Iron in PDB 6wza: Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1

The structure of Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1, PDB code: 6wza 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)	39.35 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.115, 82.115, 137.517, 90.00, 90.00, 120.00
R / Rfree (%)	24.1 / 30.6

The structure of Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1 also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Chlorine	(Cl)	6 atoms
Sodium	(Na)	5 atoms

The binding sites of Iron atom in the Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1 (pdb code 6wza). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1, PDB code: 6wza:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:25.2 occ:1.00 FE A:HEC201 0.0 25.2 1.0 ND A:HEC201 2.0 23.4 1.0 NA A:HEC201 2.0 19.4 1.0 NC A:HEC201 2.1 19.4 1.0 NB A:HEC201 2.1 18.9 1.0 NE2 A:HIS102 2.3 23.3 1.0 SD A:MET7 2.5 27.7 1.0 C1D A:HEC201 3.0 18.2 1.0 C4D A:HEC201 3.0 21.8 1.0 C1A A:HEC201 3.0 17.8 1.0 C4C A:HEC201 3.0 19.6 1.0 C4A A:HEC201 3.1 16.6 1.0 C1B A:HEC201 3.1 19.7 1.0 C1C A:HEC201 3.1 14.9 1.0 C4B A:HEC201 3.1 17.2 1.0 CD2 A:HIS102 3.2 22.8 1.0 CE1 A:HIS102 3.4 24.1 1.0 CHA A:HEC201 3.4 19.4 1.0 CHD A:HEC201 3.4 19.2 1.0 CHB A:HEC201 3.5 23.0 1.0 CG A:MET7 3.5 21.0 1.0 CHC A:HEC201 3.5 20.9 1.0 CE A:MET7 3.6 23.4 1.0 C2D A:HEC201 4.2 30.3 1.0 C3D A:HEC201 4.2 30.1 1.0 C2A A:HEC201 4.2 23.7 1.0 C3A A:HEC201 4.3 23.4 1.0 CB A:MET7 4.3 25.5 1.0 C3C A:HEC201 4.3 21.3 1.0 C2C A:HEC201 4.3 22.3 1.0 C2B A:HEC201 4.4 22.9 1.0 C3B A:HEC201 4.4 19.1 1.0 CG A:HIS102 4.4 29.4 1.0 H51 A:MPD206 4.4 44.9 1.0 ND1 A:HIS102 4.4 21.6 1.0 H53 A:MPD206 4.8 44.9 1.0

Iron binding site 2 out of 3 in the Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:25.0 occ:1.00 FE B:HEC201 0.0 25.0 1.0 ND B:HEC201 2.0 21.5 1.0 NC B:HEC201 2.0 24.0 1.0 NB B:HEC201 2.1 15.8 1.0 NA B:HEC201 2.1 22.5 1.0 NE2 B:HIS102 2.3 23.8 1.0 SD B:MET7 2.5 26.7 1.0 C1D B:HEC201 3.0 21.8 1.0 C4D B:HEC201 3.0 21.4 1.0 C4C B:HEC201 3.0 24.2 1.0 C1A B:HEC201 3.1 19.9 1.0 C4B B:HEC201 3.1 18.9 1.0 C1C B:HEC201 3.1 18.2 1.0 C1B B:HEC201 3.1 20.0 1.0 C4A B:HEC201 3.1 19.7 1.0 CD2 B:HIS102 3.2 22.9 1.0 CE B:MET7 3.3 26.5 1.0 CE1 B:HIS102 3.3 22.9 1.0 CHD B:HEC201 3.4 23.2 1.0 CHA B:HEC201 3.4 19.5 1.0 CHC B:HEC201 3.4 23.0 1.0 CG B:MET7 3.5 22.8 1.0 CHB B:HEC201 3.5 21.8 1.0 C2D B:HEC201 4.2 19.0 1.0 C3D B:HEC201 4.2 25.1 1.0 CB B:MET7 4.3 23.9 1.0 C3C B:HEC201 4.3 24.6 1.0 C2C B:HEC201 4.3 21.1 1.0 C2A B:HEC201 4.3 28.9 1.0 C2B B:HEC201 4.3 21.7 1.0 C3A B:HEC201 4.3 24.9 1.0 C3B B:HEC201 4.3 20.7 1.0 CG B:HIS102 4.4 24.3 1.0 ND1 B:HIS102 4.4 23.2 1.0

Iron binding site 3 out of 3 in the Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:25.0 occ:1.00 FE C:HEC201 0.0 25.0 1.0 NC C:HEC201 2.0 23.7 1.0 ND C:HEC201 2.0 24.9 1.0 NB C:HEC201 2.1 22.0 1.0 NA C:HEC201 2.1 27.6 1.0 NE2 C:HIS102 2.2 20.4 1.0 SD C:MET7 2.4 23.8 1.0 C4C C:HEC201 3.0 22.9 1.0 C1D C:HEC201 3.0 24.8 1.0 C1C C:HEC201 3.0 22.4 1.0 CD2 C:HIS102 3.1 23.9 1.0 C4D C:HEC201 3.1 26.1 1.0 C4B C:HEC201 3.1 23.1 1.0 C1A C:HEC201 3.1 19.9 1.0 C1B C:HEC201 3.1 26.1 1.0 C4A C:HEC201 3.2 19.1 1.0 CE1 C:HIS102 3.3 25.6 1.0 CHD C:HEC201 3.4 27.0 1.0 CHC C:HEC201 3.4 28.7 1.0 CE C:MET7 3.5 31.3 1.0 CHA C:HEC201 3.5 23.5 1.0 CG C:MET7 3.5 28.7 1.0 CHB C:HEC201 3.5 23.9 1.0 C3C C:HEC201 4.2 22.4 1.0 C2C C:HEC201 4.3 24.8 1.0 C2D C:HEC201 4.3 26.2 1.0 CG C:HIS102 4.3 23.0 1.0 C3D C:HEC201 4.3 33.6 1.0 CB C:MET7 4.3 26.5 1.0 ND1 C:HIS102 4.3 21.3 1.0 C2A C:HEC201 4.3 28.0 1.0 C2B C:HEC201 4.3 25.2 1.0 C3B C:HEC201 4.4 22.4 1.0 C3A C:HEC201 4.4 25.7 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