Calcium in PDB 8sjh: Zn-Bound Structure of Computationally Designed Homotrimer TP1

The structure of Zn-Bound Structure of Computationally Designed Homotrimer TP1, PDB code: 8sjh 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)	45.44 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.04, 77.41, 47.42, 90, 107.03, 90
R / Rfree (%)	16.5 / 19.5

The structure of Zn-Bound Structure of Computationally Designed Homotrimer TP1 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	1 atom

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

Calcium binding site 1 out of 3 in the Zn-Bound 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 Zn-Bound Structure of Computationally Designed Homotrimer TP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:68.5 occ:1.00 OD2 A:ASP5 2.4 41.6 1.0 OD1 A:ASP2 2.6 53.6 1.0 O A:HOH333 2.8 59.5 1.0 O A:HOH313 3.0 32.3 1.0 OD1 A:ASP5 3.1 39.2 1.0 CG A:ASP5 3.1 40.2 1.0 CG A:ASP2 3.6 48.2 1.0 OD2 A:ASP2 3.9 35.9 1.0 CB A:ASP5 4.6 29.1 1.0 CB A:ASP2 4.8 39.8 1.0 N A:ASP2 5.0 50.4 1.0

Calcium binding site 2 out of 3 in the Zn-Bound 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 Zn-Bound Structure of Computationally Designed Homotrimer TP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:63.6 occ:1.00 O A:HOH370 2.4 52.4 1.0 OE1 A:GLU8 2.4 42.9 1.0 OD1 A:ASP5 2.9 39.2 1.0 O A:HOH333 2.9 59.5 1.0 CD A:GLU8 3.6 33.5 1.0 O A:HOH313 3.7 32.3 1.0 CG A:ASP5 4.1 40.2 1.0 OE2 A:GLU8 4.2 41.1 1.0 CA A:ASP5 4.4 23.8 1.0 O A:HOH359 4.5 42.6 1.0 CB A:GLU8 4.6 27.4 1.0 CG A:GLU8 4.7 27.6 1.0 N A:ASP5 4.7 23.2 1.0 CB A:ASP5 4.7 29.1 1.0 O A:GLU4 4.9 23.4 1.0 C A:GLU4 5.0 25.0 1.0

Calcium binding site 3 out of 3 in the Zn-Bound 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 Zn-Bound Structure of Computationally Designed Homotrimer TP1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:106.0 occ:1.00 OE1 C:GLU8 2.5 70.9 1.0 OE2 C:GLU8 2.7 70.5 1.0 CD C:GLU8 2.9 66.0 1.0 O C:HOH303 3.9 60.0 1.0 OD2 C:ASP5 4.2 71.2 1.0 CG C:GLU8 4.4 39.0 1.0 O C:HOH365 4.5 41.1 1.0 O C:HOH321 4.5 51.6 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