Calcium in PDB 9dbb: Fe-Bound Structure of Computationally Designed Homotrimer TET4

The structure of Fe-Bound Structure of Computationally Designed Homotrimer TET4, PDB code: 9dbb 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)	40.54 / 2.50
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	70.74, 70.74, 54.08, 90, 90, 120
R / Rfree (%)	21.6 / 28.3

The structure of Fe-Bound Structure of Computationally Designed Homotrimer TET4 also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Calcium atom in the Fe-Bound Structure of Computationally Designed Homotrimer TET4 (pdb code 9dbb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Fe-Bound Structure of Computationally Designed Homotrimer TET4, PDB code: 9dbb:

Calcium binding site 1 out of 1 in the Fe-Bound Structure of Computationally Designed Homotrimer TET4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fe-Bound Structure of Computationally Designed Homotrimer TET4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:109.2 occ:1.00 O A:LYS19 3.1 134.8 1.0 OD1 A:ASP21 3.2 154.6 1.0 OD2 A:ASP21 3.3 156.5 1.0 CG A:ASP21 3.6 143.0 1.0 C A:LYS19 4.2 120.3 1.0 O A:HOH313 4.5 83.4 1.0 CB A:LYS19 4.6 115.5 1.0 CA A:LYS19 4.7 120.0 1.0

A.M.Hoffnagle, S.Srisantitham, M.Neeley, C.Y.Tsai, F.A.Tezcan. A De Novo Designed Protein with Versatile Metal Binding and Tunable Hydrolytic Activity. Biochemistry 2025.
ISSN: ISSN 0006-2960
PubMed: 40700614
DOI: 10.1021/ACS.BIOCHEM.5C00259