Iron in PDB 2oyy: Hthp: A Hexameric Tyrosine-Coordinated Heme Protein

The structure of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein, PDB code: 2oyy was solved by H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.71 / 2.50
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	173.710, 173.710, 45.880, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 26.9

The structure of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein also contains other interesting chemical elements:

Iodine

(I)

12 atoms

The binding sites of Iron atom in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein (pdb code 2oyy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein, PDB code: 2oyy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:2.0 occ:1.00 FE A:HEM201 0.0 2.0 1.0 NB A:HEM201 2.0 2.0 1.0 NA A:HEM201 2.0 2.0 1.0 OH A:TYR43 2.0 2.0 1.0 NC A:HEM201 2.1 2.0 1.0 ND A:HEM201 2.1 2.0 1.0 C1B A:HEM201 3.0 2.0 1.0 C4A A:HEM201 3.0 2.0 1.0 C4B A:HEM201 3.0 2.0 1.0 C1A A:HEM201 3.0 2.0 1.0 C1C A:HEM201 3.1 2.0 1.0 C4D A:HEM201 3.1 2.0 1.0 C4C A:HEM201 3.1 2.0 1.0 C1D A:HEM201 3.1 2.0 1.0 CZ A:TYR43 3.2 2.0 1.0 CHB A:HEM201 3.4 2.0 1.0 CHA A:HEM201 3.4 2.0 1.0 CHC A:HEM201 3.4 2.0 1.0 CHD A:HEM201 3.5 2.0 1.0 NE A:ARG23 3.9 2.3 1.0 CE1 A:TYR43 4.0 2.2 1.0 NH1 A:ARG40 4.1 2.0 1.0 CE2 A:TYR43 4.2 2.0 1.0 CZ A:ARG23 4.2 3.0 1.0 C2B A:HEM201 4.2 2.0 1.0 C3B A:HEM201 4.2 2.0 1.0 C3A A:HEM201 4.3 2.0 1.0 C2A A:HEM201 4.3 2.0 1.0 C2C A:HEM201 4.3 2.0 1.0 CD A:ARG23 4.3 2.2 1.0 C3C A:HEM201 4.3 2.0 1.0 C3D A:HEM201 4.3 2.0 1.0 C2D A:HEM201 4.4 2.0 1.0 NH2 A:ARG23 4.5 2.0 1.0 CG A:ARG23 4.5 2.0 1.0 NH1 A:ARG23 4.8 2.8 1.0 CD A:ARG40 4.9 2.0 1.0 I A:IOD9001 4.9 10.5 1.0 CZ A:ARG40 5.0 2.0 1.0

Iron binding site 2 out of 8 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:3.8 occ:1.00 FE B:HEM201 0.0 3.8 1.0 NB B:HEM201 1.9 3.6 1.0 NA B:HEM201 2.0 3.9 1.0 OH B:TYR43 2.0 2.0 1.0 NC B:HEM201 2.1 3.6 1.0 ND B:HEM201 2.2 4.5 1.0 C1B B:HEM201 2.9 4.1 1.0 C4B B:HEM201 3.0 2.7 1.0 C4A B:HEM201 3.0 3.6 1.0 C1C B:HEM201 3.1 2.9 1.0 C1A B:HEM201 3.1 5.1 1.0 C4C B:HEM201 3.1 4.2 1.0 CZ B:TYR43 3.2 2.0 1.0 C4D B:HEM201 3.2 4.7 1.0 C1D B:HEM201 3.2 4.3 1.0 CHB B:HEM201 3.3 4.7 1.0 CHC B:HEM201 3.4 2.7 1.0 CHA B:HEM201 3.5 4.4 1.0 CHD B:HEM201 3.5 4.9 1.0 CE1 B:TYR43 3.7 2.0 1.0 NE B:ARG23 3.9 4.3 1.0 C2B B:HEM201 4.1 3.8 1.0 C3B B:HEM201 4.2 3.5 1.0 CE2 B:TYR43 4.2 2.0 1.0 C3A B:HEM201 4.3 4.7 1.0 C2C B:HEM201 4.3 4.0 1.0 C2A B:HEM201 4.3 5.8 1.0 C3C B:HEM201 4.3 3.2 1.0 CD B:ARG23 4.3 3.6 1.0 NH1 B:ARG40 4.4 2.0 1.0 CZ B:ARG23 4.4 3.8 1.0 C3D B:HEM201 4.4 6.8 1.0 C2D B:HEM201 4.5 5.2 1.0 CG B:ARG23 4.6 2.5 1.0 NH2 B:ARG23 4.6 4.8 1.0 I B:IOD9001 4.8 12.2 1.0 CD B:ARG40 4.9 2.0 1.0

Iron binding site 3 out of 8 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:6.0 occ:1.00 FE C:HEM201 0.0 6.0 1.0 OH C:TYR43 2.0 2.0 1.0 NB C:HEM201 2.0 4.9 1.0 NC C:HEM201 2.0 5.6 1.0 NA C:HEM201 2.1 5.5 1.0 ND C:HEM201 2.2 6.4 1.0 C1B C:HEM201 3.0 4.4 1.0 C1C C:HEM201 3.0 5.3 1.0 C4B C:HEM201 3.0 4.1 1.0 C4C C:HEM201 3.0 6.1 1.0 C4A C:HEM201 3.1 5.2 1.0 CZ C:TYR43 3.1 2.3 1.0 C1D C:HEM201 3.2 6.7 1.0 C1A C:HEM201 3.2 6.5 1.0 C4D C:HEM201 3.2 7.2 1.0 CHB C:HEM201 3.4 4.8 1.0 CHC C:HEM201 3.4 4.8 1.0 CHD C:HEM201 3.4 6.4 1.0 CHA C:HEM201 3.6 6.2 1.0 CE1 C:TYR43 3.7 2.0 1.0 NE C:ARG23 3.8 2.0 1.0 CZ C:ARG23 4.1 2.9 1.0 NH2 C:ARG23 4.2 2.6 1.0 CE2 C:TYR43 4.2 2.3 1.0 C2C C:HEM201 4.2 5.7 1.0 C2B C:HEM201 4.2 5.0 1.0 C3C C:HEM201 4.2 4.8 1.0 C3B C:HEM201 4.2 3.8 1.0 C3A C:HEM201 4.3 4.7 1.0 NH1 C:ARG40 4.3 2.1 1.0 C2A C:HEM201 4.4 5.8 1.0 CD C:ARG23 4.4 2.0 1.0 C2D C:HEM201 4.4 7.6 1.0 C3D C:HEM201 4.5 8.6 1.0 CG C:ARG23 4.6 2.0 1.0 NH1 C:ARG23 4.8 3.0 1.0 I C:IOD9001 4.9 9.9 1.0 CD C:ARG40 5.0 2.0 1.0

Iron binding site 4 out of 8 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:8.0 occ:1.00 FE D:HEM201 0.0 8.0 1.0 NB D:HEM201 2.0 6.9 1.0 NC D:HEM201 2.0 7.2 1.0 NA D:HEM201 2.1 8.0 1.0 OH D:TYR43 2.1 2.0 1.0 ND D:HEM201 2.2 9.2 1.0 C1B D:HEM201 3.0 6.7 1.0 C4A D:HEM201 3.0 7.1 1.0 C4C D:HEM201 3.0 7.1 1.0 C1C D:HEM201 3.0 6.2 1.0 C4B D:HEM201 3.0 5.7 1.0 C1A D:HEM201 3.1 8.5 1.0 C1D D:HEM201 3.1 9.2 1.0 C4D D:HEM201 3.2 9.9 1.0 CZ D:TYR43 3.3 2.0 1.0 CHB D:HEM201 3.3 7.5 1.0 CHD D:HEM201 3.4 8.5 1.0 CHC D:HEM201 3.4 5.9 1.0 CHA D:HEM201 3.6 8.6 1.0 NE D:ARG23 3.7 2.9 1.0 CE1 D:TYR43 3.9 2.0 1.0 CZ D:ARG23 4.1 3.5 1.0 NH2 D:ARG23 4.2 3.3 1.0 C2B D:HEM201 4.2 5.3 1.0 C3C D:HEM201 4.2 6.9 1.0 C2C D:HEM201 4.2 6.3 1.0 C3B D:HEM201 4.3 6.4 1.0 NH1 D:ARG40 4.3 2.0 1.0 C3A D:HEM201 4.3 8.0 1.0 CE2 D:TYR43 4.3 2.0 1.0 CD D:ARG23 4.3 2.5 1.0 C2A D:HEM201 4.3 8.8 1.0 I D:IOD9001 4.4 12.6 1.0 C2D D:HEM201 4.4 9.4 1.0 CG D:ARG23 4.4 2.0 1.0 C3D D:HEM201 4.4 10.8 1.0 CD D:ARG40 4.8 2.0 1.0 NH1 D:ARG23 5.0 3.3 1.0

Iron binding site 5 out of 8 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe201 b:3.3 occ:1.00 FE E:HEM201 0.0 3.3 1.0 NB E:HEM201 2.0 2.9 1.0 OH E:TYR43 2.0 2.0 1.0 NC E:HEM201 2.0 3.5 1.0 ND E:HEM201 2.1 4.7 1.0 NA E:HEM201 2.1 4.2 1.0 C4C E:HEM201 3.0 3.8 1.0 C1B E:HEM201 3.0 2.8 1.0 C4B E:HEM201 3.0 2.2 1.0 C1D E:HEM201 3.0 5.0 1.0 C1C E:HEM201 3.1 2.2 1.0 C4A E:HEM201 3.1 3.5 1.0 C4D E:HEM201 3.2 4.4 1.0 C1A E:HEM201 3.2 4.5 1.0 CZ E:TYR43 3.3 2.0 1.0 CHD E:HEM201 3.3 4.2 1.0 CHB E:HEM201 3.4 3.7 1.0 CHC E:HEM201 3.5 2.4 1.0 CHA E:HEM201 3.6 4.0 1.0 NE E:ARG23 3.7 3.3 1.0 CE1 E:TYR43 3.9 2.0 1.0 C3C E:HEM201 4.2 3.2 1.0 C2B E:HEM201 4.2 2.5 1.0 C2C E:HEM201 4.2 2.0 1.0 C3B E:HEM201 4.2 2.0 1.0 CE2 E:TYR43 4.3 2.0 1.0 CD E:ARG23 4.3 3.1 1.0 CZ E:ARG23 4.3 3.4 1.0 C2D E:HEM201 4.3 5.4 1.0 C3A E:HEM201 4.4 3.5 1.0 NH1 E:ARG40 4.4 2.0 1.0 C3D E:HEM201 4.4 6.1 1.0 CG E:ARG23 4.4 2.0 1.0 C2A E:HEM201 4.4 4.3 1.0 NH2 E:ARG23 4.5 2.3 1.0 I E:IOD9001 4.9 9.6 1.0

Iron binding site 6 out of 8 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe201 b:5.8 occ:1.00 FE F:HEM201 0.0 5.8 1.0 NA F:HEM201 2.0 6.0 1.0 NB F:HEM201 2.0 5.4 1.0 NC F:HEM201 2.1 5.9 1.0 ND F:HEM201 2.2 7.5 1.0 OH F:TYR43 2.2 2.0 1.0 C1B F:HEM201 2.9 6.0 1.0 C4A F:HEM201 3.0 6.3 1.0 C4C F:HEM201 3.1 6.4 1.0 C1A F:HEM201 3.1 7.9 1.0 C4B F:HEM201 3.1 3.8 1.0 C1D F:HEM201 3.2 8.2 1.0 C1C F:HEM201 3.2 5.1 1.0 C4D F:HEM201 3.2 9.4 1.0 CHB F:HEM201 3.3 6.7 1.0 CHD F:HEM201 3.4 7.7 1.0 CZ F:TYR43 3.5 2.1 1.0 CHA F:HEM201 3.5 8.2 1.0 CHC F:HEM201 3.5 4.4 1.0 NE F:ARG23 3.9 4.1 1.0 C2B F:HEM201 4.2 5.3 1.0 CE1 F:TYR43 4.2 2.3 1.0 C3A F:HEM201 4.2 7.6 1.0 C2A F:HEM201 4.3 8.0 1.0 C3B F:HEM201 4.3 4.3 1.0 C3C F:HEM201 4.3 4.8 1.0 CD F:ARG23 4.3 3.2 1.0 CZ F:ARG23 4.3 4.4 1.0 C2C F:HEM201 4.4 4.7 1.0 CE2 F:TYR43 4.4 2.0 1.0 C2D F:HEM201 4.4 10.0 1.0 C3D F:HEM201 4.4 11.1 1.0 CG F:ARG23 4.5 2.1 1.0 NH2 F:ARG23 4.6 3.8 1.0 I F:IOD9001 4.6 14.7 1.0 NH1 F:ARG40 4.7 2.0 1.0

Iron binding site 7 out of 8 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe201 b:8.2 occ:1.00 FE G:HEM201 0.0 8.2 1.0 NB G:HEM201 2.0 9.9 1.0 OH G:TYR43 2.0 2.0 1.0 NC G:HEM201 2.0 8.8 1.0 NA G:HEM201 2.1 9.8 1.0 ND G:HEM201 2.1 11.1 1.0 C1C G:HEM201 3.0 7.8 1.0 C4B G:HEM201 3.0 8.9 1.0 C1B G:HEM201 3.0 9.7 1.0 C4C G:HEM201 3.1 8.9 1.0 C4A G:HEM201 3.1 9.7 1.0 C1A G:HEM201 3.1 10.5 1.0 C1D G:HEM201 3.1 11.4 1.0 C4D G:HEM201 3.2 11.1 1.0 CZ G:TYR43 3.3 2.0 1.0 CHC G:HEM201 3.4 9.4 1.0 CHB G:HEM201 3.4 10.0 1.0 CHD G:HEM201 3.4 10.5 1.0 CHA G:HEM201 3.5 10.8 1.0 NE G:ARG23 3.6 2.0 1.0 CZ G:ARG23 3.9 3.0 1.0 NH2 G:ARG23 4.0 2.7 1.0 CE1 G:TYR43 4.0 2.0 1.0 CD G:ARG23 4.2 2.0 1.0 C2C G:HEM201 4.2 8.2 1.0 C3C G:HEM201 4.2 8.8 1.0 C3B G:HEM201 4.2 8.5 1.0 C2B G:HEM201 4.2 8.6 1.0 CE2 G:TYR43 4.3 2.0 1.0 C3A G:HEM201 4.3 10.7 1.0 C2A G:HEM201 4.3 10.9 1.0 C2D G:HEM201 4.4 12.1 1.0 NH1 G:ARG40 4.4 2.4 1.0 C3D G:HEM201 4.4 12.5 1.0 CG G:ARG23 4.4 2.0 1.0 NH1 G:ARG23 4.8 3.0 1.0 CD G:ARG40 4.9 2.0 1.0 I G:IOD9001 4.9 11.9 1.0

Iron binding site 8 out of 8 in the Hthp: A Hexameric Tyrosine-Coordinated Heme Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Hthp: A Hexameric Tyrosine-Coordinated Heme Protein within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe201 b:3.0 occ:1.00 FE H:HEM201 0.0 3.0 1.0 NB H:HEM201 1.9 2.7 1.0 OH H:TYR43 2.0 2.0 1.0 NA H:HEM201 2.0 3.1 1.0 NC H:HEM201 2.1 2.9 1.0 ND H:HEM201 2.2 5.3 1.0 C1B H:HEM201 2.9 2.2 1.0 C4B H:HEM201 3.0 2.0 1.0 C4A H:HEM201 3.0 2.8 1.0 C1A H:HEM201 3.1 3.9 1.0 C1C H:HEM201 3.1 2.6 1.0 CZ H:TYR43 3.1 2.0 1.0 C4D H:HEM201 3.2 5.7 1.0 C4C H:HEM201 3.2 2.8 1.0 C1D H:HEM201 3.2 6.5 1.0 CHB H:HEM201 3.3 3.0 1.0 CHC H:HEM201 3.4 2.0 1.0 CHA H:HEM201 3.5 4.4 1.0 CHD H:HEM201 3.6 4.5 1.0 NE H:ARG23 3.7 3.0 1.0 CE1 H:TYR43 3.8 2.0 1.0 CE2 H:TYR43 4.1 2.0 1.0 C2B H:HEM201 4.2 2.0 1.0 CZ H:ARG23 4.2 3.5 1.0 C3B H:HEM201 4.2 2.1 1.0 NH2 H:ARG23 4.2 3.1 1.0 C3A H:HEM201 4.3 3.4 1.0 C2A H:HEM201 4.3 4.4 1.0 C2C H:HEM201 4.3 2.0 1.0 CD H:ARG23 4.4 2.0 1.0 C3C H:HEM201 4.4 2.1 1.0 C3D H:HEM201 4.4 7.9 1.0 CG H:ARG23 4.4 2.0 1.0 C2D H:HEM201 4.5 7.6 1.0 NH1 H:ARG40 4.6 2.0 1.0 I H:IOD9001 4.7 11.5 1.0 CD H:ARG40 4.8 2.0 1.0

J.H.Jeoung, D.A.Pippig, B.M.Martins, N.Wagener, H.Dobbek. Hthp: A Novel Class of Hexameric, Tyrosine-Coordinated Heme Proteins J.Mol.Biol. V. 368 1122 2007.
ISSN: ISSN 0022-2836
PubMed: 17395199
DOI: 10.1016/J.JMB.2007.02.079