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Zinc 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:

Iron (Fe) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1ygd

Go back to Zinc Binding Sites List in 1ygd
Zinc 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 Zinc with other atoms in the Zn 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
A:Zn142

b:15.0
occ:1.00
ZN A:ZNH142 0.0 15.0 1.0
O A:HOH219 2.0 25.7 1.0
NE2 A:HIS87 2.0 15.1 1.0
NA A:ZNH142 2.0 14.6 1.0
NB A:ZNH142 2.1 14.0 1.0
NC A:ZNH142 2.1 13.5 1.0
ND A:ZNH142 2.1 14.6 1.0
CE1 A:HIS87 2.8 16.5 1.0
C4A A:ZNH142 3.0 14.3 1.0
C1A A:ZNH142 3.0 15.3 1.0
C1B A:ZNH142 3.1 13.8 1.0
C4C A:ZNH142 3.1 13.2 1.0
C4D A:ZNH142 3.1 14.7 1.0
C1C A:ZNH142 3.1 12.4 1.0
C4B A:ZNH142 3.1 13.0 1.0
C1D A:ZNH142 3.1 14.7 1.0
CD2 A:HIS87 3.2 16.5 1.0
CHA A:ZNH142 3.4 15.8 1.0
CHB A:ZNH142 3.4 14.2 1.0
CHD A:ZNH142 3.5 14.0 1.0
CHC A:ZNH142 3.5 12.4 1.0
ND1 A:HIS87 4.0 16.7 1.0
CG A:HIS87 4.2 18.8 1.0
C3A A:ZNH142 4.2 15.2 1.0
C2A A:ZNH142 4.2 16.4 1.0
C3C A:ZNH142 4.3 12.5 1.0
C2B A:ZNH142 4.3 13.3 1.0
C2C A:ZNH142 4.3 11.9 1.0
C3B A:ZNH142 4.3 12.9 1.0
C3D A:ZNH142 4.4 14.5 1.0
C2D A:ZNH142 4.4 14.9 1.0
NE2 A:HIS58 4.5 20.4 1.0
CD1 A:LEU91 4.6 22.8 1.0
CE1 A:HIS58 4.6 20.4 1.0

Zinc binding site 2 out of 2 in 1ygd

Go back to Zinc Binding Sites List in 1ygd
Zinc 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 Zinc with other atoms in the Zn 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
C:Zn142

b:21.8
occ:1.00
ZN C:ZNH142 0.0 21.8 1.0
NE2 C:HIS87 2.0 21.3 1.0
NC C:ZNH142 2.0 20.5 1.0
NA C:ZNH142 2.1 20.6 1.0
ND C:ZNH142 2.1 20.6 1.0
NB C:ZNH142 2.1 19.9 1.0
O C:HOH256 2.6 42.7 1.0
CE1 C:HIS87 2.8 22.2 1.0
C4C C:ZNH142 3.0 20.6 1.0
C1C C:ZNH142 3.1 20.7 1.0
C1D C:ZNH142 3.1 21.0 1.0
C4A C:ZNH142 3.1 19.9 1.0
C1B C:ZNH142 3.1 19.4 1.0
C1A C:ZNH142 3.1 20.3 1.0
C4D C:ZNH142 3.1 20.4 1.0
C4B C:ZNH142 3.1 19.4 1.0
CD2 C:HIS87 3.1 23.2 1.0
CHD C:ZNH142 3.4 21.9 1.0
CHB C:ZNH142 3.4 19.7 1.0
CHA C:ZNH142 3.5 20.2 1.0
CHC C:ZNH142 3.5 19.8 1.0
ND1 C:HIS87 4.0 23.6 1.0
CG C:HIS87 4.2 24.5 1.0
C2C C:ZNH142 4.2 21.1 1.0
C3C C:ZNH142 4.2 20.9 1.0
C3A C:ZNH142 4.3 19.5 1.0
C2A C:ZNH142 4.3 20.0 1.0
C2B C:ZNH142 4.3 19.3 1.0
C2D C:ZNH142 4.3 20.1 1.0
C3B C:ZNH142 4.3 19.2 1.0
C3D C:ZNH142 4.3 20.2 1.0
CD1 C:LEU91 4.4 25.5 1.0
CE1 C:HIS58 4.7 25.0 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: Thu Oct 29 07:42:19 2020
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