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

Protein crystallography data

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

Other elements in 6wzc:

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

Nickel Binding Sites:

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 6wzc

Go back to Nickel Binding Sites List in 6wzc
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 6wzc

Go back to Nickel Binding Sites List in 6wzc
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

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: Wed Dec 16 01:57:05 2020

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