Calcium in PDB 8e7f: Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.

The structure of Crystal Structure of the Autotransporter Ssp From Serratia Marcescens., PDB code: 8e7f was solved by L.Hor, A.Pilapitiya, S.Panjikar, J.J.Paxman, B.Heras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.89 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.482, 55.356, 61.883, 91.52, 93.04, 102.76
R / Rfree (%)	16.3 / 20.2

The structure of Crystal Structure of the Autotransporter Ssp From Serratia Marcescens. also contains other interesting chemical elements:

Iodine

(I)

6 atoms

The binding sites of Calcium atom in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens. (pdb code 8e7f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens., PDB code: 8e7f:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.


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 Autotransporter Ssp From Serratia Marcescens. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca711 b:34.6 occ:1.00 OD2 A:ASP376 2.2 36.3 1.0 OD1 A:ASP383 2.3 36.4 1.0 O A:LEU377 2.3 34.0 1.0 O A:GLY381 2.3 35.1 1.0 O A:VAL379 2.3 41.4 1.0 O A:HOH917 2.4 30.3 1.0 CG A:ASP383 3.4 32.4 1.0 CG A:ASP376 3.4 37.7 1.0 C A:LEU377 3.5 33.6 1.0 C A:VAL379 3.5 40.4 1.0 C A:GLY381 3.5 33.8 1.0 N A:LEU377 3.7 36.0 1.0 N A:GLY381 3.9 37.8 1.0 C A:ALA380 4.0 36.1 1.0 CB A:ASP383 4.0 33.3 1.0 OD1 A:ASP376 4.1 34.5 1.0 O A:GLY387 4.2 32.6 1.0 O A:HOH870 4.2 44.9 1.0 N A:VAL379 4.2 37.7 1.0 C A:GLY378 4.3 35.6 1.0 CA A:LEU377 4.3 34.7 1.0 CA A:GLY381 4.3 37.4 1.0 OD2 A:ASP383 4.3 32.0 1.0 N A:ALA380 4.3 39.1 1.0 CA A:ALA380 4.4 36.0 1.0 N A:ASP383 4.4 32.2 1.0 O A:GLY378 4.4 41.1 1.0 N A:GLY378 4.5 38.3 1.0 O A:ALA380 4.5 34.0 1.0 CA A:VAL379 4.5 38.9 1.0 C A:ASP376 4.5 35.2 1.0 N A:ILE382 4.5 33.9 1.0 CB A:ASP376 4.6 34.1 1.0 CA A:ASP376 4.6 34.8 1.0 C A:ILE382 4.7 32.7 1.0 CA A:GLY378 4.7 36.7 1.0 CA A:ILE382 4.8 33.2 1.0 CA A:ASP383 4.9 32.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.


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 Autotransporter Ssp From Serratia Marcescens. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca712 b:39.1 occ:1.00 OE2 A:GLU45 2.3 40.5 1.0 O A:ALA127 2.3 44.6 1.0 OE2 A:GLU84 2.3 43.4 1.0 O A:MET129 2.4 36.2 1.0 OE1 A:GLU84 2.4 41.9 1.0 O A:LYS123 2.4 35.8 1.0 OD1 A:ASP125 2.6 40.2 1.0 CD A:GLU84 2.7 38.7 1.0 C A:MET129 3.5 36.5 1.0 CD A:GLU45 3.5 42.9 1.0 C A:ALA127 3.5 46.6 1.0 CG A:ASP125 3.5 39.1 1.0 C A:LYS123 3.6 34.0 1.0 OD2 A:ASP125 3.9 45.9 1.0 N A:MET129 4.0 39.6 1.0 N A:ASP125 4.0 44.6 1.0 N A:ALA127 4.1 46.6 1.0 CG A:GLU45 4.2 42.6 1.0 CG A:GLU84 4.2 38.3 1.0 CB A:HIS130 4.3 36.4 1.0 CA A:ALA127 4.3 44.7 1.0 N A:HIS130 4.3 36.1 1.0 CA A:MET129 4.3 39.6 1.0 CA A:HIS130 4.3 36.2 1.0 OE1 A:GLU45 4.5 47.8 1.0 N A:ARG124 4.5 36.3 1.0 CA A:ARG124 4.5 38.3 1.0 CA A:LYS123 4.5 37.6 1.0 N A:GLY128 4.5 45.5 1.0 C A:GLY128 4.6 45.2 1.0 N A:LYS123 4.6 33.9 1.0 O A:HOH848 4.6 52.0 1.0 CB A:ASP125 4.6 41.8 1.0 CB A:ALA127 4.7 45.7 1.0 CB A:LYS123 4.7 40.0 1.0 C A:ARG124 4.8 41.8 1.0 CA A:ASP125 4.8 43.7 1.0 CA A:GLY128 4.8 44.6 1.0 OH A:TYR334 4.9 41.5 1.0 N A:GLY126 5.0 42.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.


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 Autotransporter Ssp From Serratia Marcescens. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca713 b:40.8 occ:1.00 OE1 A:GLU553 2.3 50.1 1.0 O A:GLY532 2.3 48.2 1.0 O A:PRO529 2.3 40.1 1.0 OD2 A:ASP561 2.4 35.5 1.0 O A:HOH877 2.4 46.6 1.0 O A:HOH884 2.4 35.6 1.0 OD1 A:ASP561 2.6 41.2 1.0 CG A:ASP561 2.8 39.5 1.0 C A:GLY532 3.2 49.3 1.0 CD A:GLU553 3.4 49.0 1.0 C A:PRO529 3.5 40.6 1.0 CG A:GLU553 4.0 49.6 1.0 CA A:GLY532 4.0 50.5 1.0 N A:ILE533 4.1 51.5 1.0 CB A:GLU553 4.1 46.4 1.0 CB A:ASP561 4.2 40.0 1.0 N A:GLY532 4.3 52.6 1.0 N A:PRO529 4.3 37.0 1.0 CA A:ILE533 4.3 47.3 1.0 C A:ALA528 4.3 36.5 1.0 O A:ALA528 4.3 40.8 1.0 N A:GLY530 4.4 46.4 1.0 OE2 A:GLU553 4.4 53.3 1.0 O A:GLY530 4.4 49.8 1.0 CA A:GLY530 4.4 47.5 1.0 C A:GLY530 4.4 50.3 1.0 CA A:PRO529 4.5 37.2 1.0 N A:GLY534 4.6 40.4 1.0 O A:HOH1103 4.6 46.4 1.0 O A:ASN551 4.6 37.3 1.0 N A:GLU553 4.7 41.2 1.0 CD A:PRO529 4.7 35.9 1.0 C A:ILE533 4.8 45.1 1.0 CB A:PRO529 5.0 37.8 1.0

L.Hor, A.Pilapitiya, J.A.Mckenna, S.Panjikar, M.A.Anderson, M.Desvaux, J.J.Paxman, B.Heras. Crystal Structure of A Subtilisin-Like Autotransporter Reveals Insights Into Its Cytotoxic Function Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-36719-2