Iron in PDB 3ufh: Crystal Structure of Unda with Iron Citrate Bound

The structure of Crystal Structure of Unda with Iron Citrate Bound, PDB code: 3ufh was solved by M.J.Edwards, T.A.Clarke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.63 / 2.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.880, 106.530, 151.120, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 21.1

The structure of Crystal Structure of Unda with Iron Citrate Bound also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Unda with Iron Citrate Bound (pdb code 3ufh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 14 binding sites of Iron where determined in the Crystal Structure of Unda with Iron Citrate Bound, PDB code: 3ufh:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 14 in the Crystal Structure of Unda with Iron Citrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Unda with Iron Citrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe901 b:35.5 occ:1.00 FE A:HEC901 0.0 35.5 1.0 NE2 A:HIS827 1.9 19.6 1.0 NE2 A:HIS801 1.9 25.1 1.0 NA A:HEC901 2.0 40.9 1.0 NC A:HEC901 2.0 42.5 1.0 NB A:HEC901 2.1 42.6 1.0 ND A:HEC901 2.1 44.5 1.0 CE1 A:HIS801 2.8 32.6 1.0 CE1 A:HIS827 2.9 22.3 1.0 CD2 A:HIS827 2.9 22.7 1.0 C4A A:HEC901 3.0 37.4 1.0 C4C A:HEC901 3.0 44.5 1.0 C1A A:HEC901 3.0 42.9 1.0 C1B A:HEC901 3.0 40.5 1.0 C1D A:HEC901 3.1 43.5 1.0 C1C A:HEC901 3.1 42.9 1.0 CD2 A:HIS801 3.1 33.3 1.0 C4B A:HEC901 3.1 42.9 1.0 C4D A:HEC901 3.2 43.4 1.0 CHD A:HEC901 3.3 42.2 1.0 CHB A:HEC901 3.3 38.9 1.0 CHA A:HEC901 3.5 38.1 1.0 CHC A:HEC901 3.5 43.0 1.0 ND1 A:HIS801 4.0 31.7 1.0 ND1 A:HIS827 4.0 19.0 1.0 CG A:HIS827 4.0 23.5 1.0 CG A:HIS801 4.1 28.9 1.0 C3A A:HEC901 4.2 41.4 1.0 C3C A:HEC901 4.2 41.9 1.0 C2A A:HEC901 4.2 39.4 1.0 C2C A:HEC901 4.3 40.6 1.0 C2B A:HEC901 4.3 42.9 1.0 C2D A:HEC901 4.3 48.0 1.0 C3B A:HEC901 4.3 39.7 1.0 C3D A:HEC901 4.4 45.1 1.0

Iron binding site 2 out of 14 in the Crystal Structure of Unda with Iron Citrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Unda with Iron Citrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe902 b:20.2 occ:1.00 FE A:HEC902 0.0 20.2 1.0 NE2 A:HIS725 1.9 14.7 1.0 NE2 A:HIS755 1.9 14.7 1.0 NC A:HEC902 2.0 21.2 1.0 NA A:HEC902 2.0 25.8 1.0 NB A:HEC902 2.0 27.5 1.0 ND A:HEC902 2.2 21.5 1.0 CE1 A:HIS755 2.8 25.0 1.0 CE1 A:HIS725 2.9 22.8 1.0 CD2 A:HIS725 3.0 19.9 1.0 C4C A:HEC902 3.0 22.4 1.0 C1C A:HEC902 3.0 29.9 1.0 C4A A:HEC902 3.0 28.2 1.0 C1B A:HEC902 3.1 25.4 1.0 CD2 A:HIS755 3.1 21.5 1.0 C4B A:HEC902 3.1 30.9 1.0 C1A A:HEC902 3.1 24.4 1.0 C1D A:HEC902 3.1 20.1 1.0 C4D A:HEC902 3.2 26.8 1.0 CHB A:HEC902 3.4 24.5 1.0 CHD A:HEC902 3.4 14.4 1.0 CHC A:HEC902 3.5 24.4 1.0 CHA A:HEC902 3.5 21.7 1.0 ND1 A:HIS755 4.0 15.9 1.0 ND1 A:HIS725 4.0 18.2 1.0 CG A:HIS725 4.1 17.4 1.0 CG A:HIS755 4.1 19.9 1.0 C3C A:HEC902 4.3 21.9 1.0 C2C A:HEC902 4.3 23.7 1.0 C3A A:HEC902 4.3 25.1 1.0 C2B A:HEC902 4.3 28.4 1.0 C2A A:HEC902 4.3 21.3 1.0 C3B A:HEC902 4.3 27.9 1.0 C2D A:HEC902 4.4 20.7 1.0 C3D A:HEC902 4.4 21.5 1.0

Iron binding site 3 out of 14 in the Crystal Structure of Unda with Iron Citrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Unda with Iron Citrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe903 b:16.9 occ:1.00 FE A:HEC903 0.0 16.9 1.0 NE2 A:HIS728 2.0 13.5 1.0 NA A:HEC903 2.0 14.3 1.0 NE2 A:HIS657 2.0 15.7 1.0 NC A:HEC903 2.0 16.6 1.0 NB A:HEC903 2.1 15.8 1.0 ND A:HEC903 2.1 17.9 1.0 CE1 A:HIS657 2.9 20.8 1.0 CD2 A:HIS728 2.9 10.1 1.0 C4A A:HEC903 3.0 14.7 1.0 C1A A:HEC903 3.0 17.6 1.0 CE1 A:HIS728 3.0 16.1 1.0 C1B A:HEC903 3.0 19.5 1.0 C4C A:HEC903 3.1 21.4 1.0 C4D A:HEC903 3.1 16.6 1.0 C1C A:HEC903 3.1 19.4 1.0 C4B A:HEC903 3.1 21.3 1.0 C1D A:HEC903 3.1 15.9 1.0 CD2 A:HIS657 3.1 18.2 1.0 CHA A:HEC903 3.4 17.3 1.0 CHB A:HEC903 3.4 13.7 1.0 CHD A:HEC903 3.4 20.1 1.0 CHC A:HEC903 3.5 12.7 1.0 ND1 A:HIS657 4.0 14.6 1.0 CG A:HIS728 4.1 18.2 1.0 ND1 A:HIS728 4.1 16.3 1.0 CG A:HIS657 4.2 19.0 1.0 C3A A:HEC903 4.2 15.2 1.0 C2A A:HEC903 4.2 13.1 1.0 C2B A:HEC903 4.2 21.5 1.0 C3B A:HEC903 4.3 19.2 1.0 C3C A:HEC903 4.3 15.2 1.0 C3D A:HEC903 4.3 16.9 1.0 C2C A:HEC903 4.3 18.9 1.0 C2D A:HEC903 4.3 17.2 1.0

Iron binding site 4 out of 14 in the Crystal Structure of Unda with Iron Citrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Unda with Iron Citrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe904 b:15.2 occ:1.00 FE A:HEC904 0.0 15.2 1.0 NB A:HEC904 2.0 12.8 1.0 NE2 A:HIS709 2.0 22.1 1.0 NE2 A:HIS684 2.0 9.1 1.0 NC A:HEC904 2.1 10.9 1.0 NA A:HEC904 2.1 15.2 1.0 ND A:HEC904 2.1 11.7 1.0 CE1 A:HIS709 2.9 23.8 1.0 CE1 A:HIS684 2.9 12.0 1.0 C1B A:HEC904 3.0 13.5 1.0 C4B A:HEC904 3.0 19.0 1.0 CD2 A:HIS684 3.1 12.6 1.0 CD2 A:HIS709 3.1 17.8 1.0 C1C A:HEC904 3.1 15.7 1.0 C4C A:HEC904 3.1 15.0 1.0 C4A A:HEC904 3.1 15.1 1.0 C1A A:HEC904 3.1 14.9 1.0 C4D A:HEC904 3.1 15.7 1.0 C1D A:HEC904 3.1 13.4 1.0 CHB A:HEC904 3.4 13.6 1.0 CHD A:HEC904 3.5 14.9 1.0 CHA A:HEC904 3.5 15.7 1.0 CHC A:HEC904 3.5 15.3 1.0 ND1 A:HIS709 4.0 17.5 1.0 ND1 A:HIS684 4.1 10.3 1.0 CG A:HIS709 4.2 20.5 1.0 CG A:HIS684 4.2 10.1 1.0 C2B A:HEC904 4.2 12.0 1.0 C3B A:HEC904 4.3 14.0 1.0 C2C A:HEC904 4.3 16.2 1.0 C3C A:HEC904 4.3 12.2 1.0 C3A A:HEC904 4.3 17.5 1.0 C2A A:HEC904 4.3 13.0 1.0 C3D A:HEC904 4.3 9.8 1.0 C2D A:HEC904 4.3 15.6 1.0 NH1 A:ARG528 4.8 27.4 1.0

Iron binding site 5 out of 14 in the Crystal Structure of Unda with Iron Citrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Unda with Iron Citrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe905 b:13.6 occ:1.00 FE A:HEC905 0.0 13.6 1.0 NB A:HEC905 2.0 11.7 1.0 NA A:HEC905 2.0 15.9 1.0 NC A:HEC905 2.0 10.7 1.0 NE2 A:HIS703 2.0 13.4 1.0 ND A:HEC905 2.0 12.0 1.0 NE2 A:HIS667 2.1 10.8 1.0 CE1 A:HIS703 3.0 20.9 1.0 C4B A:HEC905 3.0 10.9 1.0 C1A A:HEC905 3.0 13.7 1.0 CD2 A:HIS703 3.0 8.3 1.0 C4C A:HEC905 3.0 9.6 1.0 C1C A:HEC905 3.0 9.8 1.0 CD2 A:HIS667 3.0 6.3 1.0 C1B A:HEC905 3.0 14.9 1.0 C1D A:HEC905 3.0 12.8 1.0 C4A A:HEC905 3.1 13.0 1.0 C4D A:HEC905 3.1 13.2 1.0 CE1 A:HIS667 3.1 11.5 1.0 CHC A:HEC905 3.4 9.6 1.0 CHA A:HEC905 3.4 10.6 1.0 CHD A:HEC905 3.4 11.5 1.0 CHB A:HEC905 3.5 15.0 1.0 ND1 A:HIS703 4.1 15.3 1.0 CG A:HIS703 4.1 16.9 1.0 CG A:HIS667 4.2 12.2 1.0 C3B A:HEC905 4.2 8.9 1.0 ND1 A:HIS667 4.2 11.3 1.0 C2A A:HEC905 4.2 11.3 1.0 C3C A:HEC905 4.2 9.3 1.0 C2B A:HEC905 4.2 11.3 1.0 C2C A:HEC905 4.3 12.7 1.0 C2D A:HEC905 4.3 4.5 1.0 C3A A:HEC905 4.3 9.3 1.0 C3D A:HEC905 4.3 8.1 1.0 ND2 A:ASN689 4.6 13.6 1.0 CZ A:PHE718 5.0 10.8 1.0

Iron binding site 6 out of 14 in the Crystal Structure of Unda with Iron Citrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Unda with Iron Citrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe906 b:22.5 occ:1.00 FE A:HEC906 0.0 22.5 1.0 ND A:HEC906 1.9 14.2 1.0 NE2 A:HIS310 1.9 21.6 1.0 NB A:HEC906 2.0 18.2 1.0 NC A:HEC906 2.0 20.7 1.0 NE2 A:HIS256 2.1 18.0 1.0 NA A:HEC906 2.1 24.7 1.0 CE1 A:HIS310 2.9 24.6 1.0 C1D A:HEC906 2.9 17.9 1.0 CE1 A:HIS256 3.0 14.5 1.0 CD2 A:HIS310 3.0 19.4 1.0 C1B A:HEC906 3.0 22.6 1.0 C4C A:HEC906 3.0 18.5 1.0 C4D A:HEC906 3.0 23.7 1.0 C4A A:HEC906 3.1 20.8 1.0 C4B A:HEC906 3.1 25.8 1.0 C1C A:HEC906 3.1 22.0 1.0 C1A A:HEC906 3.1 18.9 1.0 CD2 A:HIS256 3.1 15.4 1.0 CHD A:HEC906 3.3 18.5 1.0 CHB A:HEC906 3.4 21.0 1.0 CHA A:HEC906 3.5 21.9 1.0 CHC A:HEC906 3.5 22.3 1.0 ND1 A:HIS310 4.0 21.5 1.0 CG A:HIS310 4.1 24.1 1.0 ND1 A:HIS256 4.1 16.3 1.0 C2D A:HEC906 4.2 14.7 1.0 C2B A:HEC906 4.2 24.8 1.0 CG A:HIS256 4.2 20.9 1.0 C3D A:HEC906 4.2 19.7 1.0 C3C A:HEC906 4.3 22.2 1.0 C3B A:HEC906 4.3 17.6 1.0 C3A A:HEC906 4.3 23.4 1.0 C2C A:HEC906 4.3 22.8 1.0 C2A A:HEC906 4.3 25.6 1.0

Iron binding site 7 out of 14 in the Crystal Structure of Unda with Iron Citrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Unda with Iron Citrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe907 b:30.0 occ:1.00 FE A:HEC907 0.0 30.0 1.0 NE2 A:HIS287 2.0 13.4 1.0 NA A:HEC907 2.0 31.9 1.0 NE2 A:HIS273 2.0 26.6 1.0 NC A:HEC907 2.1 38.8 1.0 NB A:HEC907 2.1 35.8 1.0 ND A:HEC907 2.1 31.9 1.0 CE1 A:HIS287 2.5 27.1 1.0 CE1 A:HIS273 2.9 29.6 1.0 C4A A:HEC907 3.0 26.8 1.0 C1B A:HEC907 3.0 30.9 1.0 C1D A:HEC907 3.0 34.9 1.0 C4C A:HEC907 3.0 36.6 1.0 C1A A:HEC907 3.1 33.2 1.0 CD2 A:HIS273 3.1 28.7 1.0 C4D A:HEC907 3.1 32.0 1.0 C1C A:HEC907 3.1 40.7 1.0 C4B A:HEC907 3.2 37.7 1.0 CD2 A:HIS287 3.2 31.6 1.0 CHB A:HEC907 3.3 25.6 1.0 CHD A:HEC907 3.4 32.1 1.0 CHA A:HEC907 3.5 30.5 1.0 CHC A:HEC907 3.5 39.9 1.0 ND1 A:HIS287 3.8 25.0 1.0 ND1 A:HIS273 4.1 32.0 1.0 CG A:HIS287 4.2 23.9 1.0 C3A A:HEC907 4.2 29.0 1.0 CG A:HIS273 4.2 31.6 1.0 C2A A:HEC907 4.2 26.6 1.0 C2B A:HEC907 4.3 35.6 1.0 C3C A:HEC907 4.3 37.6 1.0 C2D A:HEC907 4.3 34.1 1.0 C2C A:HEC907 4.3 37.2 1.0 C3B A:HEC907 4.3 33.9 1.0 C3D A:HEC907 4.4 29.7 1.0

Iron binding site 8 out of 14 in the Crystal Structure of Unda with Iron Citrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Unda with Iron Citrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe908 b:24.2 occ:1.00 FE A:HEC908 0.0 24.2 1.0 NE2 A:HIS365 2.0 23.4 1.0 NC A:HEC908 2.0 22.8 1.0 NE2 A:HIS307 2.0 22.1 1.0 NA A:HEC908 2.0 24.1 1.0 NB A:HEC908 2.0 21.2 1.0 ND A:HEC908 2.0 24.8 1.0 CE1 A:HIS365 2.8 21.1 1.0 CE1 A:HIS307 2.9 22.8 1.0 C1C A:HEC908 3.0 17.8 1.0 C1A A:HEC908 3.0 23.2 1.0 C4D A:HEC908 3.0 23.3 1.0 C4B A:HEC908 3.0 15.1 1.0 C4C A:HEC908 3.0 21.7 1.0 C1D A:HEC908 3.1 26.7 1.0 C1B A:HEC908 3.1 21.2 1.0 CD2 A:HIS307 3.1 20.6 1.0 CD2 A:HIS365 3.1 20.9 1.0 C4A A:HEC908 3.1 24.2 1.0 CHA A:HEC908 3.3 21.4 1.0 CHC A:HEC908 3.3 17.5 1.0 CHD A:HEC908 3.5 25.0 1.0 CHB A:HEC908 3.5 22.2 1.0 ND1 A:HIS365 4.0 20.7 1.0 ND1 A:HIS307 4.1 23.1 1.0 CG A:HIS365 4.2 25.2 1.0 CG A:HIS307 4.2 22.4 1.0 C2C A:HEC908 4.2 19.0 1.0 C3B A:HEC908 4.2 15.9 1.0 C3C A:HEC908 4.2 18.4 1.0 C3D A:HEC908 4.2 28.7 1.0 C2A A:HEC908 4.3 27.7 1.0 C2B A:HEC908 4.3 18.0 1.0 C2D A:HEC908 4.3 21.8 1.0 C3A A:HEC908 4.3 20.9 1.0

Iron binding site 9 out of 14 in the Crystal Structure of Unda with Iron Citrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Unda with Iron Citrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe909 b:19.6 occ:1.00 FE A:HEC909 0.0 19.6 1.0 NA A:HEC909 1.9 21.8 1.0 NC A:HEC909 2.0 15.0 1.0 NE2 A:HIS390 2.0 19.6 1.0 NB A:HEC909 2.0 18.5 1.0 NE2 A:HIS460 2.0 20.6 1.0 ND A:HEC909 2.1 21.6 1.0 C4A A:HEC909 2.9 21.1 1.0 CD2 A:HIS390 3.0 17.3 1.0 C1B A:HEC909 3.0 15.9 1.0 C4C A:HEC909 3.0 18.2 1.0 C1A A:HEC909 3.0 22.9 1.0 CD2 A:HIS460 3.0 25.3 1.0 CE1 A:HIS460 3.0 25.5 1.0 CE1 A:HIS390 3.0 24.2 1.0 C1C A:HEC909 3.1 19.4 1.0 C4B A:HEC909 3.1 18.1 1.0 C1D A:HEC909 3.1 21.7 1.0 C4D A:HEC909 3.1 24.9 1.0 CHB A:HEC909 3.3 20.5 1.0 CHD A:HEC909 3.4 17.4 1.0 CHA A:HEC909 3.5 24.8 1.0 CHC A:HEC909 3.5 18.6 1.0 ND1 A:HIS390 4.1 15.1 1.0 CG A:HIS390 4.1 18.5 1.0 ND1 A:HIS460 4.2 20.4 1.0 C3A A:HEC909 4.2 23.8 1.0 CG A:HIS460 4.2 25.3 1.0 C2A A:HEC909 4.2 22.5 1.0 C3C A:HEC909 4.2 16.8 1.0 C2B A:HEC909 4.3 22.6 1.0 C2C A:HEC909 4.3 18.2 1.0 C3B A:HEC909 4.3 23.6 1.0 C2D A:HEC909 4.3 17.3 1.0 C3D A:HEC909 4.3 21.2 1.0

Iron binding site 10 out of 14 in the Crystal Structure of Unda with Iron Citrate Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Unda with Iron Citrate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe910 b:28.4 occ:1.00 FE A:HEC910 0.0 28.4 1.0 NE2 A:HIS448 1.8 21.4 1.0 NE2 A:HIS420 1.9 25.0 1.0 NB A:HEC910 2.0 31.1 1.0 NC A:HEC910 2.1 34.5 1.0 ND A:HEC910 2.1 30.4 1.0 NA A:HEC910 2.1 33.3 1.0 CE1 A:HIS448 2.7 29.2 1.0 CE1 A:HIS420 2.7 28.9 1.0 C1B A:HEC910 3.0 35.1 1.0 CD2 A:HIS448 3.0 26.6 1.0 C1D A:HEC910 3.0 36.0 1.0 C4C A:HEC910 3.0 30.5 1.0 C4A A:HEC910 3.0 31.0 1.0 C4B A:HEC910 3.1 40.2 1.0 C1C A:HEC910 3.1 33.4 1.0 CD2 A:HIS420 3.1 28.5 1.0 C4D A:HEC910 3.1 35.5 1.0 C1A A:HEC910 3.2 36.5 1.0 CHD A:HEC910 3.3 28.6 1.0 CHB A:HEC910 3.4 32.7 1.0 CHC A:HEC910 3.5 30.6 1.0 CHA A:HEC910 3.5 40.2 1.0 ND1 A:HIS448 3.9 25.3 1.0 ND1 A:HIS420 3.9 28.6 1.0 CG A:HIS448 4.0 22.9 1.0 CG A:HIS420 4.1 25.1 1.0 C2B A:HEC910 4.2 36.2 1.0 C3A A:HEC910 4.3 39.0 1.0 C3C A:HEC910 4.3 32.1 1.0 C2D A:HEC910 4.3 38.0 1.0 C3B A:HEC910 4.3 31.1 1.0 C2C A:HEC910 4.3 28.1 1.0 C2A A:HEC910 4.3 40.6 1.0 C3D A:HEC910 4.4 37.7 1.0

M.J.Edwards, A.Hall, L.Shi, J.K.Fredrickson, J.M.Zachara, J.N.Butt, D.J.Richardson, T.A.Clarke. The Crystal Structure of the Extracellular 11-Heme Cytochrome Unda Reveals A Conserved 10-Heme Motif and Defined Binding Site For Soluble Iron Chelates. Structure V. 20 1275 2012.
ISSN: ISSN 0969-2126
PubMed: 22682743
DOI: 10.1016/J.STR.2012.04.016