Iron in PDB 1ydz: T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set)

The structure of T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set), PDB code: 1ydz was solved by J.S.Kavanaugh, P.H.Rogers, A.Arnone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 3.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.600, 98.600, 67.100, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 30.8

The binding sites of Iron atom in the T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set) (pdb code 1ydz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set), PDB code: 1ydz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe142 b:22.0 occ:1.00 FE A:HEM142 0.0 22.0 1.0 O1 A:OXY150 1.8 24.0 1.0 NA A:HEM142 2.0 22.4 1.0 NB A:HEM142 2.0 20.5 1.0 ND A:HEM142 2.0 23.2 1.0 NC A:HEM142 2.0 21.3 1.0 NE2 A:HIS87 2.3 7.7 1.0 O2 A:OXY150 2.4 24.5 1.0 C4A A:HEM142 3.0 22.6 1.0 C1B A:HEM142 3.0 20.1 1.0 C1A A:HEM142 3.0 25.9 1.0 C4D A:HEM142 3.0 22.2 1.0 C1C A:HEM142 3.1 21.8 1.0 C1D A:HEM142 3.1 23.3 1.0 C4B A:HEM142 3.1 17.7 1.0 C4C A:HEM142 3.1 20.1 1.0 CE1 A:HIS87 3.1 10.2 1.0 CD2 A:HIS87 3.3 16.3 1.0 CHB A:HEM142 3.4 21.9 1.0 CHA A:HEM142 3.4 24.1 1.0 CHC A:HEM142 3.4 20.3 1.0 CHD A:HEM142 3.5 20.3 1.0 C3A A:HEM142 4.3 26.4 1.0 C3D A:HEM142 4.3 24.1 1.0 ND1 A:HIS87 4.3 22.6 1.0 C2B A:HEM142 4.3 16.2 1.0 C3B A:HEM142 4.3 13.1 1.0 C2C A:HEM142 4.3 20.5 1.0 C2A A:HEM142 4.3 28.1 1.0 C2D A:HEM142 4.3 23.4 1.0 C3C A:HEM142 4.3 20.4 1.0 CG A:HIS87 4.4 18.6 1.0 NE2 A:HIS58 4.5 2.0 1.0 CD1 A:LEU91 4.8 9.5 1.0 CG2 A:VAL62 4.9 2.0 1.0

Iron binding site 2 out of 4 in the T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe147 b:9.4 occ:1.00 FE B:HEM147 0.0 9.4 1.0 O1 B:OXY150 1.8 23.4 1.0 ND B:HEM147 2.0 11.0 1.0 NA B:HEM147 2.0 6.2 1.0 NC B:HEM147 2.0 6.2 1.0 NB B:HEM147 2.0 12.7 1.0 NE2 B:HIS92 2.3 6.7 1.0 CE1 B:HIS92 2.7 2.0 1.0 O2 B:OXY150 2.8 28.7 1.0 C4D B:HEM147 3.0 12.3 1.0 C1D B:HEM147 3.0 12.7 1.0 C1A B:HEM147 3.0 6.1 1.0 C4A B:HEM147 3.0 6.8 1.0 C4C B:HEM147 3.1 6.6 1.0 C1C B:HEM147 3.1 10.4 1.0 C4B B:HEM147 3.1 14.1 1.0 C1B B:HEM147 3.1 10.5 1.0 CHA B:HEM147 3.4 7.1 1.0 CHD B:HEM147 3.4 12.6 1.0 CHC B:HEM147 3.4 14.6 1.0 CHB B:HEM147 3.4 8.9 1.0 CD2 B:HIS92 3.6 4.5 1.0 ND1 B:HIS92 4.0 2.0 1.0 NE2 B:HIS63 4.2 9.3 1.0 C3D B:HEM147 4.2 13.0 1.0 C2D B:HEM147 4.3 8.7 1.0 C2A B:HEM147 4.3 9.1 1.0 C3A B:HEM147 4.3 6.9 1.0 C3C B:HEM147 4.3 8.4 1.0 C2C B:HEM147 4.3 10.0 1.0 C3B B:HEM147 4.3 14.6 1.0 C2B B:HEM147 4.3 11.0 1.0 CG B:HIS92 4.4 2.1 1.0 CD1 B:LEU96 4.7 2.0 1.0 CE1 B:HIS63 4.8 3.0 1.0 CG2 B:VAL67 4.9 7.5 1.0 CE1 B:PHE103 5.0 2.0 1.0

Iron binding site 3 out of 4 in the T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe142 b:9.8 occ:1.00 FE C:HEM142 0.0 9.8 1.0 O1 C:OXY150 1.7 8.4 1.0 NA C:HEM142 2.0 17.8 1.0 ND C:HEM142 2.0 13.5 1.0 NB C:HEM142 2.0 13.7 1.0 NC C:HEM142 2.0 11.9 1.0 NE2 C:HIS87 2.4 17.3 1.0 O2 C:OXY150 2.5 13.0 1.0 C1A C:HEM142 3.0 20.9 1.0 C4D C:HEM142 3.0 15.9 1.0 C4B C:HEM142 3.0 15.0 1.0 C1C C:HEM142 3.1 11.5 1.0 C4C C:HEM142 3.1 9.5 1.0 C4A C:HEM142 3.1 15.2 1.0 C1D C:HEM142 3.1 10.7 1.0 C1B C:HEM142 3.1 10.8 1.0 CE1 C:HIS87 3.1 19.5 1.0 CHC C:HEM142 3.4 13.6 1.0 CHA C:HEM142 3.4 16.9 1.0 CHB C:HEM142 3.5 9.2 1.0 CHD C:HEM142 3.5 6.2 1.0 CD2 C:HIS87 3.5 26.6 1.0 C2A C:HEM142 4.2 22.2 1.0 C3D C:HEM142 4.3 16.7 1.0 C3A C:HEM142 4.3 17.7 1.0 C2C C:HEM142 4.3 11.0 1.0 C2B C:HEM142 4.3 11.9 1.0 C3B C:HEM142 4.3 11.7 1.0 C3C C:HEM142 4.3 11.0 1.0 C2D C:HEM142 4.3 14.1 1.0 ND1 C:HIS87 4.3 35.3 1.0 NE2 C:HIS58 4.4 13.6 1.0 CG C:HIS87 4.6 36.6 1.0 CD1 C:LEU91 4.6 43.2 1.0 CE1 C:HIS58 4.7 19.8 1.0

Iron binding site 4 out of 4 in the T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of T-to-T(High) Quaternary Transitions in Human Hemoglobin: ALPHAY140F Oxy (2MM Ihp, 20% Peg) (1 Test Set) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe147 b:27.3 occ:1.00 FE D:HEM147 0.0 27.3 1.0 O1 D:OXY150 1.7 37.3 1.0 NB D:HEM147 2.0 27.9 1.0 NC D:HEM147 2.0 30.2 1.0 ND D:HEM147 2.0 28.5 1.0 NA D:HEM147 2.0 31.0 1.0 NE2 D:HIS92 2.3 26.2 1.0 O2 D:OXY150 2.8 44.4 1.0 C4B D:HEM147 3.0 27.2 1.0 C1C D:HEM147 3.0 31.6 1.0 C1B D:HEM147 3.0 28.2 1.0 C4A D:HEM147 3.1 30.4 1.0 C4D D:HEM147 3.1 27.1 1.0 C1D D:HEM147 3.1 27.0 1.0 C4C D:HEM147 3.1 30.1 1.0 C1A D:HEM147 3.1 32.0 1.0 CD2 D:HIS92 3.2 23.9 1.0 CE1 D:HIS92 3.3 21.5 1.0 CHC D:HEM147 3.4 30.7 1.0 CHA D:HEM147 3.4 29.9 1.0 CHB D:HEM147 3.4 29.5 1.0 CHD D:HEM147 3.4 28.6 1.0 CG2 D:VAL67 4.2 22.8 1.0 C3B D:HEM147 4.2 26.6 1.0 C2B D:HEM147 4.3 26.7 1.0 C3D D:HEM147 4.3 25.1 1.0 C2C D:HEM147 4.3 31.0 1.0 C3A D:HEM147 4.3 30.3 1.0 C2D D:HEM147 4.3 25.7 1.0 C3C D:HEM147 4.3 30.4 1.0 C2A D:HEM147 4.3 31.4 1.0 CG D:HIS92 4.4 17.4 1.0 NE2 D:HIS63 4.4 29.6 1.0 ND1 D:HIS92 4.4 18.1 1.0 CE1 D:HIS63 5.0 21.8 1.0 CD1 D:LEU96 5.0 2.0 1.0

J.S.Kavanaugh, P.H.Rogers, A.Arnone. Crystallographic Evidence For A New Ensemble of Ligand-Induced Allosteric Transitions in Hemoglobin: the T-to-T(High) Quaternary Transitions. Biochemistry V. 44 6101 2005.
ISSN: ISSN 0006-2960
PubMed: 15835899
DOI: 10.1021/BI047813A