Sodium 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
Iron	(Fe)	3 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1, PDB code: 6wza:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na203 b:46.8 occ:1.00 O A:ALA43 2.5 30.3 1.0 O A:GLN41 2.6 38.2 1.0 O A:LYS42 3.2 40.6 1.0 C A:LYS42 3.3 38.1 1.0 C A:ALA43 3.5 34.7 1.0 CD A:ARG62 3.6 32.5 1.0 N A:ALA43 3.6 38.6 1.0 C A:GLN41 3.6 38.4 1.0 CG A:ARG62 3.7 22.3 1.0 CA A:LYS42 3.9 30.4 1.0 CE A:MET58 4.1 30.6 1.0 NH1 A:ARG62 4.2 38.0 1.0 CA A:ALA43 4.2 26.5 1.0 N A:LYS42 4.2 33.0 1.0 N A:THR44 4.6 42.6 1.0 CE2 A:PHE61 4.6 27.8 1.0 CD2 A:PHE61 4.6 30.3 1.0 OG1 A:THR44 4.7 47.3 1.0 NE A:ARG62 4.7 39.9 1.0 CA A:GLN41 4.8 29.7 1.0 NE2 B:HIS59 5.0 45.5 1.0 CZ A:ARG62 5.0 34.4 1.0 CA A:THR44 5.0 38.0 1.0 CB A:ARG62 5.0 28.2 1.0

Sodium binding site 2 out of 5 in the Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na202 b:74.7 occ:1.00 OD2 B:ASP60 4.1 28.1 1.0 CE B:LYS104 4.1 54.1 1.0 CA B:GLY64 4.2 21.4 1.0 OD1 B:ASP60 4.3 30.4 1.0 O B:ASP60 4.5 30.0 1.0 CG B:ASP60 4.5 27.8 1.0 NZ B:LYS104 4.6 48.0 1.0 N B:GLY64 4.7 29.8 1.0 CB B:ALA100 4.9 31.6 1.0 N B:CYS101 5.0 29.1 1.0

Sodium binding site 3 out of 5 in the Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na202 b:52.7 occ:1.00 O2A C:HEC201 2.2 43.0 1.0 OE2 C:GLU4 2.4 59.3 1.0 O C:HOH330 2.4 56.4 1.0 O C:HOH321 2.8 49.8 1.0 OE1 C:GLU8 3.1 45.1 0.1 O C:HOH325 3.1 66.0 1.0 CGA C:HEC201 3.3 36.6 1.0 CD C:GLU4 3.5 58.3 1.0 O1A C:HEC201 3.7 35.0 1.0 CD C:GLU8 3.9 44.2 1.0 CG C:GLU4 4.0 40.7 1.0 CG C:GLU8 4.5 44.1 1.0 OE1 C:GLU4 4.6 54.1 1.0 CBA C:HEC201 4.6 25.9 1.0 OE2 C:GLU8 4.6 50.2 0.6

Sodium binding site 4 out of 5 in the Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na203 b:54.8 occ:1.00 OD1 C:ASP2 3.1 49.9 1.0 OD2 C:ASP5 3.4 53.5 1.0 OD1 C:ASP5 3.4 54.6 1.0 CG C:ASP5 3.7 53.8 1.0 CG C:ASP2 4.0 49.2 1.0 OD2 C:ASP2 4.1 64.6 1.0 OE1 C:GLU4 4.2 54.1 1.0 CD C:GLU4 4.7 58.3 1.0 CB C:GLU4 4.8 41.9 1.0 N C:ASP5 4.9 32.6 1.0

Sodium binding site 5 out of 5 in the Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ni-Bound Structure of An Engineered Metal-Dependent Protein Trimer, TRICYT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na204 b:64.2 occ:1.00 CB C:ASN99 4.7 21.3 1.0 N C:ALA100 4.9 19.4 1.0 C C:ASN99 4.9 24.8 1.0 CA C:ALA100 5.0 19.2 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