Iron in PDB 3nfe: The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State

The structure of The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State, PDB code: 3nfe 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)	39.70 / 2.01
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	62.022, 62.022, 187.926, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 25

The binding sites of Iron atom in the The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State (pdb code 3nfe). 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, PDB code: 3nfe:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:42.7 occ:1.00 FE A:HEM200 0.0 42.7 1.0 ND A:HEM200 2.0 39.0 1.0 NA A:HEM200 2.0 46.6 1.0 NB A:HEM200 2.0 35.2 1.0 NC A:HEM200 2.0 34.7 1.0 NE2 A:HIS88 2.3 47.5 1.0 NE2 A:HIS59 3.0 43.0 1.0 C4D A:HEM200 3.0 42.1 1.0 C1A A:HEM200 3.0 47.7 1.0 C1D A:HEM200 3.0 39.0 1.0 C4A A:HEM200 3.0 41.9 1.0 C1B A:HEM200 3.1 36.2 1.0 C4C A:HEM200 3.1 32.7 1.0 C4B A:HEM200 3.1 38.2 1.0 C1C A:HEM200 3.1 33.6 1.0 CE1 A:HIS88 3.3 47.7 1.0 CD2 A:HIS88 3.3 45.6 1.0 CHA A:HEM200 3.4 46.1 1.0 CHB A:HEM200 3.4 38.6 1.0 CHD A:HEM200 3.4 36.2 1.0 CHC A:HEM200 3.4 34.1 1.0 CE1 A:HIS59 3.5 42.3 1.0 CD2 A:HIS59 4.2 44.1 1.0 C2A A:HEM200 4.2 49.5 1.0 C3D A:HEM200 4.2 40.9 1.0 C3A A:HEM200 4.2 43.9 1.0 C2D A:HEM200 4.3 40.1 1.0 C2B A:HEM200 4.3 37.6 1.0 C3B A:HEM200 4.3 37.1 1.0 C3C A:HEM200 4.3 33.0 1.0 C2C A:HEM200 4.3 34.6 1.0 ND1 A:HIS88 4.4 45.4 1.0 CG2 A:VAL63 4.5 37.0 1.0 CG A:HIS88 4.5 45.1 1.0 CD1 A:LEU92 4.7 42.2 1.0 ND1 A:HIS59 4.8 42.4 1.0

Iron binding site 2 out of 4 in the The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:36.9 occ:1.00 FE B:HEM400 0.0 36.9 1.0 ND B:HEM400 2.0 34.8 1.0 NC B:HEM400 2.0 38.3 1.0 NB B:HEM400 2.0 36.4 1.0 NA B:HEM400 2.0 42.0 1.0 NE2 B:HIS92 2.2 37.1 1.0 C4D B:HEM400 3.0 38.4 1.0 CE1 B:HIS92 3.0 38.2 1.0 C4C B:HEM400 3.0 35.8 1.0 C1C B:HEM400 3.0 39.2 1.0 C1B B:HEM400 3.0 37.5 1.0 C1D B:HEM400 3.1 35.8 1.0 C4B B:HEM400 3.1 38.0 1.0 C4A B:HEM400 3.1 43.1 1.0 C1A B:HEM400 3.1 42.8 1.0 CD2 B:HIS92 3.3 35.3 1.0 CHD B:HEM400 3.4 33.7 1.0 CHC B:HEM400 3.4 37.5 1.0 CHA B:HEM400 3.4 40.4 1.0 CHB B:HEM400 3.4 41.2 1.0 ND1 B:HIS92 4.2 36.4 1.0 C2C B:HEM400 4.3 38.4 1.0 C3C B:HEM400 4.3 36.6 1.0 C3D B:HEM400 4.3 40.6 1.0 C2D B:HEM400 4.3 37.9 1.0 C2B B:HEM400 4.3 36.6 1.0 C3B B:HEM400 4.3 35.7 1.0 C3A B:HEM400 4.3 45.2 1.0 C2A B:HEM400 4.3 45.1 1.0 CG B:HIS92 4.3 36.7 1.0 CG2 B:VAL67 4.5 36.7 1.0 NE2 B:HIS63 4.6 42.3 1.0 CE1 B:PHE103 5.0 36.0 1.0

Iron binding site 3 out of 4 in the The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe600 b:47.1 occ:1.00 FE C:HEM600 0.0 47.1 1.0 ND C:HEM600 2.0 38.8 1.0 NA C:HEM600 2.0 42.2 1.0 NB C:HEM600 2.0 35.6 1.0 NC C:HEM600 2.0 36.5 1.0 NE2 C:HIS88 2.3 47.0 1.0 NE2 C:HIS59 2.9 44.9 1.0 C4D C:HEM600 3.0 42.2 1.0 C1D C:HEM600 3.0 38.2 1.0 C4A C:HEM600 3.1 40.6 1.0 C4B C:HEM600 3.1 37.4 1.0 C1B C:HEM600 3.1 37.0 1.0 C1A C:HEM600 3.1 44.4 1.0 C1C C:HEM600 3.1 35.8 1.0 C4C C:HEM600 3.1 35.9 1.0 CE1 C:HIS88 3.2 46.4 1.0 CD2 C:HIS88 3.3 47.3 1.0 CHA C:HEM600 3.4 45.4 1.0 CHB C:HEM600 3.4 35.6 1.0 CHD C:HEM600 3.4 35.5 1.0 CHC C:HEM600 3.4 34.0 1.0 CE1 C:HIS59 3.8 46.9 1.0 CD2 C:HIS59 3.9 45.9 1.0 CG2 C:VAL63 4.2 27.9 1.0 C3D C:HEM600 4.3 41.4 1.0 C2D C:HEM600 4.3 38.7 1.0 C3A C:HEM600 4.3 45.8 1.0 C2B C:HEM600 4.3 38.4 1.0 C2A C:HEM600 4.3 46.0 1.0 C3B C:HEM600 4.3 36.6 1.0 C2C C:HEM600 4.3 37.2 1.0 C3C C:HEM600 4.3 36.5 1.0 ND1 C:HIS88 4.4 45.4 1.0 CG C:HIS88 4.4 44.9 1.0 CD1 C:LEU92 4.6 40.0 1.0 ND1 C:HIS59 4.9 48.4 1.0

Iron binding site 4 out of 4 in the The Crystal Structure of Hemoglobin I From Trematomus Newnesi in Deoxygenated State


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe800 b:39.5 occ:1.00 FE D:HEM800 0.0 39.5 1.0 NA D:HEM800 2.0 36.8 1.0 ND D:HEM800 2.0 34.8 1.0 NB D:HEM800 2.0 30.3 1.0 NC D:HEM800 2.0 34.8 1.0 NE2 D:HIS92 2.2 32.8 1.0 CE1 D:HIS92 3.0 32.3 1.0 C4D D:HEM800 3.0 35.4 1.0 C1A D:HEM800 3.0 39.3 1.0 C4A D:HEM800 3.0 35.3 1.0 C1D D:HEM800 3.1 35.8 1.0 C1B D:HEM800 3.1 30.4 1.0 C1C D:HEM800 3.1 35.3 1.0 C4B D:HEM800 3.1 34.2 1.0 C4C D:HEM800 3.1 34.3 1.0 CD2 D:HIS92 3.2 32.9 1.0 CHA D:HEM800 3.4 37.8 1.0 CHB D:HEM800 3.4 32.6 1.0 CHC D:HEM800 3.4 34.5 1.0 CHD D:HEM800 3.4 34.6 1.0 CG2 D:VAL67 3.5 37.4 1.0 ND1 D:HIS92 4.2 31.5 1.0 NE2 D:HIS63 4.2 48.6 1.0 C3D D:HEM800 4.3 36.6 1.0 C2A D:HEM800 4.3 39.4 1.0 C2D D:HEM800 4.3 37.3 1.0 C3A D:HEM800 4.3 38.2 1.0 C2B D:HEM800 4.3 30.9 1.0 C3B D:HEM800 4.3 34.4 1.0 C2C D:HEM800 4.3 35.2 1.0 C3C D:HEM800 4.3 33.1 1.0 CG D:HIS92 4.3 32.8 1.0 CE1 D:HIS63 4.9 48.9 1.0 CB D:VAL67 4.9 34.5 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