Calcium in PDB 8sji: Apo Structure of Computationally Designed Homotrimer TP1

The structure of Apo Structure of Computationally Designed Homotrimer TP1, PDB code: 8sji was solved by A.M.Hoffnagle, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.74 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.06, 77.43, 47.44, 90, 106.58, 90
R / Rfree (%)	16.8 / 20.6

The structure of Apo Structure of Computationally Designed Homotrimer TP1 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Apo Structure of Computationally Designed Homotrimer TP1 (pdb code 8sji). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Apo Structure of Computationally Designed Homotrimer TP1, PDB code: 8sji:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Apo Structure of Computationally Designed Homotrimer TP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Apo Structure of Computationally Designed Homotrimer TP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:52.8 occ:1.00 OD2 A:ASP5 2.4 47.9 1.0 OD1 A:ASP2 2.5 59.8 1.0 OD1 A:ASP5 3.1 41.2 1.0 CG A:ASP5 3.1 44.8 1.0 O A:HOH305 3.4 31.5 1.0 CG A:ASP2 3.6 54.4 1.0 OD2 A:ASP2 4.1 46.9 1.0 CB A:ASP5 4.6 31.1 1.0 CB A:ASP2 4.7 38.6 1.0 N A:ASP2 4.8 54.9 1.0

Calcium binding site 2 out of 4 in the Apo Structure of Computationally Designed Homotrimer TP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Apo Structure of Computationally Designed Homotrimer TP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:53.9 occ:0.50 O B:HOH303 2.3 40.9 1.0 OE1 B:GLU8 2.3 59.4 1.0 O B:HOH362 2.5 46.4 1.0 O B:HOH343 2.6 50.7 1.0 CD B:GLU8 3.6 62.6 1.0 OD1 B:ASP5 4.1 38.1 1.0 CA B:CA202 4.2 54.8 1.0 OE2 B:GLU8 4.3 66.3 1.0 O B:HOH380 4.3 51.2 1.0 CB B:GLU8 4.5 29.7 1.0 O B:HOH364 4.6 62.2 1.0 CG B:GLU8 4.6 42.6 1.0 O B:HOH377 4.8 46.3 1.0

Calcium binding site 3 out of 4 in the Apo Structure of Computationally Designed Homotrimer TP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Apo Structure of Computationally Designed Homotrimer TP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:54.8 occ:1.00 O B:HOH377 2.4 46.3 1.0 OE2 B:GLU8 2.5 66.3 1.0 CD B:GLU8 3.0 62.6 1.0 OE1 B:GLU8 3.1 59.4 1.0 O B:HOH302 3.2 60.6 1.0 CA B:CA201 4.2 53.9 0.5 O B:HOH312 4.2 43.3 1.0 CG B:GLU8 4.3 42.6 1.0 O B:HOH380 4.4 51.2 1.0

Calcium binding site 4 out of 4 in the Apo Structure of Computationally Designed Homotrimer TP1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Apo Structure of Computationally Designed Homotrimer TP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:37.6 occ:1.00 O C:HOH340 2.3 38.1 1.0 O C:LYS19 2.3 28.2 1.0 OD1 C:ASP21 2.7 49.4 1.0 OD2 C:ASP21 2.8 53.5 1.0 O C:HOH373 2.9 46.9 1.0 CG C:ASP21 3.1 51.6 1.0 C C:LYS19 3.6 26.4 1.0 CA C:LYS19 4.3 24.0 1.0 CB C:LYS19 4.3 25.6 1.0 C C:ALA20 4.5 29.8 1.0 CB C:ASP21 4.6 52.5 1.0 N C:ALA20 4.6 27.2 1.0 O C:HOH348 4.6 43.3 1.0 N C:ASP21 4.6 32.5 1.0 CA C:ALA20 4.7 24.1 1.0 O C:ALA20 4.9 28.9 1.0

A.M.Hoffnagle, F.A.Tezcan. Atomically Accurate Design of Metalloproteins with Predefined Coordination Geometries. J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
PubMed: 37352018
DOI: 10.1021/JACS.3C04047