Iron 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:

Nickel

(Ni)

24 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron 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 Iron atom.
In total 12 binding sites of Iron where determined in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form, PDB code: 3foo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe150 b:39.3 occ:1.00 FE A:HEM150 0.0 39.3 1.0 ND A:HEM150 2.0 39.9 1.0 NE2 A:HIS102 2.0 37.8 1.0 NA A:HEM150 2.1 41.0 1.0 NC A:HEM150 2.1 39.7 1.0 NB A:HEM150 2.1 40.3 1.0 SD A:MET7 2.5 38.1 1.0 CD2 A:HIS102 3.0 38.3 1.0 C1D A:HEM150 3.0 40.1 1.0 C4D A:HEM150 3.1 41.2 1.0 CE1 A:HIS102 3.1 37.7 1.0 C4C A:HEM150 3.1 39.0 1.0 C4A A:HEM150 3.1 41.4 1.0 C1A A:HEM150 3.1 41.6 1.0 C1B A:HEM150 3.1 41.0 1.0 C1C A:HEM150 3.1 39.5 1.0 C4B A:HEM150 3.1 40.0 1.0 CHD A:HEM150 3.4 39.8 1.0 CHA A:HEM150 3.4 40.9 1.0 CHB A:HEM150 3.5 41.2 1.0 CHC A:HEM150 3.5 39.9 1.0 CG A:MET7 3.6 39.9 1.0 CE A:MET7 3.7 38.7 1.0 CG A:HIS102 4.1 38.9 1.0 ND1 A:HIS102 4.2 37.7 1.0 C2D A:HEM150 4.3 39.9 1.0 C3D A:HEM150 4.3 40.7 1.0 CB A:MET7 4.3 39.9 1.0 C3A A:HEM150 4.3 42.5 1.0 C3C A:HEM150 4.3 39.4 1.0 C2A A:HEM150 4.3 42.7 1.0 C2C A:HEM150 4.3 39.4 1.0 C2B A:HEM150 4.3 40.0 1.0 C3B A:HEM150 4.4 39.8 1.0

Iron binding site 2 out of 12 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 B:Fe150 b:35.3 occ:1.00 FE B:HEM150 0.0 35.3 1.0 NE2 B:HIS102 2.0 36.8 1.0 NA B:HEM150 2.1 36.9 1.0 ND B:HEM150 2.1 36.8 1.0 NC B:HEM150 2.1 36.2 1.0 NB B:HEM150 2.2 37.0 1.0 SD B:MET7 2.3 38.4 1.0 CD2 B:HIS102 2.9 38.2 1.0 CE1 B:HIS102 3.0 38.3 1.0 C1D B:HEM150 3.0 37.4 1.0 C1A B:HEM150 3.1 38.5 1.0 C4D B:HEM150 3.1 37.7 1.0 C4C B:HEM150 3.1 36.4 1.0 C4A B:HEM150 3.1 37.1 1.0 C1C B:HEM150 3.1 35.7 1.0 C1B B:HEM150 3.2 37.3 1.0 C4B B:HEM150 3.2 36.8 1.0 CHD B:HEM150 3.4 37.2 1.0 CHA B:HEM150 3.4 37.9 1.0 CHB B:HEM150 3.5 37.9 1.0 CG B:MET7 3.5 40.0 1.0 CHC B:HEM150 3.5 36.8 1.0 CE B:MET7 3.7 39.3 1.0 ND1 B:HIS102 4.1 37.1 1.0 CG B:HIS102 4.1 38.4 1.0 CB B:MET7 4.2 40.0 1.0 C3A B:HEM150 4.3 39.3 1.0 C2A B:HEM150 4.3 41.0 1.0 C2D B:HEM150 4.3 37.3 1.0 C3D B:HEM150 4.3 37.6 1.0 C3C B:HEM150 4.3 35.9 1.0 C2C B:HEM150 4.3 36.6 1.0 C2B B:HEM150 4.4 37.2 1.0 C3B B:HEM150 4.4 37.2 1.0

Iron binding site 3 out of 12 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 C:Fe150 b:40.6 occ:1.00 FE C:HEM150 0.0 40.6 1.0 ND C:HEM150 2.0 40.7 1.0 NE2 C:HIS102 2.0 38.4 1.0 NC C:HEM150 2.0 41.1 1.0 NB C:HEM150 2.1 40.4 1.0 NA C:HEM150 2.1 42.3 1.0 SD C:MET7 2.3 39.4 1.0 CE1 C:HIS102 2.9 38.5 1.0 C1D C:HEM150 3.0 42.5 1.0 C4C C:HEM150 3.0 41.3 1.0 C4D C:HEM150 3.0 42.8 1.0 C1C C:HEM150 3.1 40.4 1.0 C4B C:HEM150 3.1 40.7 1.0 CD2 C:HIS102 3.1 38.5 1.0 C1A C:HEM150 3.1 43.1 1.0 C1B C:HEM150 3.1 40.9 1.0 C4A C:HEM150 3.2 42.8 1.0 CHD C:HEM150 3.4 42.0 1.0 CHA C:HEM150 3.4 42.9 1.0 CHC C:HEM150 3.4 40.9 1.0 CE C:MET7 3.5 39.4 1.0 CHB C:HEM150 3.5 42.0 1.0 CG C:MET7 3.6 39.5 1.0 ND1 C:HIS102 4.1 37.8 1.0 CG C:HIS102 4.2 38.9 1.0 C3C C:HEM150 4.2 40.4 1.0 C2D C:HEM150 4.3 42.5 1.0 C3D C:HEM150 4.3 43.8 1.0 C2C C:HEM150 4.3 40.9 1.0 C3B C:HEM150 4.3 40.8 1.0 C2B C:HEM150 4.3 41.1 1.0 CB C:MET7 4.3 40.2 1.0 C2A C:HEM150 4.3 45.1 1.0 C3A C:HEM150 4.4 44.0 1.0

Iron binding site 4 out of 12 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 D:Fe150 b:37.7 occ:1.00 FE D:HEM150 0.0 37.7 1.0 NC D:HEM150 2.0 37.2 1.0 NE2 D:HIS102 2.0 37.8 1.0 ND D:HEM150 2.0 37.4 1.0 NB D:HEM150 2.1 36.6 1.0 NA D:HEM150 2.2 38.4 1.0 SD D:MET7 2.4 37.4 1.0 CD2 D:HIS102 3.0 37.8 1.0 C4C D:HEM150 3.0 37.2 1.0 CE1 D:HIS102 3.0 38.2 1.0 C1C D:HEM150 3.0 36.5 1.0 C1D D:HEM150 3.0 37.8 1.0 C4B D:HEM150 3.0 36.6 1.0 C4D D:HEM150 3.0 38.6 1.0 C1B D:HEM150 3.1 36.9 1.0 C1A D:HEM150 3.1 39.6 1.0 C4A D:HEM150 3.2 39.1 1.0 CHD D:HEM150 3.4 37.9 1.0 CE D:MET7 3.4 39.0 1.0 CHC D:HEM150 3.4 36.8 1.0 CHA D:HEM150 3.4 39.4 1.0 CG D:MET7 3.5 39.9 1.0 CHB D:HEM150 3.5 38.1 1.0 ND1 D:HIS102 4.1 37.5 1.0 CG D:HIS102 4.1 38.4 1.0 C3C D:HEM150 4.2 38.1 1.0 C2C D:HEM150 4.2 37.9 1.0 C2D D:HEM150 4.3 38.0 1.0 C3B D:HEM150 4.3 36.5 1.0 C3D D:HEM150 4.3 39.2 1.0 CB D:MET7 4.3 40.4 1.0 C2B D:HEM150 4.3 36.5 1.0 C2A D:HEM150 4.4 41.9 1.0 C3A D:HEM150 4.4 40.9 1.0

Iron binding site 5 out of 12 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 E:Fe150 b:34.2 occ:1.00 FE E:HEM150 0.0 34.2 1.0 NE2 E:HIS102 2.0 37.4 1.0 NC E:HEM150 2.0 33.9 1.0 ND E:HEM150 2.1 33.9 1.0 NB E:HEM150 2.1 34.8 1.0 NA E:HEM150 2.1 35.1 1.0 SD E:MET7 2.4 37.0 1.0 CE1 E:HIS102 3.0 38.3 1.0 CD2 E:HIS102 3.0 38.9 1.0 C1C E:HEM150 3.0 33.6 1.0 C4B E:HEM150 3.1 35.4 1.0 C4D E:HEM150 3.1 35.1 1.0 C4C E:HEM150 3.1 34.7 1.0 C1A E:HEM150 3.1 35.9 1.0 C1D E:HEM150 3.1 34.3 1.0 C1B E:HEM150 3.1 34.7 1.0 C4A E:HEM150 3.2 35.3 1.0 CHC E:HEM150 3.4 34.9 1.0 CHA E:HEM150 3.4 35.1 1.0 CHD E:HEM150 3.5 34.2 1.0 CG E:MET7 3.5 38.9 1.0 CE E:MET7 3.5 37.6 1.0 CHB E:HEM150 3.5 35.6 1.0 ND1 E:HIS102 4.1 38.7 1.0 CB E:MET7 4.1 39.8 1.0 CG E:HIS102 4.2 39.2 1.0 C2C E:HEM150 4.3 33.3 1.0 C3C E:HEM150 4.3 34.1 1.0 C3B E:HEM150 4.3 35.0 1.0 C3D E:HEM150 4.3 35.1 1.0 C2D E:HEM150 4.3 34.6 1.0 C2A E:HEM150 4.3 37.6 1.0 C2B E:HEM150 4.3 34.9 1.0 C3A E:HEM150 4.4 37.1 1.0

Iron binding site 6 out of 12 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 F:Fe150 b:32.1 occ:1.00 FE F:HEM150 0.0 32.1 1.0 NE2 F:HIS102 2.0 37.2 1.0 NA F:HEM150 2.0 33.1 1.0 NB F:HEM150 2.1 31.4 1.0 ND F:HEM150 2.1 32.2 1.0 NC F:HEM150 2.1 32.6 1.0 SD F:MET7 2.3 36.2 1.0 CD2 F:HIS102 2.9 38.3 1.0 CE1 F:HIS102 3.0 38.4 1.0 C1A F:HEM150 3.0 33.9 1.0 C4B F:HEM150 3.1 32.3 1.0 C4D F:HEM150 3.1 32.6 1.0 C4A F:HEM150 3.1 33.8 1.0 C1B F:HEM150 3.1 32.2 1.0 C1D F:HEM150 3.1 32.8 1.0 C1C F:HEM150 3.1 32.0 1.0 C4C F:HEM150 3.1 32.9 1.0 CE F:MET7 3.3 39.4 1.0 CHA F:HEM150 3.4 33.3 1.0 CG F:MET7 3.4 39.1 1.0 CHC F:HEM150 3.4 31.9 1.0 CHD F:HEM150 3.5 32.8 1.0 CHB F:HEM150 3.5 33.4 1.0 CG F:HIS102 4.1 39.1 1.0 ND1 F:HIS102 4.1 38.5 1.0 CB F:MET7 4.2 40.4 1.0 C2A F:HEM150 4.3 34.9 1.0 C3B F:HEM150 4.3 32.8 1.0 C3A F:HEM150 4.3 34.5 1.0 C2B F:HEM150 4.3 31.9 1.0 C3D F:HEM150 4.3 33.3 1.0 C2D F:HEM150 4.3 33.3 1.0 C2C F:HEM150 4.3 33.4 1.0 C3C F:HEM150 4.4 33.1 1.0

Iron binding site 7 out of 12 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 G:Fe150 b:35.7 occ:1.00 FE G:HEM150 0.0 35.7 1.0 NE2 G:HIS102 2.0 37.0 1.0 ND G:HEM150 2.0 35.8 1.0 NA G:HEM150 2.0 36.4 1.0 NB G:HEM150 2.1 35.2 1.0 NC G:HEM150 2.1 35.4 1.0 SD G:MET7 2.3 38.2 1.0 CE1 G:HIS102 2.9 37.7 1.0 C4D G:HEM150 3.0 37.0 1.0 C1A G:HEM150 3.0 38.0 1.0 C4A G:HEM150 3.0 36.8 1.0 C1D G:HEM150 3.1 36.6 1.0 C1B G:HEM150 3.1 35.5 1.0 CD2 G:HIS102 3.1 38.1 1.0 C4B G:HEM150 3.1 36.2 1.0 C4C G:HEM150 3.1 34.2 1.0 C1C G:HEM150 3.1 35.1 1.0 CHA G:HEM150 3.4 37.4 1.0 CHB G:HEM150 3.4 36.7 1.0 CE G:MET7 3.4 38.1 1.0 CHD G:HEM150 3.4 35.7 1.0 CHC G:HEM150 3.5 35.4 1.0 CG G:MET7 3.6 39.6 1.0 ND1 G:HIS102 4.1 37.5 1.0 CG G:HIS102 4.2 38.7 1.0 C3A G:HEM150 4.2 38.4 1.0 C2A G:HEM150 4.2 38.5 1.0 C3D G:HEM150 4.3 38.2 1.0 CB G:MET7 4.3 39.9 1.0 C2D G:HEM150 4.3 36.9 1.0 C2B G:HEM150 4.3 36.0 1.0 C3B G:HEM150 4.3 36.0 1.0 C3C G:HEM150 4.4 34.5 1.0 C2C G:HEM150 4.4 35.0 1.0

Iron binding site 8 out of 12 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 H:Fe150 b:40.2 occ:1.00 FE H:HEM150 0.0 40.2 1.0 NE2 H:HIS102 2.0 37.9 1.0 ND H:HEM150 2.0 41.5 1.0 NA H:HEM150 2.1 42.6 1.0 NC H:HEM150 2.1 41.0 1.0 NB H:HEM150 2.1 40.3 1.0 SD H:MET7 2.3 39.7 1.0 CE1 H:HIS102 3.0 37.7 1.0 CD2 H:HIS102 3.0 38.3 1.0 C1D H:HEM150 3.0 41.5 1.0 C4D H:HEM150 3.1 42.1 1.0 C4C H:HEM150 3.1 40.9 1.0 C4A H:HEM150 3.1 42.1 1.0 C1A H:HEM150 3.1 42.8 1.0 C1B H:HEM150 3.1 41.0 1.0 C1C H:HEM150 3.2 40.6 1.0 C4B H:HEM150 3.2 40.7 1.0 CHD H:HEM150 3.4 41.1 1.0 CE H:MET7 3.4 39.0 1.0 CHA H:HEM150 3.4 41.8 1.0 CHB H:HEM150 3.5 41.7 1.0 CG H:MET7 3.5 40.0 1.0 CHC H:HEM150 3.6 40.6 1.0 ND1 H:HIS102 4.1 37.5 1.0 CG H:HIS102 4.1 38.8 1.0 CB H:MET7 4.2 40.3 1.0 C2D H:HEM150 4.3 41.4 1.0 C3D H:HEM150 4.3 42.4 1.0 C3A H:HEM150 4.3 43.3 1.0 C2A H:HEM150 4.3 43.7 1.0 C3C H:HEM150 4.3 41.2 1.0 C2B H:HEM150 4.4 41.1 1.0 C2C H:HEM150 4.4 41.4 1.0 C3B H:HEM150 4.4 40.5 1.0

Iron binding site 9 out of 12 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 I:Fe150 b:41.4 occ:1.00 FE I:HEM150 0.0 41.4 1.0 NE2 I:HIS102 2.0 37.8 1.0 NB I:HEM150 2.0 41.2 1.0 NC I:HEM150 2.1 41.3 1.0 ND I:HEM150 2.1 42.4 1.0 NA I:HEM150 2.1 43.1 1.0 SD I:MET7 2.4 38.9 1.0 CD2 I:HIS102 2.9 38.5 1.0 CE1 I:HIS102 3.0 38.3 1.0 C4B I:HEM150 3.0 41.0 1.0 C1C I:HEM150 3.1 40.6 1.0 C1B I:HEM150 3.1 40.9 1.0 C4C I:HEM150 3.1 41.4 1.0 C1A I:HEM150 3.1 43.8 1.0 C4D I:HEM150 3.1 43.0 1.0 C1D I:HEM150 3.1 42.4 1.0 C4A I:HEM150 3.1 42.8 1.0 CHC I:HEM150 3.4 41.0 1.0 CE I:MET7 3.4 38.3 1.0 CHA I:HEM150 3.4 43.2 1.0 CHD I:HEM150 3.4 42.1 1.0 CHB I:HEM150 3.5 42.0 1.0 CG I:MET7 3.6 39.6 1.0 ND1 I:HIS102 4.1 38.4 1.0 CG I:HIS102 4.1 39.1 1.0 C3B I:HEM150 4.2 39.9 1.0 C2B I:HEM150 4.3 39.8 1.0 C2C I:HEM150 4.3 40.9 1.0 C3C I:HEM150 4.3 40.8 1.0 C2A I:HEM150 4.3 44.5 1.0 C2D I:HEM150 4.3 42.5 1.0 C3D I:HEM150 4.3 43.4 1.0 C3A I:HEM150 4.3 43.8 1.0 CB I:MET7 4.4 40.3 1.0

Iron binding site 10 out of 12 in the A Triangular Cytochrome B562 Superstructure Mediated By Ni Coordination - Monoclinic Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 J:Fe150 b:34.6 occ:1.00 FE J:HEM150 0.0 34.6 1.0 ND J:HEM150 2.0 36.2 1.0 NE2 J:HIS102 2.0 37.3 1.0 NC J:HEM150 2.1 34.7 1.0 NB J:HEM150 2.1 34.9 1.0 NA J:HEM150 2.1 35.8 1.0 SD J:MET7 2.3 38.4 1.0 CE1 J:HIS102 3.0 37.9 1.0 C1D J:HEM150 3.0 36.0 1.0 C4C J:HEM150 3.1 34.6 1.0 CD2 J:HIS102 3.1 38.0 1.0 C4D J:HEM150 3.1 36.4 1.0 C1A J:HEM150 3.1 37.1 1.0 C1B J:HEM150 3.1 35.6 1.0 C1C J:HEM150 3.1 34.7 1.0 C4A J:HEM150 3.1 35.8 1.0 C4B J:HEM150 3.1 35.5 1.0 CHD J:HEM150 3.3 35.2 1.0 CE J:MET7 3.4 39.0 1.0 CHA J:HEM150 3.4 36.5 1.0 CHB J:HEM150 3.5 36.4 1.0 CHC J:HEM150 3.5 35.3 1.0 CG J:MET7 3.5 39.7 1.0 ND1 J:HIS102 4.1 37.5 1.0 CG J:HIS102 4.2 39.2 1.0 CB J:MET7 4.2 39.9 1.0 C2D J:HEM150 4.2 36.4 1.0 C3D J:HEM150 4.3 37.3 1.0 C3C J:HEM150 4.3 36.0 1.0 C2C J:HEM150 4.3 35.0 1.0 C3A J:HEM150 4.3 38.3 1.0 C2A J:HEM150 4.4 39.1 1.0 C2B J:HEM150 4.4 35.7 1.0 C3B J:HEM150 4.4 35.7 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