Nickel in PDB 3fop: A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form

The structure of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form, PDB code: 3fop was solved by F.A.Tezcan, R.J.Radford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.91 / 3.00
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	104.897, 104.897, 107.925, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 27.7

The structure of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Nickel atom in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form (pdb code 3fop). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form, PDB code: 3fop:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni109 b:35.8 occ:1.00 NAK A:PXX151 2.1 37.0 1.0 NAJ A:PXX151 2.1 37.4 1.0 O A:HOH115 2.3 23.3 1.0 O A:HOH116 2.4 11.1 1.0 CAR A:PXX151 2.9 37.0 1.0 CAQ A:PXX151 2.9 37.3 1.0 CAF A:PXX151 3.1 37.4 1.0 CAE A:PXX151 3.1 37.7 1.0 O A:LYS42 3.9 40.0 1.0 CAP A:PXX151 4.3 37.2 1.0 CAO A:PXX151 4.3 37.2 1.0 CAD A:PXX151 4.4 37.4 1.0 CAC A:PXX151 4.4 37.4 1.0 CAH A:PXX151 4.9 37.1 1.0 CAG A:PXX151 4.9 37.1 1.0 C A:LYS42 4.9 40.1 1.0

Nickel binding site 2 out of 4 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni110 b:53.0 occ:1.00 O A:ALA1 2.0 50.7 1.0 N A:ALA1 2.3 50.5 1.0 OD2 A:ASP39 2.4 38.9 1.0 C A:ALA1 2.8 50.8 1.0 O A:HOH111 3.1 25.1 1.0 CA A:ALA1 3.1 50.8 1.0 CG A:ASP39 3.2 37.8 1.0 OD1 A:ASP39 3.3 38.3 1.0 N A:ASP2 4.0 51.0 1.0 CB A:ALA1 4.1 51.1 1.0 ND2 A:ASN6 4.5 45.1 1.0 CA A:ASP2 4.6 51.7 1.0 CB A:ASP39 4.6 37.5 1.0 O A:ASP39 4.8 37.4 1.0

Nickel binding site 3 out of 4 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni109 b:32.4 occ:1.00 NAJ B:PXX151 2.1 34.7 1.0 NAK B:PXX151 2.1 35.1 1.0 O B:HOH116 2.2 16.7 1.0 CAQ B:PXX151 2.9 35.0 1.0 CAR B:PXX151 2.9 34.7 1.0 CAE B:PXX151 3.1 35.3 1.0 CAF B:PXX151 3.1 35.4 1.0 O B:LYS42 4.0 40.0 1.0 CAP B:PXX151 4.2 34.7 1.0 CAO B:PXX151 4.2 35.0 1.0 CAC B:PXX151 4.4 35.1 1.0 CAD B:PXX151 4.4 35.0 1.0 CAG B:PXX151 4.8 35.0 1.0 CAH B:PXX151 4.8 34.6 1.0 C B:LYS42 5.0 40.0 1.0

Nickel binding site 4 out of 4 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Hexagonal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni110 b:49.1 occ:1.00 O B:ALA1 2.0 50.7 1.0 OD2 B:ASP39 2.2 38.5 1.0 N B:ALA1 2.2 50.7 1.0 C B:ALA1 2.9 50.9 1.0 CG B:ASP39 3.0 37.0 1.0 CA B:ALA1 3.1 50.9 1.0 OD1 B:ASP39 3.2 36.6 1.0 N B:ASP2 4.1 51.0 1.0 CB B:ALA1 4.2 51.2 1.0 ND2 B:ASN6 4.4 45.8 1.0 CB B:ASP39 4.5 37.0 1.0 O B:ASP39 4.7 37.6 1.0 CA B:ASP2 4.7 51.5 1.0

R.J.Radford, F.A.Tezcan. A Superprotein Triangle Driven By Nickel(II) Coordination: Exploiting Non-Natural Metal Ligands in Protein Self-Assembly. J.Am.Chem.Soc. V. 131 9136 2009.
ISSN: ISSN 0002-7863
PubMed: 19527025
DOI: 10.1021/JA9000695