6 47.4 1.0 CB A:CYS231 4.6 61.2 1.0 CA A:ILE233 4.6 63.9 1.0 C A:CYS231 4.7 63.0 1.0 N A:TYR394 4.7 43.0 1.0 O A:LEU392 4.7 40.0 1.0 O A:HOH777 4.8 25.5 1.0 C A:ASN234 4.9 62.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli


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 Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:48.0 occ:1.00 OE2 B:GLU393 2.4 48.4 1.0 O B:GLU393 2.4 50.2 1.0 O B:HOH701 2.5 31.4 1.0 O B:ILE233 2.5 49.9 1.0 O B:HOH756 2.6 48.0 1.0 OH B:TYR481 2.9 42.5 1.0 C B:GLU393 3.4 48.3 1.0 CD B:GLU393 3.5 46.5 1.0 C B:ILE233 3.7 49.9 1.0 CZ B:TYR481 3.8 42.7 1.0 CE2 B:TYR481 3.8 43.6 1.0 CA B:GLU393 3.8 46.6 1.0 O B:LEU395 3.9 38.8 1.0 CG B:GLU393 4.1 45.6 1.0 CA B:ASN234 4.3 60.8 1.0 O B:CYS231 4.4 51.0 1.0 N B:ASN234 4.4 62.8 1.0 O B:LEU392 4.4 48.0 1.0 N B:ILE233 4.5 54.1 1.0 OE1 B:GLU393 4.5 45.3 1.0 N B:TYR394 4.6 41.0 1.0 C B:GLY232 4.6 53.9 1.0 O B:GLY232 4.6 52.4 1.0 N B:VAL235 4.6 54.1 1.0 CB B:GLU393 4.6 44.9 1.0 CA B:ILE233 4.7 51.8 1.0 O B:HOH784 4.8 27.4 1.0 CB B:CYS231 4.8 48.2 1.0 C B:CYS231 4.9 50.9 1.0 C B:LEU395 5.0 38.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli


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 Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:47.0 occ:1.00 O C:HOH723 2.2 46.6 1.0 O C:HOH752 2.4 32.9 1.0 OE1 C:GLU393 2.5 38.5 1.0 O C:ILE233 2.5 38.9 1.0 O C:GLU393 2.7 38.6 1.0 OH C:TYR481 3.0 36.0 1.0 C C:ILE233 3.6 40.6 1.0 CD C:GLU393 3.6 36.7 1.0 C C:GLU393 3.8 36.6 1.0 O C:GLY232 3.9 43.0 1.0 CZ C:TYR481 3.9 36.0 1.0 CE2 C:TYR481 4.0 36.2 1.0 CA C:ASN234 4.1 39.3 1.0 C C:GLY232 4.1 45.0 1.0 CG C:GLU393 4.2 35.3 1.0 O C:CYS231 4.2 44.8 1.0 N C:ASN234 4.2 41.0 1.0 CA C:GLU393 4.2 34.9 1.0 O C:LEU395 4.4 40.8 1.0 N C:VAL235 4.5 44.1 1.0 N C:ILE233 4.5 41.3 1.0 C C:CYS231 4.5 44.5 1.0 OE2 C:GLU393 4.6 36.2 1.0 CB C:CYS231 4.6 40.8 1.0 CA C:ILE233 4.6 43.0 1.0 CA C:GLY232 4.8 47.5 1.0 N C:GLY232 4.8 47.3 1.0 CB C:GLU393 4.8 33.8 1.0 C C:ASN234 4.8 42.1 1.0 N C:TYR394 5.0 33.9 1.0 O C:LEU392 5.0 39.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli


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 Albireti Toxin, A Diphtheria Toxin Homolog, From Streptomyces Albireticuli within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca603 b:52.5 occ:1.00 O D:HOH717 2.2 48.8 1.0 OE1 D:GLU393 2.4 58.0 1.0 O D:GLU393 2.5 58.2 1.0 O D:ILE233 2.5 46.8 1.0 O D:HOH737 2.6 28.8 1.0 O D:HOH745 2.6 50.1 1.0 OH D:TYR481 2.7 42.5 1.0 CD D:GLU393 3.5 57.6 1.0 C D:GLU393 3.6 57.3 1.0 C D:ILE233 3.7 48.3 1.0 CZ D:TYR481 3.7 41.8 1.0 CE2 D:TYR481 3.8 43.1 1.0 CG D:GLU393 4.0 57.4 1.0 CA D:GLU393 4.0 56.5 1.0 O D:CYS231 4.1 55.7 1.0 CA D:ASN234 4.3 49.1 1.0 O D:LEU395 4.3 42.1 1.0 O D:GLY232 4.4 51.5 1.0 C D:GLY232 4.4 53.1 1.0 N D:ASN234 4.4 50.8 1.0 N D:VAL235 4.5 49.3 1.0 OE2 D:GLU393 4.5 57.5 1.0 C D:CYS231 4.6 55.0 1.0 N D:ILE233 4.6 49.1 1.0 CB D:GLU393 4.6 56.4 1.0 CB D:CYS231 4.7 51.7 1.0 N D:TYR394 4.7 42.5 1.0 CA D:ILE233 4.8 50.2 1.0 O D:LEU392 4.8 45.8 1.0 O D:HOH804 4.9 46.2 1.0 N D:GLY232 4.9 52.3 1.0 C D:ASN234 5.0 49.5 1.0 CE1 D:TYR481 5.0 40.0 1.0 CA D:GLY232 5.0 53.7 1.0

S.N.Sugiman-Marangos, S.K.Gill, M.J.Mansfield, K.E.Orrell, A.C.Doxey, R.A.Melnyk. Structures of Distant Diphtheria Toxin Homologs Reveal Functional Determinants of An Evolutionarily Conserved Toxin Scaffold. Commun Biol V. 5 375 2022.
ISSN: ESSN 2399-3642
PubMed: 35440624
DOI: 10.1038/S42003-022-03333-9