Calcium in PDB 9ppo: Zn-Bound Structure of the H77C Variant of TRICYT2

The structure of Zn-Bound Structure of the H77C Variant of TRICYT2, PDB code: 9ppo was solved by V.H.Eng, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.80 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.52, 71.39, 75.84, 90, 90, 90
R / Rfree (%)	19.3 / 22.3

The structure of Zn-Bound Structure of the H77C Variant of TRICYT2 also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Calcium atom in the Zn-Bound Structure of the H77C Variant of TRICYT2 (pdb code 9ppo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Zn-Bound Structure of the H77C Variant of TRICYT2, PDB code: 9ppo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Zn-Bound Structure of the H77C Variant of TRICYT2


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 the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:44.7 occ:1.00 O A:HOH325 2.3 36.0 1.0 OE2 A:GLU4 2.3 42.9 1.0 CD A:GLU4 3.2 44.9 1.0 CG A:GLU4 3.5 36.0 1.0 OE1 A:GLU4 4.3 40.4 1.0 OE1 A:GLU8 4.4 48.6 1.0 O A:HOH314 4.5 45.2 1.0 OD1 A:ASP5 4.8 44.7 1.0 CB A:GLU4 4.9 33.8 1.0

Calcium binding site 2 out of 4 in the Zn-Bound Structure of the H77C Variant of TRICYT2


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 the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:47.2 occ:1.00 O A:LYS47 2.4 31.3 1.0 OD1 A:ASP50 3.4 53.5 1.0 OD2 A:ASP50 3.4 55.3 1.0 C A:LYS47 3.6 36.4 1.0 CG A:ASP50 3.8 52.4 1.0 CA A:LYS47 4.3 34.5 1.0 CB A:LYS47 4.5 39.3 1.0 O A:HOH334 4.5 43.0 1.0 N A:LEU48 4.6 33.3 1.0 O A:HOH302 4.6 48.0 1.0 CA A:LEU48 4.7 30.9 1.0 CE A:LYS51 4.8 43.8 1.0

Calcium binding site 3 out of 4 in the Zn-Bound Structure of the H77C Variant of TRICYT2


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 the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:60.8 occ:1.00 O B:HOH354 2.6 49.9 1.0 NA B:NA203 2.6 52.5 1.0 OE1 B:GLU8 2.8 42.0 1.0 O B:HOH358 2.8 43.4 1.0 CD B:GLU8 3.5 40.8 1.0 CG B:GLU8 4.1 31.8 1.0 O B:HOH306 4.1 46.5 1.0 CB B:GLU8 4.2 29.2 1.0 OE2 B:GLU8 4.3 38.0 1.0 OD2 B:ASP12 4.4 39.9 1.0 O B:HOH360 4.6 56.4 1.0

Calcium binding site 4 out of 4 in the Zn-Bound Structure of the H77C Variant of TRICYT2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Zn-Bound Structure of the H77C Variant of TRICYT2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:54.3 occ:1.00 OD1 B:ASP5 2.3 43.9 1.0 OE2 B:GLU8 2.5 38.0 1.0 O B:HOH306 2.6 46.5 1.0 OE1 B:GLU4 2.6 41.7 1.0 O B:HOH360 3.0 56.4 1.0 CD B:GLU8 3.4 40.8 1.0 CG B:ASP5 3.4 46.8 1.0 O B:HOH302 3.5 47.8 1.0 CD B:GLU4 3.6 43.1 1.0 OE1 B:GLU8 3.7 42.0 1.0 OE2 B:GLU4 3.9 36.8 1.0 OD2 B:ASP5 3.9 46.6 1.0 CB B:ASP5 4.6 33.9 1.0 CA B:ASP5 4.6 28.1 1.0 CG B:GLU8 4.7 31.8 1.0 N B:ASP5 4.8 29.8 1.0 CG B:GLU4 4.8 35.3 1.0

V.H.Eng, M.Gascon, A.Kakkis, F.A.Tezcan. Design of A Protein Scaffold with A Selective, Bi-Containing Heterodinuclear Metal Coordination Motif. J.Inorg.Biochem. V. 274 13104 2025.
ISSN: ISSN 0162-0134
PubMed: 41072111
DOI: 10.1016/J.JINORGBIO.2025.113104