Calcium in PDB 6wz1: Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3

The structure of Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3, PDB code: 6wz1 was solved by F.A.Tezcan, A.Kakkis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.79 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.759, 77.392, 47.940, 90.00, 110.70, 90.00
R / Rfree (%)	17.6 / 22.9

The structure of Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3 also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Iron	(Fe)	3 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Calcium atom in the Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3 (pdb code 6wz1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3, PDB code: 6wz1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:13.1 occ:1.00 OE2 B:GLU4 2.2 12.3 1.0 O2D B:HEC201 2.3 18.7 1.0 O B:HOH335 2.4 16.1 1.0 O1D B:HEC201 2.9 15.9 1.0 CGD B:HEC201 3.0 22.3 1.0 CD B:GLU4 3.4 14.3 1.0 CA B:CA203 3.8 20.8 1.0 O B:HOH303 4.0 21.8 1.0 CG B:GLU4 4.1 13.3 1.0 OE1 B:GLU4 4.4 18.2 0.9 CBD B:HEC201 4.4 17.8 1.0 CG B:PRO46 4.6 18.0 1.0 O B:HOH307 4.7 18.9 1.0 O B:HOH324 4.7 20.9 1.0

Calcium binding site 2 out of 4 in the Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:20.8 occ:1.00 OE2 B:GLU4 2.6 12.3 1.0 OE1 B:GLU4 2.6 18.2 0.9 CD B:GLU4 2.9 14.3 1.0 CA B:CA202 3.8 13.1 1.0 CA B:CA204 3.9 18.2 0.8 O B:HOH348 4.3 18.6 1.0 CG B:GLU4 4.4 13.3 1.0 O B:HOH335 4.6 16.1 1.0 O B:HOH313 4.8 18.9 1.0

Calcium binding site 3 out of 4 in the Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:18.2 occ:0.80 O B:HOH348 2.2 18.6 1.0 O B:HOH313 2.4 18.9 1.0 OE1 B:GLU4 2.5 18.2 0.9 O B:HOH310 2.8 24.4 1.0 O B:HOH372 3.7 31.2 1.0 CD B:GLU4 3.7 14.3 1.0 CB B:GLU4 3.9 22.1 1.0 CA B:CA203 3.9 20.8 1.0 CG B:GLU4 4.4 13.3 1.0 O B:HOH369 4.6 26.4 1.0 OE2 B:GLU4 4.6 12.3 1.0 OD1 B:ASP5 4.6 25.2 1.0 O1A B:HEC201 4.7 24.5 1.0 OD2 B:ASP2 4.8 40.6 0.7

Calcium binding site 4 out of 4 in the Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mn-Bound Structure of An Engineered Protein Trimer, TRICYT3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:43.1 occ:1.00 OD2 C:ASP2 2.5 34.6 1.0 OD1 C:ASP5 3.0 32.1 1.0 OD1 C:ASP2 3.1 26.4 1.0 O C:HOH306 3.1 29.2 1.0 CG C:ASP2 3.1 27.3 1.0 CG C:ASP5 3.4 31.0 1.0 OD2 C:ASP5 3.4 37.9 1.0 O C:HOH315 4.0 38.5 1.0 N C:ASP5 4.2 15.9 1.0 O C:HOH316 4.3 21.3 1.0 CB C:ASP5 4.4 21.0 1.0 CB C:GLU4 4.4 14.2 1.0 CB C:ASP2 4.6 21.3 1.0 CA C:ASP5 4.8 21.4 1.0 O C:HOH359 4.9 24.1 1.0 C C:GLU4 5.0 19.5 1.0 O C:HOH314 5.0 35.8 1.0

F.A.Tezcan, A.Kakkis, D.Gagnon, J.Esselborn, R.D.Britt. Metal-Templated Design of Chemically Switchable Protein Assemblies with High-Affinity Coordination Sites. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32830423
DOI: 10.1002/ANIE.202009226