Iron in PDB 3ng6: The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added

The structure of The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added, PDB code: 3ng6 was solved by A.Vergara, L.Vitagliano, A.Merlino, F.Sica, K.Marino, L.Mazzarella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.60 / 2.20
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	61.882, 61.882, 187.014, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.7

The binding sites of Iron atom in the The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added (pdb code 3ng6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added, PDB code: 3ng6:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:59.0 occ:1.00 FE A:HEM200 0.0 59.0 1.0 NE2 A:HIS88 2.0 66.8 1.0 NB A:HEM200 2.0 43.3 1.0 NA A:HEM200 2.0 60.4 1.0 NC A:HEM200 2.0 42.7 1.0 ND A:HEM200 2.0 53.6 1.0 NE2 A:HIS59 2.5 56.2 1.0 CE1 A:HIS88 2.7 65.6 1.0 C4B A:HEM200 3.0 44.4 1.0 C1B A:HEM200 3.0 46.0 1.0 C4A A:HEM200 3.0 57.0 1.0 C1C A:HEM200 3.0 43.7 1.0 C1A A:HEM200 3.1 61.3 1.0 C4D A:HEM200 3.1 56.4 1.0 C4C A:HEM200 3.1 43.9 1.0 C1D A:HEM200 3.1 50.9 1.0 CD2 A:HIS88 3.2 68.2 1.0 CE1 A:HIS59 3.3 56.6 1.0 CHC A:HEM200 3.4 46.2 1.0 CHB A:HEM200 3.4 50.1 1.0 CHA A:HEM200 3.4 59.4 1.0 CHD A:HEM200 3.4 47.5 1.0 CD2 A:HIS59 3.7 54.8 1.0 ND1 A:HIS88 3.9 66.6 1.0 CG A:HIS88 4.2 68.5 1.0 C3B A:HEM200 4.3 44.2 1.0 C2B A:HEM200 4.3 45.6 1.0 C3A A:HEM200 4.3 61.6 1.0 C2A A:HEM200 4.3 63.6 1.0 C2C A:HEM200 4.3 40.2 1.0 C3D A:HEM200 4.3 55.3 1.0 C3C A:HEM200 4.3 43.0 1.0 C2D A:HEM200 4.3 50.8 1.0 ND1 A:HIS59 4.5 57.7 1.0 CG2 A:VAL63 4.6 34.2 1.0 CG A:HIS59 4.7 56.4 1.0 CD1 A:LEU92 4.8 66.1 1.0

Iron binding site 2 out of 4 in the The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:47.5 occ:1.00 FE B:HEM400 0.0 47.5 1.0 ND B:HEM400 2.0 49.5 1.0 NA B:HEM400 2.0 53.2 1.0 NC B:HEM400 2.0 52.2 1.0 NB B:HEM400 2.1 47.2 1.0 NE2 B:HIS92 2.3 45.6 1.0 C4D B:HEM400 3.0 51.1 1.0 C1D B:HEM400 3.1 50.0 1.0 C1A B:HEM400 3.1 55.1 1.0 C4A B:HEM400 3.1 52.4 1.0 C4C B:HEM400 3.1 50.3 1.0 C1B B:HEM400 3.1 48.1 1.0 C1C B:HEM400 3.1 51.6 1.0 C4B B:HEM400 3.1 48.1 1.0 CD2 B:HIS92 3.2 43.9 1.0 CE1 B:HIS92 3.3 47.6 1.0 CHA B:HEM400 3.4 53.0 1.0 CHD B:HEM400 3.4 48.6 1.0 CHB B:HEM400 3.4 50.1 1.0 CHC B:HEM400 3.5 49.7 1.0 C3D B:HEM400 4.3 51.8 1.0 C2D B:HEM400 4.3 50.8 1.0 C2A B:HEM400 4.3 56.2 1.0 C3A B:HEM400 4.3 53.7 1.0 C2B B:HEM400 4.3 48.6 1.0 C3C B:HEM400 4.3 51.0 1.0 C2C B:HEM400 4.3 51.3 1.0 C3B B:HEM400 4.3 47.6 1.0 CG B:HIS92 4.3 46.0 1.0 ND1 B:HIS92 4.3 48.3 1.0 CG2 B:VAL67 4.5 40.5 1.0 NE2 B:HIS63 4.6 55.0 1.0 CE1 B:HIS63 5.0 54.9 1.0 CE1 B:PHE103 5.0 41.7 1.0

Iron binding site 3 out of 4 in the The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe600 b:53.1 occ:1.00 FE C:HEM600 0.0 53.1 1.0 NE2 C:HIS88 1.9 65.7 1.0 ND C:HEM600 2.0 52.8 1.0 NA C:HEM600 2.0 55.1 1.0 NB C:HEM600 2.0 46.2 1.0 NC C:HEM600 2.0 45.1 1.0 NE2 C:HIS59 2.6 57.8 1.0 CE1 C:HIS88 2.6 65.6 1.0 C4D C:HEM600 3.0 55.4 1.0 C1B C:HEM600 3.1 50.0 1.0 C1D C:HEM600 3.1 50.8 1.0 C1A C:HEM600 3.1 56.9 1.0 C4A C:HEM600 3.1 52.9 1.0 C4B C:HEM600 3.1 46.5 1.0 C1C C:HEM600 3.1 43.8 1.0 C4C C:HEM600 3.1 45.2 1.0 CD2 C:HIS88 3.1 65.5 1.0 CE1 C:HIS59 3.3 56.1 1.0 CHA C:HEM600 3.4 56.8 1.0 CHB C:HEM600 3.4 50.2 1.0 CHC C:HEM600 3.4 45.1 1.0 CHD C:HEM600 3.4 46.9 1.0 CD2 C:HIS59 3.7 57.4 1.0 ND1 C:HIS88 3.8 64.6 1.0 CG C:HIS88 4.1 65.6 1.0 C3D C:HEM600 4.3 56.3 1.0 C2D C:HEM600 4.3 50.9 1.0 C2B C:HEM600 4.3 50.1 1.0 C2A C:HEM600 4.3 56.6 1.0 C3A C:HEM600 4.3 54.5 1.0 C3B C:HEM600 4.3 46.9 1.0 C2C C:HEM600 4.3 43.0 1.0 C3C C:HEM600 4.3 45.1 1.0 CG2 C:VAL63 4.3 26.2 1.0 ND1 C:HIS59 4.5 54.9 1.0 CD1 C:LEU92 4.5 58.6 1.0 CG C:HIS59 4.7 55.1 1.0

Iron binding site 4 out of 4 in the The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State Obtained Through An Oxidation/Reduction Cycle in Which Potassium Hexacyanoferrate and Sodium Dithionite Were Alternatively Added within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe800 b:56.7 occ:1.00 FE D:HEM800 0.0 56.7 1.0 ND D:HEM800 2.0 53.9 1.0 NC D:HEM800 2.0 48.3 1.0 NB D:HEM800 2.0 47.5 1.0 NA D:HEM800 2.0 57.2 1.0 NE2 D:HIS92 2.3 49.6 1.0 C4C D:HEM800 3.1 48.7 1.0 C1B D:HEM800 3.1 48.4 1.0 C4B D:HEM800 3.1 48.5 1.0 C1D D:HEM800 3.1 53.4 1.0 C1C D:HEM800 3.1 47.5 1.0 C4D D:HEM800 3.1 54.8 1.0 C1A D:HEM800 3.1 58.7 1.0 C4A D:HEM800 3.1 55.0 1.0 CD2 D:HIS92 3.2 47.5 1.0 CE1 D:HIS92 3.4 47.6 1.0 CHC D:HEM800 3.4 47.0 1.0 CHD D:HEM800 3.4 50.5 1.0 CHA D:HEM800 3.4 56.5 1.0 CHB D:HEM800 3.4 52.5 1.0 CG2 D:VAL67 3.8 45.4 1.0 NE2 D:HIS63 4.2 59.6 1.0 C2B D:HEM800 4.3 47.6 1.0 C3B D:HEM800 4.3 48.0 1.0 C3C D:HEM800 4.3 48.0 1.0 C2C D:HEM800 4.3 48.1 1.0 C2D D:HEM800 4.3 55.0 1.0 C3D D:HEM800 4.3 55.7 1.0 C2A D:HEM800 4.3 59.5 1.0 C3A D:HEM800 4.3 55.6 1.0 CG D:HIS92 4.4 45.1 1.0 ND1 D:HIS92 4.4 45.3 1.0 CE1 D:HIS63 4.6 59.6 1.0 CE1 D:PHE103 4.9 39.9 1.0

A.Vergara, L.Vitagliano, A.Merlino, F.Sica, K.Marino, C.Verde, G.Di Prisco, L.Mazzarella. An Order-Disorder Transition Plays A Role in Switching Off the Root Effect in Fish Hemoglobins. J.Biol.Chem. V. 285 32568 2010.
ISSN: ISSN 0021-9258
PubMed: 20610398
DOI: 10.1074/JBC.M110.143537