Nickel 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:

Iron	(Fe)	1 atom
Calcium	(Ca)	4 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the Ni-Bound Structure of An Engineered Protein Trimer, TRICYT3, PDB code: 6wzc:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Ni-Bound Structure of An Engineered Protein Trimer, TRICYT3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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:Ni202 b:35.0 occ:1.00 N A:ALA1 2.0 26.6 1.0 O A:HOH361 2.1 33.3 1.0 O A:ALA1 2.1 30.9 1.0 O A:HOH320 2.2 32.0 1.0 O A:HOH360 2.2 43.7 1.0 OD2 A:ASP39 2.2 27.0 1.0 C A:ALA1 2.8 28.6 1.0 CA A:ALA1 2.9 25.6 1.0 CG A:ASP39 3.0 22.4 1.0 OD1 A:ASP39 3.1 27.3 1.0 CB A:ALA1 3.9 27.1 1.0 O A:HOH350 4.0 30.5 1.0 N A:ASP2 4.1 27.5 1.0 O A:HOH381 4.1 52.5 1.0 ND2 A:ASN6 4.2 23.2 1.0 O A:HOH391 4.4 38.2 1.0 CB A:ASP39 4.4 20.2 1.0 O A:ASP39 4.6 22.3 1.0 CA A:ASP2 4.7 26.4 1.0

Nickel binding site 2 out of 2 in the Ni-Bound Structure of An Engineered Protein Trimer, TRICYT3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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:Ni203 b:20.9 occ:0.33 NE2 A:HIS73 2.1 27.2 1.0 NE2 A:HIS77 2.2 50.1 1.0 CE1 A:HIS73 2.8 41.5 1.0 CE1 A:HIS77 3.1 40.1 1.0 CD2 A:HIS73 3.3 21.6 1.0 CD2 A:HIS77 3.3 40.7 1.0 ND1 A:HIS73 4.0 34.8 1.0 ND1 A:HIS77 4.3 53.8 1.0 CG A:HIS73 4.3 27.1 1.0 CG A:HIS77 4.4 53.1 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