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Iron in PDB 2w6v: Structure of Human Deoxy Hemoglobin A in Complex with Xenon

Protein crystallography data

The structure of Structure of Human Deoxy Hemoglobin A in Complex with Xenon, PDB code: 2w6v was solved by A.E.Miele, F.Draghi, G.Sciara, K.A.Johnson, F.Renzi, B.Vallone, M.Brunori, C.Savino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.90 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.645, 82.328, 53.552, 90.00, 99.79, 90.00
R / Rfree (%) 16.2 / 21.6

Other elements in 2w6v:

The structure of Structure of Human Deoxy Hemoglobin A in Complex with Xenon also contains other interesting chemical elements:

Xenon (Xe) 15 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon (pdb code 2w6v). 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 Human Deoxy Hemoglobin A in Complex with Xenon, PDB code: 2w6v:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2w6v

Go back to Iron Binding Sites List in 2w6v
Iron binding site 1 out of 4 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1142

b:19.6
occ:1.00
FE A:HEM1142 0.0 19.6 1.0
NB A:HEM1142 2.1 18.4 1.0
NA A:HEM1142 2.1 19.7 1.0
NC A:HEM1142 2.2 19.0 1.0
ND A:HEM1142 2.2 17.2 1.0
NE2 A:HIS87 2.3 18.4 1.0
C4B A:HEM1142 3.1 17.3 1.0
CE1 A:HIS87 3.1 16.8 1.0
C1B A:HEM1142 3.1 19.0 1.0
C1C A:HEM1142 3.1 18.4 1.0
C1A A:HEM1142 3.1 17.3 1.0
C4D A:HEM1142 3.1 18.6 1.0
C4A A:HEM1142 3.2 18.8 1.0
C4C A:HEM1142 3.2 17.7 1.0
C1D A:HEM1142 3.2 16.3 1.0
CD2 A:HIS87 3.4 16.7 1.0
CHC A:HEM1142 3.4 16.6 1.0
CHB A:HEM1142 3.5 16.6 1.0
O A:HOH2071 3.5 23.0 1.0
CHA A:HEM1142 3.5 17.7 1.0
CHD A:HEM1142 3.6 16.9 1.0
ND1 A:HIS87 4.3 17.0 1.0
C3B A:HEM1142 4.3 17.0 1.0
CE1 A:HIS58 4.3 23.7 1.0
C2B A:HEM1142 4.3 17.8 1.0
C2A A:HEM1142 4.4 20.3 1.0
C2C A:HEM1142 4.4 17.4 1.0
C3D A:HEM1142 4.4 17.8 1.0
C3A A:HEM1142 4.4 18.5 1.0
C3C A:HEM1142 4.4 17.1 1.0
NE2 A:HIS58 4.4 21.1 1.0
C2D A:HEM1142 4.4 17.1 1.0
CG A:HIS87 4.4 18.4 1.0
CD1 A:LEU91 4.5 17.4 1.0

Iron binding site 2 out of 4 in 2w6v

Go back to Iron Binding Sites List in 2w6v
Iron binding site 2 out of 4 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1147

b:17.0
occ:1.00
FE B:HEM1147 0.0 17.0 1.0
NB B:HEM1147 2.1 15.7 1.0
NC B:HEM1147 2.1 13.7 1.0
ND B:HEM1147 2.2 15.4 1.0
NA B:HEM1147 2.2 14.2 1.0
NE2 B:HIS92 2.2 14.3 1.0
C1B B:HEM1147 3.1 14.8 1.0
CE1 B:HIS92 3.1 13.3 1.0
C1C B:HEM1147 3.1 14.6 1.0
C4B B:HEM1147 3.1 13.7 1.0
C1D B:HEM1147 3.1 17.1 1.0
C4C B:HEM1147 3.1 15.9 1.0
C1A B:HEM1147 3.1 16.3 1.0
C4A B:HEM1147 3.2 15.3 1.0
C4D B:HEM1147 3.2 16.5 1.0
CD2 B:HIS92 3.2 16.5 1.0
CHD B:HEM1147 3.5 14.4 1.0
CHB B:HEM1147 3.5 16.2 1.0
CHC B:HEM1147 3.5 15.0 1.0
CHA B:HEM1147 3.5 16.1 1.0
CG2 B:VAL67 4.1 18.4 1.0
NE2 B:HIS63 4.2 21.0 1.0
ND1 B:HIS92 4.2 13.5 1.0
CG B:HIS92 4.3 16.0 1.0
C2B B:HEM1147 4.4 15.4 1.0
C3B B:HEM1147 4.4 14.5 1.0
C2A B:HEM1147 4.4 17.9 1.0
C2C B:HEM1147 4.4 16.4 1.0
C3A B:HEM1147 4.4 16.3 1.0
C2D B:HEM1147 4.4 16.4 1.0
C3D B:HEM1147 4.4 17.2 1.0
C3C B:HEM1147 4.4 14.8 1.0
CE1 B:HIS63 4.5 21.8 1.0
CD1 B:LEU96 4.9 16.0 1.0

Iron binding site 3 out of 4 in 2w6v

Go back to Iron Binding Sites List in 2w6v
Iron binding site 3 out of 4 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1142

b:17.3
occ:1.00
FE C:HEM1142 0.0 17.3 1.0
NA C:HEM1142 2.1 17.9 1.0
ND C:HEM1142 2.1 15.2 1.0
NB C:HEM1142 2.1 15.7 1.0
NC C:HEM1142 2.2 15.1 1.0
NE2 C:HIS87 2.2 14.7 1.0
CE1 C:HIS87 3.0 14.9 1.0
C1D C:HEM1142 3.1 14.1 1.0
C4D C:HEM1142 3.1 15.5 1.0
C4A C:HEM1142 3.1 17.3 1.0
C1A C:HEM1142 3.1 14.7 1.0
C1C C:HEM1142 3.2 14.6 1.0
C1B C:HEM1142 3.2 16.5 1.0
C4B C:HEM1142 3.2 16.9 1.0
C4C C:HEM1142 3.2 14.4 1.0
CD2 C:HIS87 3.3 13.6 1.0
CHA C:HEM1142 3.5 15.3 1.0
CHB C:HEM1142 3.5 16.7 1.0
CHC C:HEM1142 3.5 15.3 1.0
CHD C:HEM1142 3.5 13.4 1.0
O C:HOH2143 3.5 27.6 1.0
CE1 C:HIS58 4.2 22.1 1.0
ND1 C:HIS87 4.2 14.0 1.0
C2D C:HEM1142 4.3 17.0 1.0
C3D C:HEM1142 4.3 17.0 1.0
NE2 C:HIS58 4.3 21.0 1.0
CG C:HIS87 4.4 14.5 1.0
C2A C:HEM1142 4.4 15.5 1.0
C3A C:HEM1142 4.4 17.3 1.0
C2C C:HEM1142 4.4 13.4 1.0
C3C C:HEM1142 4.4 12.4 1.0
C3B C:HEM1142 4.4 17.8 1.0
C2B C:HEM1142 4.4 16.9 1.0
CD1 C:LEU91 4.4 17.0 1.0

Iron binding site 4 out of 4 in 2w6v

Go back to Iron Binding Sites List in 2w6v
Iron binding site 4 out of 4 in the Structure of Human Deoxy Hemoglobin A in Complex with Xenon


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Human Deoxy Hemoglobin A in Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1147

b:17.5
occ:1.00
FE D:HEM1147 0.0 17.5 1.0
NB D:HEM1147 2.1 15.3 1.0
NA D:HEM1147 2.1 15.8 1.0
ND D:HEM1147 2.1 16.4 1.0
NE2 D:HIS92 2.1 16.4 1.0
NC D:HEM1147 2.2 15.8 1.0
CE1 D:HIS92 3.1 17.4 1.0
C1A D:HEM1147 3.1 18.1 1.0
C1B D:HEM1147 3.1 16.4 1.0
C4D D:HEM1147 3.1 16.9 1.0
C4B D:HEM1147 3.1 15.5 1.0
C4A D:HEM1147 3.1 15.2 1.0
C1D D:HEM1147 3.1 17.7 1.0
CD2 D:HIS92 3.2 17.2 1.0
C4C D:HEM1147 3.2 14.2 1.0
C1C D:HEM1147 3.2 15.8 1.0
CHA D:HEM1147 3.4 15.5 1.0
CHB D:HEM1147 3.5 16.6 1.0
CHC D:HEM1147 3.5 13.4 1.0
CHD D:HEM1147 3.5 14.0 1.0
ND1 D:HIS92 4.2 15.8 1.0
NE2 D:HIS63 4.2 18.7 1.0
CG D:HIS92 4.3 17.1 1.0
C3B D:HEM1147 4.3 17.4 1.0
C2B D:HEM1147 4.3 18.1 1.0
C2A D:HEM1147 4.3 16.8 1.0
C3D D:HEM1147 4.3 15.4 1.0
C3A D:HEM1147 4.4 15.9 1.0
C2D D:HEM1147 4.4 17.7 1.0
C2C D:HEM1147 4.4 16.2 1.0
C3C D:HEM1147 4.4 14.9 1.0
CG2 D:VAL67 4.5 17.6 1.0
CD1 D:LEU96 4.7 13.1 1.0
CE1 D:HIS63 4.7 16.9 1.0

Reference:

C.Savino, A.E.Miele, F.Draghi, K.A.Johnson, G.Sciara, M.Brunori, B.Vallone. Pattern of Cavities in Globins: the Case of Human Hemoglobin. Biopolymers V. 91 1097 2009.
ISSN: ISSN 0006-3525
PubMed: 19365817
DOI: 10.1002/BIP.21201
Page generated: Sun Dec 13 14:55:04 2020

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