Calcium in PDB 8deo: Structure of Aap A Domain and B-Repeats (Residues 351-813) From Staphylococcus Epidermidis

The structure of Structure of Aap A Domain and B-Repeats (Residues 351-813) From Staphylococcus Epidermidis, PDB code: 8deo was solved by G.Harris, F.Whelan, L.Clark, J.P.Turkenburg, J.R.Potts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.71 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.482, 66.565, 66.873, 84.7, 80.49, 89.66
R / Rfree (%)	19.8 / 24.3

The structure of Structure of Aap A Domain and B-Repeats (Residues 351-813) From Staphylococcus Epidermidis also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Structure of Aap A Domain and B-Repeats (Residues 351-813) From Staphylococcus Epidermidis (pdb code 8deo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Aap A Domain and B-Repeats (Residues 351-813) From Staphylococcus Epidermidis, PDB code: 8deo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Aap A Domain and B-Repeats (Residues 351-813) From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Aap A Domain and B-Repeats (Residues 351-813) From Staphylococcus Epidermidis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:30.1 occ:1.00 O A:HOH1011 2.3 24.9 1.0 O A:GLY468 2.3 35.2 1.0 OD1 A:ASP466 2.4 31.1 1.0 OD2 A:ASP466 2.4 31.0 1.0 OD2 A:ASP476 2.4 41.0 1.0 OD1 A:ASP476 2.5 33.0 1.0 O A:HOH1047 2.5 31.6 1.0 OE1 A:GLN481 2.6 34.8 1.0 CG A:ASP466 2.7 30.6 1.0 CG A:ASP476 2.8 37.3 1.0 C A:GLY468 3.5 35.7 1.0 CD A:GLN481 3.6 34.6 1.0 NE2 A:GLN481 4.0 31.9 1.0 NH1 A:ARG464 4.1 28.6 1.0 OH A:TYR489 4.2 26.1 1.0 CB A:ASP476 4.2 35.5 1.0 CB A:ASP466 4.3 29.5 1.0 O A:LEU452 4.3 34.4 1.0 CA A:TYR469 4.3 38.7 1.0 N A:TYR469 4.3 37.1 1.0 N A:TYR470 4.4 40.8 1.0 N A:GLY468 4.4 32.9 1.0 CA A:GLY468 4.5 34.4 1.0 OD2 A:ASP473 4.5 42.0 1.0 CE1 A:TYR489 4.6 28.4 1.0 CZ A:TYR489 4.7 28.1 1.0 C A:TYR469 4.7 39.7 1.0 O A:ASP431 4.7 34.4 1.0 CG A:GLN481 4.9 37.1 1.0 CZ A:ARG464 5.0 30.6 1.0

Calcium binding site 2 out of 2 in the Structure of Aap A Domain and B-Repeats (Residues 351-813) From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Aap A Domain and B-Repeats (Residues 351-813) From Staphylococcus Epidermidis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:31.6 occ:1.00 O B:HOH1023 2.2 34.1 1.0 O B:GLY468 2.3 31.4 1.0 OD2 B:ASP466 2.4 30.3 1.0 OD1 B:ASP466 2.4 31.0 1.0 OD1 B:ASP476 2.5 32.0 1.0 OD2 B:ASP476 2.5 35.9 1.0 OE1 B:GLN481 2.5 36.1 1.0 O B:HOH1029 2.7 27.3 1.0 CG B:ASP466 2.7 27.9 1.0 CG B:ASP476 2.7 34.7 1.0 C B:GLY468 3.5 32.3 1.0 CD B:GLN481 3.6 34.2 1.0 O B:HOH1030 4.0 34.5 1.0 NE2 B:GLN481 4.0 30.8 1.0 NH1 B:ARG464 4.1 29.0 1.0 OH B:TYR489 4.2 29.9 1.0 CB B:ASP476 4.2 34.5 1.0 CB B:ASP466 4.3 28.7 1.0 CA B:TYR469 4.3 36.8 1.0 N B:TYR469 4.3 33.4 1.0 O B:LEU452 4.3 30.7 1.0 N B:TYR470 4.4 40.2 1.0 N B:GLY468 4.4 30.1 1.0 CA B:GLY468 4.5 31.1 1.0 OD2 B:ASP473 4.6 38.8 1.0 CE2 B:TYR489 4.6 28.2 1.0 CZ B:TYR489 4.6 27.9 1.0 O B:ASP431 4.7 28.8 1.0 C B:TYR469 4.7 38.2 1.0 CG B:GLN481 4.9 36.3 1.0 CZ B:ARG464 5.0 31.6 1.0

L.C.Clark, K.E.Atkin, F.Whelan, A.S.Brentnall, G.Harris, A.M.Towell, J.P.Turkenburg, Y.Liu, T.Feizi, S.C.Griffiths, J.A.Geoghegan, J.R.Potts. Staphylococcal Periscope Proteins Aap, Sasg, and Pls Project Noncanonical Legume-Like Lectin Adhesin Domains From the Bacterial Surface. J.Biol.Chem. V. 299 02936 2023.
ISSN: ESSN 1083-351X
PubMed: 36702253
DOI: 10.1016/J.JBC.2023.102936