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

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

Resolution Low / High (Å)	98.53 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.339, 107.396, 102.051, 90.00, 105.52, 90.00
R / Rfree (%)	20.9 / 26.8

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

Iron

(Fe)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Nickel atom in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form (pdb code 3foo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 24 binding sites of Nickel where determined in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form, PDB code: 3foo:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic 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 - Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni107 b:66.2 occ:1.00 O A:ALA1 2.3 45.5 1.0 OD2 A:ASP39 2.6 43.5 1.0 N A:ALA1 2.8 45.8 1.0 O A:HOH166 3.0 35.5 1.0 OD1 A:ASP39 3.1 42.2 1.0 C A:ALA1 3.1 45.8 1.0 CG A:ASP39 3.2 42.2 1.0 CA A:ALA1 3.4 45.8 1.0 CB A:ALA1 4.0 45.8 1.0 N A:ASP2 4.3 45.7 1.0 ND2 A:ASN6 4.4 41.6 1.0 CB A:ASP39 4.6 41.5 1.0 O A:ASP39 4.7 41.1 1.0 CA A:ASP2 5.0 45.6 1.0

Nickel binding site 2 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic 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 - Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni108 b:34.8 occ:1.00 NAK C:PXX151 2.1 31.1 1.0 NAJ C:PXX151 2.1 30.3 1.0 ND1 A:HIS77 2.1 34.9 1.0 O C:HOH125 2.2 37.4 1.0 O C:HOH124 2.7 19.4 1.0 CAR C:PXX151 2.9 30.1 1.0 CAQ C:PXX151 2.9 30.1 1.0 CE1 A:HIS77 3.0 34.0 1.0 CAF C:PXX151 3.1 30.5 1.0 CAE C:PXX151 3.1 31.0 1.0 CG A:HIS77 3.2 35.5 1.0 CB A:HIS77 3.6 36.2 1.0 NE2 A:HIS77 4.1 33.4 1.0 CD2 A:HIS77 4.2 34.3 1.0 CAP C:PXX151 4.2 30.8 1.0 CAO C:PXX151 4.3 30.9 1.0 CA A:HIS77 4.3 36.8 1.0 CAD C:PXX151 4.4 30.7 1.0 CAC C:PXX151 4.4 30.2 1.0 O C:HOH170 4.6 28.8 1.0 O C:LYS42 4.6 40.7 1.0 CAH C:PXX151 4.8 30.1 1.0 CAG C:PXX151 4.9 30.3 1.0

Nickel binding site 3 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic 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 - Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni107 b:76.5 occ:1.00 O B:ALA1 1.9 46.1 1.0 N B:ALA1 2.4 46.4 1.0 OD2 B:ASP39 2.5 42.5 1.0 O B:HOH171 2.7 35.3 1.0 C B:ALA1 2.8 46.0 1.0 CA B:ALA1 3.1 46.3 1.0 CG B:ASP39 3.3 41.6 1.0 OD1 B:ASP39 3.5 42.2 1.0 N B:ASP2 4.0 45.7 1.0 CB B:ALA1 4.1 46.4 1.0 ND2 B:ASN6 4.6 41.4 1.0 CA B:ASP2 4.6 45.6 1.0 CB B:ASP39 4.6 41.3 1.0 O B:ASP39 4.6 40.9 1.0

Nickel binding site 4 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic 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 - Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni108 b:31.7 occ:1.00 NAJ A:PXX151 2.1 28.9 1.0 NAK A:PXX151 2.1 29.0 1.0 ND1 B:HIS77 2.1 33.7 1.0 CAQ A:PXX151 2.9 29.1 1.0 CAR A:PXX151 2.9 28.6 1.0 O B:HOH121 2.9 16.3 1.0 CE1 B:HIS77 3.0 33.5 1.0 CAE A:PXX151 3.1 28.6 1.0 CAF A:PXX151 3.1 28.6 1.0 CG B:HIS77 3.2 34.9 1.0 O A:HOH120 3.5 28.8 1.0 CB B:HIS77 3.6 36.2 1.0 NE2 B:HIS77 4.2 33.5 1.0 CAO A:PXX151 4.2 28.8 1.0 CAP A:PXX151 4.3 28.4 1.0 CD2 B:HIS77 4.3 34.3 1.0 CAC A:PXX151 4.4 28.5 1.0 O A:LYS42 4.4 40.3 1.0 CAD A:PXX151 4.4 29.1 1.0 CA B:HIS77 4.4 36.5 1.0 CAG A:PXX151 4.9 28.6 1.0 CAH A:PXX151 4.9 27.9 1.0

Nickel binding site 5 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni107 b:73.6 occ:1.00 N C:ALA1 2.1 46.0 1.0 OD2 C:ASP39 2.4 42.6 1.0 O C:ALA1 2.4 45.6 1.0 C C:ALA1 3.1 45.9 1.0 CA C:ALA1 3.1 45.9 1.0 CG C:ASP39 3.4 41.9 1.0 OD1 C:ASP39 3.7 43.4 1.0 CB C:ALA1 4.3 46.0 1.0 N C:ASP2 4.4 45.8 1.0 ND2 C:ASN6 4.6 41.7 1.0 CB C:ASP39 4.7 41.1 1.0 O C:ASP39 4.8 40.9 1.0

Nickel binding site 6 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni108 b:31.1 occ:1.00 O C:HOH123 2.0 27.6 1.0 NAJ B:PXX151 2.1 26.8 1.0 NAK B:PXX151 2.1 26.6 1.0 ND1 C:HIS77 2.1 33.2 1.0 O B:HOH122 2.2 27.8 1.0 CAQ B:PXX151 2.9 26.3 1.0 CAR B:PXX151 2.9 26.1 1.0 CE1 C:HIS77 3.0 33.0 1.0 CAE B:PXX151 3.1 26.0 1.0 CAF B:PXX151 3.1 26.2 1.0 CG C:HIS77 3.2 34.9 1.0 CB C:HIS77 3.6 35.9 1.0 NE2 C:HIS77 4.2 33.1 1.0 CAO B:PXX151 4.2 26.0 1.0 CAP B:PXX151 4.3 25.9 1.0 CD2 C:HIS77 4.3 34.4 1.0 CAC B:PXX151 4.3 26.4 1.0 O B:LYS42 4.4 39.9 1.0 CA C:HIS77 4.4 36.4 1.0 CAD B:PXX151 4.4 25.9 1.0 CAG B:PXX151 4.8 25.7 1.0 CAH B:PXX151 4.9 25.6 1.0

Nickel binding site 7 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni107 b:74.3 occ:1.00 N D:ALA1 2.2 45.9 1.0 O D:ALA1 2.3 45.8 1.0 OD2 D:ASP39 2.5 43.9 1.0 C D:ALA1 3.0 45.9 1.0 CA D:ALA1 3.2 45.9 1.0 CG D:ASP39 3.2 42.3 1.0 O D:HOH145 3.4 39.1 1.0 OD1 D:ASP39 3.4 43.4 1.0 N D:ASP2 4.3 45.7 1.0 CB D:ALA1 4.3 46.2 1.0 CB D:ASP39 4.6 41.2 1.0 ND2 D:ASN6 4.7 41.9 1.0 O D:ASP39 4.8 41.0 1.0 CA D:ASP2 4.9 45.6 1.0

Nickel binding site 8 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni108 b:32.5 occ:1.00 NAK F:PXX151 2.1 30.5 1.0 NAJ F:PXX151 2.1 30.6 1.0 ND1 D:HIS77 2.1 33.2 1.0 O F:HOH119 2.5 33.6 1.0 CAQ F:PXX151 2.9 30.5 1.0 CAR F:PXX151 2.9 30.7 1.0 O F:HOH118 3.0 14.5 1.0 CE1 D:HIS77 3.1 33.3 1.0 CAF F:PXX151 3.1 30.7 1.0 CAE F:PXX151 3.1 30.4 1.0 CG D:HIS77 3.2 35.2 1.0 CB D:HIS77 3.5 36.2 1.0 NE2 D:HIS77 4.2 33.8 1.0 CAO F:PXX151 4.2 30.7 1.0 CAP F:PXX151 4.3 30.9 1.0 CD2 D:HIS77 4.3 34.2 1.0 CA D:HIS77 4.3 36.6 1.0 CAD F:PXX151 4.4 30.7 1.0 CAC F:PXX151 4.4 30.5 1.0 O F:LYS42 4.5 40.1 1.0 O D:HOH148 4.7 32.5 1.0 CAG F:PXX151 4.9 30.4 1.0 CAH F:PXX151 4.9 30.0 1.0

Nickel binding site 9 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni107 b:60.0 occ:1.00 N E:ALA1 2.2 45.5 1.0 O E:ALA1 2.3 45.8 1.0 OD2 E:ASP39 2.3 44.3 1.0 O E:HOH149 2.5 27.5 1.0 C E:ALA1 3.0 45.8 1.0 CA E:ALA1 3.2 45.6 1.0 CG E:ASP39 3.3 42.8 1.0 OD1 E:ASP39 3.6 44.0 1.0 CB E:ALA1 4.1 45.7 1.0 N E:ASP2 4.3 45.5 1.0 CB E:ASP39 4.6 41.2 1.0 ND2 E:ASN6 4.6 42.9 1.0 O E:ASP39 4.7 41.3 1.0 CA E:ASP2 4.9 45.5 1.0

Nickel binding site 10 out of 24 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni108 b:36.5 occ:1.00 NAK D:PXX151 2.1 31.8 1.0 NAJ D:PXX151 2.1 31.1 1.0 ND1 E:HIS77 2.1 34.3 1.0 O D:HOH113 2.5 24.0 1.0 O D:HOH114 2.6 23.4 1.0 CE1 E:HIS77 2.9 33.4 1.0 CAQ D:PXX151 2.9 30.4 1.0 CAR D:PXX151 2.9 31.0 1.0 CAF D:PXX151 3.1 30.7 1.0 CAE D:PXX151 3.1 31.1 1.0 CG E:HIS77 3.3 35.1 1.0 CB E:HIS77 3.8 36.2 1.0 NE2 E:HIS77 4.1 33.5 1.0 CAO D:PXX151 4.3 30.4 1.0 CAP D:PXX151 4.3 31.0 1.0 CD2 E:HIS77 4.3 33.8 1.0 CAD D:PXX151 4.4 30.4 1.0 CAC D:PXX151 4.4 30.8 1.0 O D:LYS42 4.4 40.1 1.0 CA E:HIS77 4.5 36.7 1.0 CAH D:PXX151 4.9 30.2 1.0 CAG D:PXX151 4.9 30.8 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