Calcium in PDB 6wzc: Ni-Bound Structure of An Engineered Protein Trimer, TRICYT3

The structure of Ni-Bound Structure of An Engineered Protein Trimer, TRICYT3, PDB code: 6wzc 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)	35.71 / 2.20
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.460, 82.460, 53.118, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.9

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

Nickel	(Ni)	2 atoms
Iron	(Fe)	1 atom
Chlorine	(Cl)	3 atoms

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

Calcium binding site 1 out of 4 in the Ni-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 Ni-Bound Structure of An Engineered Protein Trimer, TRICYT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:34.3 occ:0.50 O A:HOH363 2.3 47.8 0.5 OD1 A:ASP21 2.4 36.7 1.0 O A:LYS19 2.5 36.0 1.0 CA A:CA205 2.7 59.9 1.0 CG A:ASP21 3.4 33.9 1.0 C A:LYS19 3.5 34.5 1.0 OD2 A:ASP21 3.8 47.3 1.0 CA A:LYS19 4.0 35.0 1.0 CB A:LYS19 4.2 28.3 1.0 O A:ALA20 4.3 31.9 1.0 C A:ALA20 4.3 36.0 1.0 N A:ALA20 4.5 34.9 1.0 N A:ASP21 4.6 35.6 1.0 CB A:ASP21 4.7 34.7 1.0 CA A:ALA20 4.8 40.8 1.0 CA A:ASP21 4.9 37.2 1.0

Calcium binding site 2 out of 4 in the Ni-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 Ni-Bound Structure of An Engineered Protein Trimer, TRICYT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:59.9 occ:1.00 CA A:CA204 2.7 34.3 0.5 CA A:LYS19 3.5 35.0 1.0 O A:LYS19 3.7 36.0 1.0 CD A:LYS19 3.8 37.1 1.0 C A:LYS19 3.9 34.5 1.0 O A:HOH385 3.9 48.7 1.0 O A:GLU18 4.1 29.4 1.0 CB A:LYS19 4.1 28.3 1.0 CG A:LYS19 4.6 31.3 1.0 N A:LYS19 4.6 29.4 1.0 OD1 A:ASP21 4.6 36.7 1.0 C A:GLU18 4.8 28.1 1.0 O A:HOH325 4.9 49.8 1.0 O A:ALA20 4.9 31.9 1.0 N A:ALA20 4.9 34.9 1.0 O A:HOH363 4.9 47.8 0.5 CE A:LYS19 5.0 46.7 1.0

Calcium binding site 3 out of 4 in the Ni-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 Ni-Bound Structure of An Engineered Protein Trimer, TRICYT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:92.6 occ:1.00 OE1 A:GLU4 2.5 72.2 1.0 O A:HOH379 2.8 72.4 1.0 OE2 A:GLU4 3.2 67.6 1.0 CA A:CA207 3.2 56.5 0.5 CD A:GLU4 3.2 73.0 1.0 CG A:GLU4 4.7 59.8 1.0 O2A A:HEC201 5.0 54.1 1.0

Calcium binding site 4 out of 4 in the Ni-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 Ni-Bound Structure of An Engineered Protein Trimer, TRICYT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca207 b:56.5 occ:0.50 O1A A:HEC201 2.5 52.7 1.0 OE1 A:GLU4 2.5 72.2 1.0 O2A A:HEC201 2.5 54.1 1.0 CGA A:HEC201 2.8 50.1 1.0 CD A:GLU4 3.1 73.0 1.0 CA A:CA206 3.2 92.6 1.0 CG A:GLU4 3.7 59.8 1.0 OE2 A:GLU4 3.7 67.6 1.0 CBA A:HEC201 4.3 40.9 1.0 OE1 A:GLU8 4.6 67.0 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