Iron in PDB 3dhr: Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia)

The structure of Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia), PDB code: 3dhr was solved by P.Sathya Moorthy, K.Neelagandan, M.Balasubramanian, M.N.Ponnuswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	54.659, 65.322, 103.733, 78.78, 89.90, 65.30
R / Rfree (%)	24.3 / 27.6

The binding sites of Iron atom in the Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia) (pdb code 3dhr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia), PDB code: 3dhr:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe142 b:21.8 occ:1.00 FE A:HEM142 0.0 21.8 1.0 O A:HOH144 2.1 18.1 1.0 ND A:HEM142 2.1 22.2 1.0 NC A:HEM142 2.1 21.5 1.0 NA A:HEM142 2.1 22.7 1.0 NB A:HEM142 2.1 21.8 1.0 NE2 A:HIS87 2.2 31.0 1.0 C1A A:HEM142 3.0 23.2 1.0 C4D A:HEM142 3.0 22.7 1.0 C1C A:HEM142 3.1 21.3 1.0 C4B A:HEM142 3.1 21.9 1.0 CE1 A:HIS87 3.1 31.2 1.0 C1D A:HEM142 3.1 22.1 1.0 C4C A:HEM142 3.1 21.4 1.0 C4A A:HEM142 3.1 23.1 1.0 C1B A:HEM142 3.1 22.3 1.0 CD2 A:HIS87 3.3 31.0 1.0 CHA A:HEM142 3.4 22.8 1.0 CHC A:HEM142 3.4 21.4 1.0 CHD A:HEM142 3.5 21.8 1.0 CHB A:HEM142 3.5 22.7 1.0 NE2 A:HIS58 4.2 24.7 1.0 ND1 A:HIS87 4.3 31.0 1.0 C2A A:HEM142 4.3 24.2 1.0 C3D A:HEM142 4.3 23.1 1.0 C3A A:HEM142 4.3 23.6 1.0 C2C A:HEM142 4.3 21.3 1.0 C3B A:HEM142 4.3 22.3 1.0 C3C A:HEM142 4.3 21.1 1.0 C2D A:HEM142 4.3 22.5 1.0 C2B A:HEM142 4.3 22.4 1.0 CG A:HIS87 4.4 31.5 1.0 CE1 A:HIS58 4.6 24.8 1.0 CG2 A:VAL62 5.0 26.1 1.0

Iron binding site 2 out of 8 in the Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe147 b:36.9 occ:1.00 FE B:HEM147 0.0 36.9 1.0 O B:HOH148 1.9 31.6 1.0 NB B:HEM147 2.1 37.1 1.0 NC B:HEM147 2.1 37.0 1.0 NA B:HEM147 2.1 37.3 1.0 ND B:HEM147 2.1 37.1 1.0 CE1 B:HIS92 2.4 40.7 1.0 C1C B:HEM147 3.1 36.8 1.0 C4C B:HEM147 3.1 36.9 1.0 C4B B:HEM147 3.1 37.1 1.0 C4D B:HEM147 3.1 37.3 1.0 C1A B:HEM147 3.1 37.5 1.0 C1D B:HEM147 3.1 37.1 1.0 C1B B:HEM147 3.1 37.0 1.0 C4A B:HEM147 3.1 37.3 1.0 NE2 B:HIS92 3.3 40.9 1.0 ND1 B:HIS92 3.3 40.8 1.0 CHA B:HEM147 3.4 37.4 1.0 CHC B:HEM147 3.4 36.9 1.0 CHD B:HEM147 3.4 37.0 1.0 CHB B:HEM147 3.5 37.1 1.0 NE2 B:HIS63 4.2 37.9 1.0 C2C B:HEM147 4.3 36.7 1.0 C3C B:HEM147 4.3 36.8 1.0 C3B B:HEM147 4.3 37.1 1.0 C2A B:HEM147 4.3 37.7 1.0 C3D B:HEM147 4.3 37.5 1.0 C2D B:HEM147 4.3 37.2 1.0 C2B B:HEM147 4.3 37.0 1.0 C3A B:HEM147 4.3 37.6 1.0 CD2 B:HIS92 4.5 40.9 1.0 CG B:HIS92 4.5 41.0 1.0 CE1 B:HIS63 4.7 37.9 1.0 CG2 B:VAL67 4.8 38.0 1.0

Iron binding site 3 out of 8 in the Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe142 b:23.5 occ:1.00 FE C:HEM142 0.0 23.5 1.0 NC C:HEM142 2.1 24.0 1.0 NA C:HEM142 2.1 24.7 1.0 ND C:HEM142 2.1 24.3 1.0 NB C:HEM142 2.1 24.0 1.0 O C:HOH144 2.2 15.9 1.0 NE2 C:HIS87 2.2 30.4 1.0 C1A C:HEM142 3.1 25.3 1.0 C4D C:HEM142 3.1 24.6 1.0 C1C C:HEM142 3.1 23.6 1.0 C4C C:HEM142 3.1 23.8 1.0 C4B C:HEM142 3.1 23.7 1.0 C1D C:HEM142 3.1 23.9 1.0 CE1 C:HIS87 3.1 30.7 1.0 C4A C:HEM142 3.1 24.9 1.0 C1B C:HEM142 3.1 24.2 1.0 CD2 C:HIS87 3.3 30.7 1.0 CHA C:HEM142 3.4 24.9 1.0 CHC C:HEM142 3.4 23.7 1.0 CHD C:HEM142 3.5 23.8 1.0 CHB C:HEM142 3.5 24.6 1.0 NE2 C:HIS58 4.2 25.1 1.0 C2A C:HEM142 4.3 26.1 1.0 ND1 C:HIS87 4.3 30.6 1.0 C2C C:HEM142 4.3 23.6 1.0 C3C C:HEM142 4.3 23.5 1.0 C3A C:HEM142 4.3 25.6 1.0 C3D C:HEM142 4.3 24.8 1.0 C2D C:HEM142 4.3 24.0 1.0 C3B C:HEM142 4.3 24.2 1.0 C2B C:HEM142 4.3 24.4 1.0 CG C:HIS87 4.4 31.2 1.0 CE1 C:HIS58 4.6 25.3 1.0 CG2 C:VAL62 4.9 27.6 1.0

Iron binding site 4 out of 8 in the Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe147 b:33.9 occ:1.00 FE D:HEM147 0.0 33.9 1.0 O D:HOH148 2.0 17.6 1.0 NA D:HEM147 2.1 34.6 1.0 NC D:HEM147 2.1 34.0 1.0 ND D:HEM147 2.1 34.5 1.0 NB D:HEM147 2.1 34.2 1.0 NE2 D:HIS92 2.4 41.7 1.0 C4D D:HEM147 3.1 34.9 1.0 C1A D:HEM147 3.1 35.0 1.0 C1D D:HEM147 3.1 34.6 1.0 C4C D:HEM147 3.1 34.0 1.0 C1C D:HEM147 3.1 33.7 1.0 C4B D:HEM147 3.1 34.0 1.0 C4A D:HEM147 3.1 34.7 1.0 C1B D:HEM147 3.1 34.3 1.0 CD2 D:HIS92 3.3 42.0 1.0 CE1 D:HIS92 3.4 41.8 1.0 CHA D:HEM147 3.4 34.9 1.0 CHD D:HEM147 3.4 34.2 1.0 CHC D:HEM147 3.5 33.8 1.0 CHB D:HEM147 3.5 34.4 1.0 NE2 D:HIS63 4.2 38.0 1.0 C3D D:HEM147 4.3 35.3 1.0 C2D D:HEM147 4.3 34.9 1.0 C2A D:HEM147 4.3 35.3 1.0 C3C D:HEM147 4.3 33.8 1.0 C2C D:HEM147 4.3 33.7 1.0 C3B D:HEM147 4.3 34.1 1.0 C3A D:HEM147 4.3 35.1 1.0 C2B D:HEM147 4.3 34.2 1.0 CG D:HIS92 4.5 42.3 1.0 ND1 D:HIS92 4.5 41.9 1.0 CE1 D:HIS63 4.5 38.1 1.0 CG2 D:VAL67 4.8 38.0 1.0

Iron binding site 5 out of 8 in the Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia) within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe142 b:24.8 occ:1.00 FE E:HEM142 0.0 24.8 1.0 O E:HOH143 2.0 15.1 1.0 ND E:HEM142 2.1 24.6 1.0 NA E:HEM142 2.1 24.9 1.0 NB E:HEM142 2.1 24.8 1.0 NC E:HEM142 2.1 24.3 1.0 CE1 E:HIS87 2.3 29.8 1.0 C4D E:HEM142 3.0 24.6 1.0 C1A E:HEM142 3.1 25.2 1.0 C1D E:HEM142 3.1 24.4 1.0 C4B E:HEM142 3.1 24.7 1.0 C1C E:HEM142 3.1 24.2 1.0 C4C E:HEM142 3.1 24.2 1.0 C4A E:HEM142 3.1 25.1 1.0 NE2 E:HIS87 3.1 30.0 1.0 C1B E:HEM142 3.1 24.9 1.0 ND1 E:HIS87 3.3 29.9 1.0 CHA E:HEM142 3.4 24.9 1.0 CHC E:HEM142 3.4 24.4 1.0 CHD E:HEM142 3.5 24.3 1.0 CHB E:HEM142 3.5 25.1 1.0 NE2 E:HIS58 4.2 28.9 1.0 C3D E:HEM142 4.3 24.5 1.0 C2A E:HEM142 4.3 25.9 1.0 C3A E:HEM142 4.3 25.4 1.0 C2D E:HEM142 4.3 24.4 1.0 C3B E:HEM142 4.3 24.9 1.0 C2C E:HEM142 4.3 24.1 1.0 C2B E:HEM142 4.3 25.0 1.0 C3C E:HEM142 4.3 24.0 1.0 CD2 E:HIS87 4.3 29.7 1.0 CG E:HIS87 4.4 30.3 1.0 CE1 E:HIS58 4.6 29.5 1.0 CG2 E:VAL62 4.9 27.6 1.0

Iron binding site 6 out of 8 in the Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia) within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe147 b:26.9 occ:1.00 FE F:HEM147 0.0 26.9 1.0 NA F:HEM147 2.1 27.5 1.0 NC F:HEM147 2.1 26.6 1.0 ND F:HEM147 2.1 27.3 1.0 NB F:HEM147 2.1 26.9 1.0 O F:HOH148 2.1 24.9 1.0 NE2 F:HIS92 2.3 28.8 1.0 C4C F:HEM147 3.1 26.4 1.0 C1D F:HEM147 3.1 27.3 1.0 C1A F:HEM147 3.1 27.8 1.0 C4A F:HEM147 3.1 27.6 1.0 C1C F:HEM147 3.1 26.3 1.0 C1B F:HEM147 3.1 27.0 1.0 C4D F:HEM147 3.1 28.0 1.0 C4B F:HEM147 3.1 26.7 1.0 CE1 F:HIS92 3.1 28.6 1.0 CD2 F:HIS92 3.4 28.8 1.0 CHD F:HEM147 3.4 26.9 1.0 CHB F:HEM147 3.4 27.2 1.0 CHA F:HEM147 3.4 27.9 1.0 CHC F:HEM147 3.5 26.3 1.0 NE2 F:HIS63 4.2 27.1 1.0 C3C F:HEM147 4.3 26.3 1.0 C2C F:HEM147 4.3 26.2 1.0 C3A F:HEM147 4.3 27.9 1.0 C2A F:HEM147 4.3 28.3 1.0 ND1 F:HIS92 4.3 28.7 1.0 C2D F:HEM147 4.3 27.8 1.0 C2B F:HEM147 4.3 27.0 1.0 C3B F:HEM147 4.3 27.0 1.0 C3D F:HEM147 4.3 28.4 1.0 CG F:HIS92 4.4 29.2 1.0 CE1 F:HIS63 4.7 26.9 1.0 CG2 F:VAL67 4.9 27.9 1.0

Iron binding site 7 out of 8 in the Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia) within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe142 b:24.7 occ:1.00 FE G:HEM142 0.0 24.7 1.0 ND G:HEM142 2.1 24.8 1.0 NC G:HEM142 2.1 24.0 1.0 NA G:HEM142 2.1 25.0 1.0 NB G:HEM142 2.1 24.5 1.0 O G:HOH144 2.1 16.4 1.0 CE1 G:HIS87 2.3 28.4 1.0 C4D G:HEM142 3.1 24.8 1.0 C1D G:HEM142 3.1 24.5 1.0 C1A G:HEM142 3.1 25.5 1.0 C1C G:HEM142 3.1 23.9 1.0 C4C G:HEM142 3.1 23.9 1.0 NE2 G:HIS87 3.1 28.6 1.0 C4B G:HEM142 3.1 24.1 1.0 C1B G:HEM142 3.1 24.6 1.0 C4A G:HEM142 3.1 25.4 1.0 ND1 G:HIS87 3.3 28.3 1.0 CHA G:HEM142 3.4 25.1 1.0 CHD G:HEM142 3.4 24.0 1.0 CHC G:HEM142 3.4 23.9 1.0 CHB G:HEM142 3.5 24.9 1.0 NE2 G:HIS58 4.2 27.7 1.0 C3D G:HEM142 4.3 25.0 1.0 C2C G:HEM142 4.3 23.8 1.0 C2D G:HEM142 4.3 24.6 1.0 C3C G:HEM142 4.3 23.5 1.0 C2A G:HEM142 4.3 26.2 1.0 C3B G:HEM142 4.3 24.3 1.0 CD2 G:HIS87 4.3 28.4 1.0 C3A G:HEM142 4.3 25.7 1.0 C2B G:HEM142 4.3 24.4 1.0 CG G:HIS87 4.4 28.8 1.0 CE1 G:HIS58 4.6 28.1 1.0 CG2 G:VAL62 4.9 27.3 1.0

Iron binding site 8 out of 8 in the Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure Determination of Methemoglobin From Pigeon at 2 Angstrom Resolution (Columba Livia) within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe147 b:25.1 occ:1.00 FE H:HEM147 0.0 25.1 1.0 O H:HOH149 2.0 19.1 1.0 NB H:HEM147 2.1 25.4 1.0 NC H:HEM147 2.1 25.2 1.0 NA H:HEM147 2.1 26.1 1.0 ND H:HEM147 2.1 25.5 1.0 CE1 H:HIS92 2.3 29.3 1.0 NE2 H:HIS92 3.1 29.2 1.0 C4B H:HEM147 3.1 25.3 1.0 C4C H:HEM147 3.1 25.0 1.0 C1D H:HEM147 3.1 25.9 1.0 C1C H:HEM147 3.1 24.9 1.0 C1B H:HEM147 3.1 25.6 1.0 C4D H:HEM147 3.1 26.2 1.0 C4A H:HEM147 3.1 26.2 1.0 C1A H:HEM147 3.1 26.6 1.0 CHD H:HEM147 3.4 25.1 1.0 CHC H:HEM147 3.4 24.8 1.0 ND1 H:HIS92 3.4 29.7 1.0 CHA H:HEM147 3.4 26.2 1.0 CHB H:HEM147 3.5 25.9 1.0 NE2 H:HIS63 4.2 27.3 1.0 C3B H:HEM147 4.3 25.7 1.0 C2C H:HEM147 4.3 24.7 1.0 C2B H:HEM147 4.3 25.6 1.0 C3C H:HEM147 4.3 24.8 1.0 C2D H:HEM147 4.3 26.0 1.0 C3A H:HEM147 4.3 26.8 1.0 C2A H:HEM147 4.3 27.0 1.0 C3D H:HEM147 4.3 26.5 1.0 CD2 H:HIS92 4.3 29.4 1.0 CG H:HIS92 4.5 30.0 1.0 CE1 H:HIS63 4.5 27.3 1.0 CG2 H:VAL67 4.8 27.8 1.0

P.Sathya Moorthy, K.Neelagandan, M.Balasubramanian, M.N.Ponnuswamy. Purification, Crystallization and X-Ray Diffraction Studies of Pigeon Hemoglobin To Be Published.