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Iron in PDB 2z8a: Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe

Protein crystallography data

The structure of Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe, PDB code: 2z8a was solved by J.E.Knapp, W.E.Royer Jr., K.Nienhaus, P.Palladino, G.U.Nienhaus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.30 / 1.06
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 92.660, 43.390, 82.290, 90.00, 122.02, 90.00
R / Rfree (%) 14.3 / 16.2

Other elements in 2z8a:

The structure of Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe also contains other interesting chemical elements:

Xenon (Xe) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe (pdb code 2z8a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe, PDB code: 2z8a:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 2z8a

Go back to Iron Binding Sites List in 2z8a
Iron binding site 1 out of 2 in the Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1147

b:6.9
occ:1.00
FE A:HEM1147 0.0 6.9 1.0
C A:CMO1148 1.8 9.2 1.0
NB A:HEM1147 2.0 8.2 1.0
ND A:HEM1147 2.0 8.1 1.0
NC A:HEM1147 2.0 8.1 1.0
NA A:HEM1147 2.0 7.8 1.0
NE2 A:HIS1101 2.0 7.7 1.0
O A:CMO1148 3.0 9.9 1.0
C4B A:HEM1147 3.0 8.2 1.0
CE1 A:HIS1101 3.0 8.3 1.0
C4D A:HEM1147 3.0 8.4 1.0
C1C A:HEM1147 3.0 8.0 1.0
C1A A:HEM1147 3.0 8.4 1.0
C4A A:HEM1147 3.0 8.2 1.0
C1D A:HEM1147 3.0 8.2 1.0
C4C A:HEM1147 3.0 8.2 1.0
C1B A:HEM1147 3.0 8.7 1.0
CD2 A:HIS1101 3.1 8.0 1.0
CHC A:HEM1147 3.4 8.7 1.0
CHD A:HEM1147 3.4 8.9 1.0
CHA A:HEM1147 3.4 8.3 1.0
CHB A:HEM1147 3.4 8.9 1.0
ND1 A:HIS1101 4.1 8.5 1.0
CG A:HIS1101 4.2 7.9 1.0
C3B A:HEM1147 4.3 8.8 1.0
C2B A:HEM1147 4.3 9.2 1.0
C2D A:HEM1147 4.3 8.8 1.0
C2C A:HEM1147 4.3 8.5 1.0
C3C A:HEM1147 4.3 8.3 1.0
C3D A:HEM1147 4.3 8.9 1.0
C2A A:HEM1147 4.3 8.7 1.0
C3A A:HEM1147 4.3 8.6 1.0
CD1 A:LEU1073 4.5 11.9 1.0
CE1 A:HIS1069 4.6 10.6 1.0
CE1 A:PHE1111 4.8 10.8 1.0

Iron binding site 2 out of 2 in 2z8a

Go back to Iron Binding Sites List in 2z8a
Iron binding site 2 out of 2 in the Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis: I25W with Co Bound to Heme and in the Presence of 3 Atoms of Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe2147

b:6.8
occ:1.00
FE B:HEM2147 0.0 6.8 1.0
C B:CMO2148 1.8 8.8 1.0
NB B:HEM2147 2.0 7.8 1.0
ND B:HEM2147 2.0 7.9 1.0
NA B:HEM2147 2.0 7.9 1.0
NC B:HEM2147 2.0 7.8 1.0
NE2 B:HIS2101 2.0 7.7 1.0
O B:CMO2148 3.0 9.9 1.0
C4B B:HEM2147 3.0 7.8 1.0
CE1 B:HIS2101 3.0 8.1 1.0
C1A B:HEM2147 3.0 8.5 1.0
C4D B:HEM2147 3.0 8.2 1.0
C1B B:HEM2147 3.0 8.0 1.0
C1C B:HEM2147 3.0 7.5 1.0
C4A B:HEM2147 3.0 8.4 1.0
C1D B:HEM2147 3.0 8.7 1.0
C4C B:HEM2147 3.0 7.9 1.0
CD2 B:HIS2101 3.1 8.2 1.0
CHC B:HEM2147 3.4 8.0 1.0
CHA B:HEM2147 3.4 8.6 1.0
CHD B:HEM2147 3.4 8.6 1.0
CHB B:HEM2147 3.4 8.3 1.0
ND1 B:HIS2101 4.2 8.7 1.0
CG B:HIS2101 4.2 8.2 1.0
C2B B:HEM2147 4.3 8.5 1.0
C3B B:HEM2147 4.3 8.2 1.0
C2D B:HEM2147 4.3 9.7 1.0
C2A B:HEM2147 4.3 9.0 1.0
C2C B:HEM2147 4.3 7.9 1.0
C3C B:HEM2147 4.3 8.3 1.0
C3D B:HEM2147 4.3 9.2 1.0
C3A B:HEM2147 4.3 9.0 1.0
CD1 B:LEU2073 4.5 10.7 1.0
CE1 B:HIS2069 4.7 9.4 1.0
CE2 B:PHE2111 4.9 10.5 1.0
CZ B:PHE2051 5.0 11.6 1.0
CE1 B:PHE2051 5.0 11.2 1.0

Reference:

K.Nienhaus, J.E.Knapp, P.Palladino, W.E.Royer Jr., G.U.Nienhaus. Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca Inaequivalvis Biochemistry V. 46 14018 2007.
ISSN: ISSN 0006-2960
PubMed: 18001141
DOI: 10.1021/BI7016798
Page generated: Sun Dec 13 14:58:45 2020

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