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Iron in PDB 1ygd: T-to-T(High) Quaternary Transitions in Human Hemoglobin: BETAW37E Alpha Zinc Beta Oxy (10 Test Sets)

Protein crystallography data

The structure of T-to-T(High) Quaternary Transitions in Human Hemoglobin: BETAW37E Alpha Zinc Beta Oxy (10 Test Sets), PDB code: 1ygd 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 / 2.73
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.300, 99.100, 66.800, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 26.6

Other elements in 1ygd:

The structure of T-to-T(High) Quaternary Transitions in Human Hemoglobin: BETAW37E Alpha Zinc Beta Oxy (10 Test Sets) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the T-to-T(High) Quaternary Transitions in Human Hemoglobin: BETAW37E Alpha Zinc Beta Oxy (10 Test Sets) (pdb code 1ygd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the T-to-T(High) Quaternary Transitions in Human Hemoglobin: BETAW37E Alpha Zinc Beta Oxy (10 Test Sets), PDB code: 1ygd:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 1ygd

Go back to Iron Binding Sites List in 1ygd
Iron binding site 1 out of 2 in the T-to-T(High) Quaternary Transitions in Human Hemoglobin: BETAW37E Alpha Zinc Beta Oxy (10 Test Sets)


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: BETAW37E Alpha Zinc Beta Oxy (10 Test Sets) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe147

b:8.4
occ:1.00
FE B:HEM147 0.0 8.4 1.0
O1 B:OXY150 1.8 9.8 1.0
NA B:HEM147 1.9 5.8 1.0
NE2 B:HIS92 1.9 6.8 1.0
NB B:HEM147 2.0 6.1 1.0
NC B:HEM147 2.0 5.8 1.0
ND B:HEM147 2.2 7.2 1.0
O2 B:OXY150 2.6 14.9 1.0
C4A B:HEM147 2.8 5.3 1.0
CE1 B:HIS92 2.8 7.4 1.0
C1B B:HEM147 2.9 5.4 1.0
CD2 B:HIS92 3.0 7.7 1.0
C4C B:HEM147 3.0 4.9 1.0
C1A B:HEM147 3.0 5.0 1.0
C4B B:HEM147 3.1 6.3 1.0
C1C B:HEM147 3.1 4.8 1.0
C1D B:HEM147 3.2 6.7 1.0
CHB B:HEM147 3.2 6.1 1.0
C4D B:HEM147 3.3 7.8 1.0
CHD B:HEM147 3.4 2.2 1.0
CHC B:HEM147 3.5 6.5 1.0
CHA B:HEM147 3.6 6.1 1.0
ND1 B:HIS92 4.0 8.4 1.0
C3A B:HEM147 4.1 2.1 1.0
CG B:HIS92 4.1 8.9 1.0
C2B B:HEM147 4.2 6.4 1.0
C2A B:HEM147 4.2 3.8 1.0
C3C B:HEM147 4.2 5.1 1.0
C3B B:HEM147 4.2 6.6 1.0
C2C B:HEM147 4.3 2.0 1.0
C2D B:HEM147 4.5 7.1 1.0
C3D B:HEM147 4.5 8.4 1.0
CG2 B:VAL67 4.6 12.9 1.0
NE2 B:HIS63 4.6 12.9 1.0

Iron binding site 2 out of 2 in 1ygd

Go back to Iron Binding Sites List in 1ygd
Iron binding site 2 out of 2 in the T-to-T(High) Quaternary Transitions in Human Hemoglobin: BETAW37E Alpha Zinc Beta Oxy (10 Test Sets)


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: BETAW37E Alpha Zinc Beta Oxy (10 Test Sets) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe147

b:19.1
occ:1.00
FE D:HEM147 0.0 19.1 1.0
O1 D:OXY150 1.8 23.0 1.0
NE2 D:HIS92 1.8 20.3 1.0
NC D:HEM147 1.9 20.2 1.0
NB D:HEM147 2.0 21.0 1.0
NA D:HEM147 2.1 21.2 1.0
ND D:HEM147 2.1 20.9 1.0
O2 D:OXY150 2.6 27.2 1.0
CE1 D:HIS92 2.7 19.2 1.0
C4C D:HEM147 2.9 19.4 1.0
C1B D:HEM147 3.0 21.3 1.0
C1C D:HEM147 3.0 19.5 1.0
CD2 D:HIS92 3.0 19.4 1.0
C4B D:HEM147 3.0 20.9 1.0
C1D D:HEM147 3.1 21.0 1.0
C4A D:HEM147 3.1 21.5 1.0
C1A D:HEM147 3.2 21.7 1.0
C4D D:HEM147 3.2 21.2 1.0
CHD D:HEM147 3.3 20.0 1.0
CHB D:HEM147 3.3 21.1 1.0
CHC D:HEM147 3.4 20.3 1.0
CHA D:HEM147 3.6 21.5 1.0
ND1 D:HIS92 3.9 19.0 1.0
CG D:HIS92 4.0 19.6 1.0
C3C D:HEM147 4.2 19.0 1.0
C2C D:HEM147 4.2 19.4 1.0
C2B D:HEM147 4.2 21.4 1.0
C3B D:HEM147 4.2 21.7 1.0
C2D D:HEM147 4.3 20.5 1.0
C3A D:HEM147 4.3 21.7 1.0
C2A D:HEM147 4.4 22.3 1.0
C3D D:HEM147 4.4 21.1 1.0
NE2 D:HIS63 4.6 28.1 1.0
CG2 D:VAL67 4.8 26.9 1.0

Reference:

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
Page generated: Wed Jul 16 22:41:48 2025

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