Iron in PDB 3b75: Crystal Structure of Glycated Human Haemoglobin

The structure of Crystal Structure of Glycated Human Haemoglobin, PDB code: 3b75 was solved by N.T.Saraswathi, V.E.Syakhovich, S.B.Bokut, D.Moras, M.Ruff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.90 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	237.987, 59.267, 137.024, 90.00, 125.36, 90.00
R / Rfree (%)	24.4 / 33.1

The binding sites of Iron atom in the Crystal Structure of Glycated Human Haemoglobin (pdb code 3b75). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Crystal Structure of Glycated Human Haemoglobin, PDB code: 3b75:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in the Crystal Structure of Glycated Human Haemoglobin


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 Glycated Human Haemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe150 b:38.7 occ:1.00 FE A:HEM150 0.0 38.7 1.0 O1 A:OXY151 1.8 40.6 1.0 NE2 A:HIS87 2.0 34.6 1.0 ND A:HEM150 2.1 38.9 1.0 NA A:HEM150 2.1 40.6 1.0 NC A:HEM150 2.1 37.5 1.0 NB A:HEM150 2.1 39.7 1.0 O2 A:OXY151 2.4 47.4 1.0 CD2 A:HIS87 3.0 33.6 1.0 C4D A:HEM150 3.0 37.0 1.0 C1A A:HEM150 3.0 41.2 1.0 CE1 A:HIS87 3.1 34.7 1.0 C1D A:HEM150 3.1 38.1 1.0 C4C A:HEM150 3.1 36.8 1.0 C1C A:HEM150 3.1 34.8 1.0 C4B A:HEM150 3.1 38.7 1.0 C1B A:HEM150 3.2 40.1 1.0 C4A A:HEM150 3.2 41.2 1.0 CHA A:HEM150 3.3 39.4 1.0 CHD A:HEM150 3.5 35.9 1.0 CHC A:HEM150 3.5 36.0 1.0 CHB A:HEM150 3.6 40.2 1.0 ND1 A:HIS87 4.2 36.1 1.0 CG A:HIS87 4.2 37.7 1.0 C3D A:HEM150 4.2 36.5 1.0 CE1 A:HIS58 4.3 44.7 1.0 C2A A:HEM150 4.3 40.9 1.0 C2D A:HEM150 4.3 35.3 1.0 C3C A:HEM150 4.3 31.6 1.0 C2C A:HEM150 4.3 34.3 1.0 C3A A:HEM150 4.4 39.7 1.0 C3B A:HEM150 4.4 38.8 1.0 C2B A:HEM150 4.4 39.4 1.0 NE2 A:HIS58 4.4 44.6 1.0 CG2 A:VAL62 4.9 42.3 1.0

Iron binding site 2 out of 10 in the Crystal Structure of Glycated Human Haemoglobin


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 Glycated Human Haemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe150 b:29.4 occ:1.00 FE B:HEM150 0.0 29.4 1.0 O1 B:OXY151 1.8 33.9 1.0 NC B:HEM150 2.0 29.0 1.0 NB B:HEM150 2.1 30.9 1.0 ND B:HEM150 2.1 29.7 1.0 NE2 B:HIS92 2.1 28.4 1.0 NA B:HEM150 2.1 33.4 1.0 O2 B:OXY151 2.9 40.3 1.0 CD2 B:HIS92 3.0 28.9 1.0 C4C B:HEM150 3.0 26.6 1.0 C1D B:HEM150 3.1 30.5 1.0 C1B B:HEM150 3.1 32.2 1.0 C4B B:HEM150 3.1 31.7 1.0 CE1 B:HIS92 3.1 25.3 1.0 C1C B:HEM150 3.1 28.7 1.0 C4D B:HEM150 3.1 29.4 1.0 C1A B:HEM150 3.1 31.6 1.0 C4A B:HEM150 3.1 33.7 1.0 CHD B:HEM150 3.4 27.4 1.0 CHA B:HEM150 3.5 28.6 1.0 CHC B:HEM150 3.5 27.3 1.0 CHB B:HEM150 3.5 32.2 1.0 CG B:HIS92 4.2 28.4 1.0 ND1 B:HIS92 4.2 25.5 1.0 C3C B:HEM150 4.3 22.4 1.0 NE2 B:HIS63 4.3 35.0 1.0 C2B B:HEM150 4.3 31.1 1.0 C3B B:HEM150 4.3 31.7 1.0 C2C B:HEM150 4.3 24.0 1.0 C2D B:HEM150 4.3 29.2 1.0 C3D B:HEM150 4.3 29.6 1.0 C2A B:HEM150 4.4 33.8 1.0 C3A B:HEM150 4.4 34.4 1.0 CG2 B:VAL67 4.8 32.5 1.0 CE1 B:HIS63 4.9 37.5 1.0

Iron binding site 3 out of 10 in the Crystal Structure of Glycated Human Haemoglobin


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 Glycated Human Haemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe150 b:38.2 occ:1.00 FE C:HEM150 0.0 38.2 1.0 O1 C:OXY151 1.8 37.5 1.0 NE2 C:HIS87 2.0 33.8 1.0 NB C:HEM150 2.1 37.6 1.0 ND C:HEM150 2.1 38.0 1.0 NC C:HEM150 2.1 36.6 1.0 NA C:HEM150 2.1 40.5 1.0 O2 C:OXY151 2.7 44.5 1.0 CE1 C:HIS87 2.9 30.4 1.0 C4B C:HEM150 3.0 37.3 1.0 C4D C:HEM150 3.0 39.2 1.0 C1C C:HEM150 3.1 33.0 1.0 C1A C:HEM150 3.1 40.6 1.0 CD2 C:HIS87 3.1 34.3 1.0 C1B C:HEM150 3.1 39.4 1.0 C1D C:HEM150 3.1 38.0 1.0 C4C C:HEM150 3.1 35.1 1.0 C4A C:HEM150 3.2 40.4 1.0 CHC C:HEM150 3.3 34.6 1.0 CHA C:HEM150 3.4 39.7 1.0 CHD C:HEM150 3.5 36.1 1.0 CHB C:HEM150 3.5 39.5 1.0 ND1 C:HIS87 4.1 31.2 1.0 CG C:HIS87 4.2 35.3 1.0 C3B C:HEM150 4.2 38.5 1.0 C3D C:HEM150 4.3 37.1 1.0 C2C C:HEM150 4.3 34.0 1.0 C2B C:HEM150 4.3 39.9 1.0 C2A C:HEM150 4.3 43.6 1.0 C2D C:HEM150 4.3 36.5 1.0 C3C C:HEM150 4.3 32.7 1.0 C3A C:HEM150 4.4 42.7 1.0 NE2 C:HIS58 4.5 43.1 1.0 CE1 C:HIS58 4.5 43.0 1.0 CG2 C:VAL62 4.8 46.0 1.0

Iron binding site 4 out of 10 in the Crystal Structure of Glycated Human Haemoglobin


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 Glycated Human Haemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe150 b:45.7 occ:1.00 FE D:HEM150 0.0 45.7 1.0 O1 D:OXY151 1.8 45.8 1.0 NE2 D:HIS92 2.0 41.1 1.0 NA D:HEM150 2.1 45.8 1.0 NC D:HEM150 2.1 45.1 1.0 ND D:HEM150 2.1 48.3 1.0 NB D:HEM150 2.1 46.0 1.0 CE1 D:HIS92 2.8 43.0 1.0 O2 D:OXY151 3.0 48.4 1.0 C1A D:HEM150 3.1 46.5 1.0 C4C D:HEM150 3.1 45.1 1.0 C4A D:HEM150 3.1 46.0 1.0 C4D D:HEM150 3.1 48.2 1.0 C1D D:HEM150 3.1 48.2 1.0 C1C D:HEM150 3.1 45.4 1.0 C1B D:HEM150 3.1 45.0 1.0 C4B D:HEM150 3.2 44.8 1.0 CD2 D:HIS92 3.2 42.0 1.0 CHA D:HEM150 3.4 46.7 1.0 CHD D:HEM150 3.5 46.4 1.0 CHB D:HEM150 3.5 45.4 1.0 CHC D:HEM150 3.5 44.7 1.0 ND1 D:HIS92 4.0 43.3 1.0 CG D:HIS92 4.2 44.5 1.0 C2A D:HEM150 4.3 48.0 1.0 C3A D:HEM150 4.3 47.1 1.0 C3C D:HEM150 4.3 44.5 1.0 C2C D:HEM150 4.3 45.1 1.0 C3D D:HEM150 4.3 47.9 1.0 NE2 D:HIS63 4.3 42.5 1.0 C2D D:HEM150 4.4 47.4 1.0 C2B D:HEM150 4.4 45.8 1.0 C3B D:HEM150 4.4 44.3 1.0 CG2 D:VAL67 4.9 48.5 1.0

Iron binding site 5 out of 10 in the Crystal Structure of Glycated Human Haemoglobin


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 Glycated Human Haemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe150 b:75.8 occ:1.00 FE E:HEM150 0.0 75.8 1.0 O1 E:OXY151 1.9 76.7 1.0 NB E:HEM150 2.0 73.2 1.0 NA E:HEM150 2.1 74.8 1.0 ND E:HEM150 2.1 73.0 1.0 NC E:HEM150 2.1 73.7 1.0 NE2 E:HIS87 2.2 83.4 1.0 CE1 E:HIS87 2.8 84.8 1.0 C1B E:HEM150 3.0 73.6 1.0 C4A E:HEM150 3.1 75.0 1.0 O2 E:OXY151 3.1 76.3 1.0 C1D E:HEM150 3.1 72.6 1.0 C4B E:HEM150 3.1 73.4 1.0 C1A E:HEM150 3.1 74.7 1.0 C4D E:HEM150 3.1 72.9 1.0 C1C E:HEM150 3.1 72.7 1.0 C4C E:HEM150 3.1 72.9 1.0 CHB E:HEM150 3.4 74.6 1.0 CD2 E:HIS87 3.4 85.4 1.0 CHD E:HEM150 3.4 73.1 1.0 CHC E:HEM150 3.5 72.9 1.0 CHA E:HEM150 3.5 73.5 1.0 ND1 E:HIS87 4.1 85.8 1.0 C2B E:HEM150 4.3 73.4 1.0 C3A E:HEM150 4.3 75.1 1.0 C3B E:HEM150 4.3 73.6 1.0 C2A E:HEM150 4.3 75.5 1.0 C2D E:HEM150 4.3 72.9 1.0 C3D E:HEM150 4.3 73.0 1.0 C2C E:HEM150 4.4 73.0 1.0 CG E:HIS87 4.4 87.0 1.0 C3C E:HEM150 4.4 71.7 1.0 CE1 E:HIS58 4.7 84.1 1.0 CG2 E:VAL62 4.7 81.6 1.0 NE2 E:HIS58 5.0 83.8 1.0

Iron binding site 6 out of 10 in the Crystal Structure of Glycated Human Haemoglobin


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 Glycated Human Haemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe150 b:39.0 occ:1.00 FE F:HEM150 0.0 39.0 1.0 O1 F:OXY151 1.9 46.1 1.0 NC F:HEM150 2.0 38.8 1.0 NE2 F:HIS92 2.0 30.9 1.0 NA F:HEM150 2.1 40.5 1.0 NB F:HEM150 2.1 39.4 1.0 ND F:HEM150 2.1 40.9 1.0 CE1 F:HIS92 2.8 26.0 1.0 C4C F:HEM150 3.0 39.9 1.0 O2 F:OXY151 3.0 49.0 1.0 C4A F:HEM150 3.0 40.3 1.0 C1B F:HEM150 3.1 37.9 1.0 C1C F:HEM150 3.1 39.5 1.0 C1D F:HEM150 3.1 40.6 1.0 C1A F:HEM150 3.1 42.6 1.0 C4B F:HEM150 3.1 37.0 1.0 C4D F:HEM150 3.2 41.5 1.0 CD2 F:HIS92 3.2 27.1 1.0 CHB F:HEM150 3.4 40.3 1.0 CHD F:HEM150 3.4 41.3 1.0 CHC F:HEM150 3.5 38.3 1.0 CHA F:HEM150 3.5 41.5 1.0 ND1 F:HIS92 4.0 30.5 1.0 NE2 F:HIS63 4.2 69.6 1.0 C3C F:HEM150 4.2 38.4 1.0 CG F:HIS92 4.2 31.4 1.0 C2C F:HEM150 4.3 37.8 1.0 C2B F:HEM150 4.3 38.2 1.0 C3A F:HEM150 4.3 40.8 1.0 C3B F:HEM150 4.3 37.1 1.0 C2A F:HEM150 4.3 43.4 1.0 C2D F:HEM150 4.4 42.8 1.0 C3D F:HEM150 4.4 43.9 1.0 CD1 F:LEU96 4.8 30.4 1.0 CE1 F:HIS63 4.8 69.8 1.0 CG2 F:VAL67 4.9 55.7 1.0

Iron binding site 7 out of 10 in the Crystal Structure of Glycated Human Haemoglobin


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 Glycated Human Haemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe150 b:50.5 occ:1.00 FE G:HEM150 0.0 50.5 1.0 O1 G:OXY151 1.8 50.7 1.0 NE2 G:HIS87 2.0 61.0 1.0 NB G:HEM150 2.0 49.2 1.0 ND G:HEM150 2.1 49.4 1.0 NA G:HEM150 2.1 51.2 1.0 NC G:HEM150 2.1 49.1 1.0 O2 G:OXY151 2.6 53.2 1.0 CE1 G:HIS87 2.9 63.5 1.0 C4D G:HEM150 3.1 51.0 1.0 C1B G:HEM150 3.1 51.8 1.0 C1D G:HEM150 3.1 49.9 1.0 C4B G:HEM150 3.1 50.6 1.0 C1A G:HEM150 3.1 52.0 1.0 C4A G:HEM150 3.1 50.9 1.0 CD2 G:HIS87 3.1 63.4 1.0 C4C G:HEM150 3.1 46.2 1.0 C1C G:HEM150 3.2 47.5 1.0 CHA G:HEM150 3.4 50.7 1.0 CHD G:HEM150 3.5 48.5 1.0 CHB G:HEM150 3.5 51.1 1.0 CHC G:HEM150 3.5 48.5 1.0 NE2 G:HIS58 4.0 60.3 1.0 ND1 G:HIS87 4.1 63.5 1.0 CG G:HIS87 4.2 64.7 1.0 C2B G:HEM150 4.3 51.7 1.0 C3B G:HEM150 4.3 51.5 1.0 C3D G:HEM150 4.3 50.0 1.0 C2D G:HEM150 4.3 48.0 1.0 C2A G:HEM150 4.3 53.1 1.0 C3A G:HEM150 4.4 52.6 1.0 C3C G:HEM150 4.4 46.1 1.0 C2C G:HEM150 4.4 48.1 1.0 CE1 G:HIS58 4.6 60.3 1.0

Iron binding site 8 out of 10 in the Crystal Structure of Glycated Human Haemoglobin


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 Glycated Human Haemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe150 b:70.0 occ:1.00 FE H:HEM150 0.0 70.0 1.0 O1 H:OXY151 1.9 70.3 1.0 CE1 H:HIS92 1.9 72.1 1.0 NE2 H:HIS92 2.0 72.2 1.0 NC H:HEM150 2.1 69.0 1.0 ND H:HEM150 2.1 70.0 1.0 NA H:HEM150 2.1 69.7 1.0 NB H:HEM150 2.1 69.8 1.0 O2 H:OXY151 2.8 71.3 1.0 C1C H:HEM150 3.0 67.4 1.0 C4D H:HEM150 3.1 69.6 1.0 C1D H:HEM150 3.1 69.6 1.0 C1A H:HEM150 3.1 69.7 1.0 C4C H:HEM150 3.1 67.6 1.0 C4B H:HEM150 3.1 68.2 1.0 C4A H:HEM150 3.1 69.9 1.0 C1B H:HEM150 3.1 69.2 1.0 ND1 H:HIS92 3.2 72.1 1.0 CD2 H:HIS92 3.4 72.3 1.0 CHC H:HEM150 3.4 67.6 1.0 CHA H:HEM150 3.4 69.3 1.0 CHD H:HEM150 3.4 68.3 1.0 CHB H:HEM150 3.5 69.2 1.0 CG H:HIS92 3.9 73.2 1.0 C2C H:HEM150 4.3 67.2 1.0 C3C H:HEM150 4.3 66.8 1.0 C2D H:HEM150 4.3 69.4 1.0 C3D H:HEM150 4.3 70.1 1.0 C2A H:HEM150 4.3 70.0 1.0 C3B H:HEM150 4.3 67.9 1.0 C3A H:HEM150 4.3 70.1 1.0 C2B H:HEM150 4.3 67.9 1.0 NE2 H:HIS63 4.6 84.5 1.0 CE1 H:HIS63 4.8 84.2 1.0

Iron binding site 9 out of 10 in the Crystal Structure of Glycated Human Haemoglobin


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 Glycated Human Haemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ S:Fe150 b:50.6 occ:1.00 FE S:HEM150 0.0 50.6 1.0 O1 S:OXY151 1.8 52.1 1.0 NE2 S:HIS87 2.0 49.9 1.0 ND S:HEM150 2.0 47.5 1.0 NC S:HEM150 2.0 47.2 1.0 NB S:HEM150 2.1 47.2 1.0 NA S:HEM150 2.1 48.8 1.0 CE1 S:HIS87 2.9 49.7 1.0 C4D S:HEM150 3.0 47.4 1.0 C1C S:HEM150 3.0 44.6 1.0 C4B S:HEM150 3.0 46.3 1.0 CD2 S:HIS87 3.1 50.7 1.0 O2 S:OXY151 3.1 56.9 1.0 C1A S:HEM150 3.1 47.6 1.0 C1D S:HEM150 3.1 49.5 1.0 C4C S:HEM150 3.1 47.4 1.0 C1B S:HEM150 3.2 47.4 1.0 C4A S:HEM150 3.2 48.7 1.0 CHC S:HEM150 3.3 45.8 1.0 CHA S:HEM150 3.4 47.0 1.0 CHD S:HEM150 3.5 47.5 1.0 CHB S:HEM150 3.6 48.0 1.0 ND1 S:HIS87 4.0 50.0 1.0 CG S:HIS87 4.2 50.8 1.0 C3D S:HEM150 4.2 48.1 1.0 C2C S:HEM150 4.3 45.1 1.0 C3B S:HEM150 4.3 45.9 1.0 C2D S:HEM150 4.3 47.7 1.0 C3C S:HEM150 4.3 44.3 1.0 C2B S:HEM150 4.3 46.6 1.0 C2A S:HEM150 4.4 49.1 1.0 C3A S:HEM150 4.4 49.4 1.0 NE2 S:HIS58 4.8 66.0 1.0 CE1 S:HIS58 4.8 65.8 1.0 CG2 S:VAL62 4.8 65.4 1.0

Iron binding site 10 out of 10 in the Crystal Structure of Glycated Human Haemoglobin


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 Glycated Human Haemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ T:Fe150 b:74.2 occ:1.00 FE T:HEM150 0.0 74.2 1.0 O1 T:OXY151 1.9 74.6 1.0 NE2 T:HIS92 2.0 73.5 1.0 NB T:HEM150 2.1 76.8 1.0 NA T:HEM150 2.1 77.1 1.0 NC T:HEM150 2.1 77.0 1.0 ND T:HEM150 2.1 77.1 1.0 CE1 T:HIS92 2.5 73.3 1.0 O2 T:OXY151 3.1 73.0 1.0 C1C T:HEM150 3.1 76.1 1.0 C4C T:HEM150 3.1 77.1 1.0 C4B T:HEM150 3.1 76.4 1.0 C4D T:HEM150 3.1 77.4 1.0 C1A T:HEM150 3.1 77.1 1.0 C4A T:HEM150 3.1 77.2 1.0 C1B T:HEM150 3.1 76.8 1.0 C1D T:HEM150 3.1 77.6 1.0 CD2 T:HIS92 3.2 74.8 1.0 CHC T:HEM150 3.4 76.4 1.0 CHA T:HEM150 3.5 77.4 1.0 CHD T:HEM150 3.5 77.4 1.0 CHB T:HEM150 3.5 76.8 1.0 ND1 T:HIS92 3.8 74.8 1.0 CG T:HIS92 4.1 76.3 1.0 C2C T:HEM150 4.3 76.7 1.0 C3C T:HEM150 4.3 76.4 1.0 C3A T:HEM150 4.3 77.3 1.0 C3B T:HEM150 4.3 76.4 1.0 C2A T:HEM150 4.3 77.6 1.0 C2B T:HEM150 4.3 76.4 1.0 C3D T:HEM150 4.4 77.9 1.0 C2D T:HEM150 4.4 78.0 1.0 CE1 T:HIS63 4.4 88.0 1.0 CG2 T:VAL67 4.5 89.3 1.0 CD1 T:LEU91 4.9 81.8 1.0

N.T.Saraswathi, V.E.Syakhovich, S.B.Bokut, D.Moras, M.Ruff. The Effect of Hemoglobin Glycosylation on Diabete Linked Oxidative Stress To Be Published.