Iron in PDB 2zfo: Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins

The structure of Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins, PDB code: 2zfo was solved by N.Numoto, T.Nakagawa, A.Kita, Y.Sasayama, Y.Fukumori, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.22 / 1.95
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	110.960, 110.960, 271.580, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 20.2

The binding sites of Iron atom in the Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins (pdb code 2zfo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins, PDB code: 2zfo:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:27.1 occ:1.00 FE A:HEM200 0.0 27.1 1.0 O1 A:OXY201 1.8 38.5 1.0 NA A:HEM200 2.0 25.8 1.0 ND A:HEM200 2.0 29.5 1.0 NB A:HEM200 2.1 25.0 1.0 NC A:HEM200 2.1 27.5 1.0 NE2 A:HIS94 2.1 27.5 1.0 O2 A:OXY201 3.0 41.7 1.0 C4A A:HEM200 3.1 26.5 1.0 C1D A:HEM200 3.1 30.3 1.0 C4C A:HEM200 3.1 27.4 1.0 CD2 A:HIS94 3.1 27.9 1.0 C4D A:HEM200 3.1 28.5 1.0 C1A A:HEM200 3.1 26.9 1.0 C1B A:HEM200 3.1 26.1 1.0 C1C A:HEM200 3.1 27.3 1.0 C4B A:HEM200 3.1 26.1 1.0 CE1 A:HIS94 3.1 29.1 1.0 CHD A:HEM200 3.4 29.9 1.0 CHB A:HEM200 3.4 24.7 1.0 CHC A:HEM200 3.4 24.4 1.0 CHA A:HEM200 3.4 27.7 1.0 CG A:HIS94 4.2 29.1 1.0 ND1 A:HIS94 4.2 29.5 1.0 C2D A:HEM200 4.3 30.2 1.0 C3D A:HEM200 4.3 30.8 1.0 C3A A:HEM200 4.3 24.8 1.0 C2A A:HEM200 4.3 26.5 1.0 C3C A:HEM200 4.3 28.3 1.0 C2B A:HEM200 4.3 25.4 1.0 C2C A:HEM200 4.3 25.7 1.0 C3B A:HEM200 4.3 25.5 1.0 CG2 A:VAL66 4.5 20.8 1.0

Iron binding site 2 out of 4 in the Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:24.2 occ:1.00 FE B:HEM200 0.0 24.2 1.0 ND B:HEM200 2.0 23.1 1.0 NA B:HEM200 2.1 23.0 1.0 NB B:HEM200 2.1 22.9 1.0 NC B:HEM200 2.1 22.8 1.0 NE2 B:HIS94 2.2 25.0 1.0 C1D B:HEM200 3.0 23.1 1.0 C4D B:HEM200 3.1 24.3 1.0 C4C B:HEM200 3.1 23.2 1.0 CD2 B:HIS94 3.1 27.3 1.0 C4A B:HEM200 3.1 22.8 1.0 C1B B:HEM200 3.1 22.0 1.0 C4B B:HEM200 3.1 24.7 1.0 C1A B:HEM200 3.1 22.6 1.0 C1C B:HEM200 3.1 24.3 1.0 CE1 B:HIS94 3.2 27.1 1.0 CHD B:HEM200 3.4 22.8 1.0 CHA B:HEM200 3.4 24.4 1.0 CHB B:HEM200 3.4 23.3 1.0 CHC B:HEM200 3.4 23.7 1.0 CG2 B:VAL66 4.2 19.2 1.0 CG B:HIS94 4.3 27.5 1.0 C2D B:HEM200 4.3 24.8 1.0 C3D B:HEM200 4.3 25.4 1.0 ND1 B:HIS94 4.3 26.1 1.0 C2B B:HEM200 4.3 23.5 1.0 C3C B:HEM200 4.3 24.9 1.0 C2A B:HEM200 4.3 26.5 1.0 C2C B:HEM200 4.3 24.1 1.0 C3B B:HEM200 4.3 23.7 1.0 C3A B:HEM200 4.3 25.1 1.0 CG1 B:VAL66 4.7 21.6 1.0

Iron binding site 3 out of 4 in the Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:39.5 occ:1.00 FE C:HEM200 0.0 39.5 1.0 ND C:HEM200 2.1 40.3 1.0 NA C:HEM200 2.1 39.8 1.0 NB C:HEM200 2.1 39.5 1.0 NC C:HEM200 2.1 40.5 1.0 NE2 C:HIS98 2.3 43.5 1.0 C4C C:HEM200 3.1 41.3 1.0 C1D C:HEM200 3.1 41.8 1.0 C4A C:HEM200 3.1 39.9 1.0 C4B C:HEM200 3.1 39.6 1.0 C1C C:HEM200 3.1 41.3 1.0 C4D C:HEM200 3.1 41.3 1.0 C1A C:HEM200 3.1 42.2 1.0 C1B C:HEM200 3.1 38.9 1.0 CD2 C:HIS98 3.3 44.1 1.0 CE1 C:HIS98 3.3 43.2 1.0 CHD C:HEM200 3.4 41.1 1.0 CHB C:HEM200 3.4 40.0 1.0 CHC C:HEM200 3.4 40.4 1.0 CHA C:HEM200 3.4 41.0 1.0 C2D C:HEM200 4.3 41.4 1.0 C3D C:HEM200 4.3 41.4 1.0 C3C C:HEM200 4.3 42.2 1.0 C2C C:HEM200 4.3 42.0 1.0 C3B C:HEM200 4.3 38.9 1.0 C3A C:HEM200 4.3 40.9 1.0 C2A C:HEM200 4.3 42.2 1.0 C2B C:HEM200 4.3 40.4 1.0 CG2 C:VAL70 4.4 23.7 1.0 NH2 C:ARG101 4.4 60.6 1.0 ND1 C:HIS98 4.4 43.3 1.0 CG1 C:VAL70 4.4 26.6 1.0 CG C:HIS98 4.4 44.4 1.0 O C:HOH1463 4.8 49.7 1.0

Iron binding site 4 out of 4 in the Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:26.9 occ:1.00 FE D:HEM200 0.0 26.9 1.0 NB D:HEM200 2.0 25.1 1.0 ND D:HEM200 2.1 28.2 1.0 NA D:HEM200 2.1 26.4 1.0 NC D:HEM200 2.1 25.0 1.0 NE2 D:HIS96 2.2 27.2 1.0 C4A D:HEM200 3.1 25.8 1.0 C4B D:HEM200 3.1 25.7 1.0 C1B D:HEM200 3.1 24.9 1.0 C1A D:HEM200 3.1 26.6 1.0 C1D D:HEM200 3.1 28.5 1.0 C4D D:HEM200 3.1 29.1 1.0 C1C D:HEM200 3.1 25.9 1.0 C4C D:HEM200 3.1 27.6 1.0 CE1 D:HIS96 3.1 27.2 1.0 CD2 D:HIS96 3.2 27.6 1.0 CHC D:HEM200 3.4 23.6 1.0 CHB D:HEM200 3.4 24.8 1.0 CHA D:HEM200 3.4 27.9 1.0 CHD D:HEM200 3.4 26.6 1.0 CG2 D:VAL68 4.1 26.8 1.0 ND1 D:HIS96 4.3 26.7 1.0 CG D:HIS96 4.3 28.0 1.0 C3D D:HEM200 4.3 31.1 1.0 C2D D:HEM200 4.3 29.8 1.0 C3A D:HEM200 4.3 25.1 1.0 C3B D:HEM200 4.3 23.4 1.0 C2A D:HEM200 4.3 26.7 1.0 C2B D:HEM200 4.3 25.9 1.0 C2C D:HEM200 4.3 25.8 1.0 C3C D:HEM200 4.3 25.5 1.0 CG1 D:VAL68 4.8 25.3 1.0

N.Numoto, T.Nakagawa, A.Kita, Y.Sasayama, Y.Fukumori, K.Miki. Structure of the Partially Unliganded Met State of 400 kDa Hemoglobin: Insights Into Ligand-Induced Structural Changes of Giant Hemoglobins Proteins V. 73 113 2008.
ISSN: ISSN 0887-3585
PubMed: 18398907
DOI: 10.1002/PROT.22040