Atomistry » Sodium » PDB 6w3r-6wza » 6wza
Atomistry »
  Sodium »
    PDB 6w3r-6wza »
      6wza »

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

Protein crystallography data

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

Other elements in 6wza:

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

Sodium Binding Sites:

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 6wza

Go back to Sodium Binding Sites List in 6wza
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 6wza

Go back to Sodium Binding Sites List in 6wza
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 6wza

Go back to Sodium Binding Sites List in 6wza
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 6wza

Go back to Sodium Binding Sites List in 6wza
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 6wza

Go back to Sodium Binding Sites List in 6wza
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

Reference:

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
Page generated: Tue Dec 15 15:51:09 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy