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Iron in PDB 6xd9: Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039)

Protein crystallography data

The structure of Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039), PDB code: 6xd9 was solved by P.P.Pagare, M.K.Safo, F.N.Musayev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.34 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.778, 82.628, 104.997, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25.8

Iron Binding Sites:

The binding sites of Iron atom in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039) (pdb code 6xd9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039), PDB code: 6xd9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6xd9

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Iron binding site 1 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:26.6
occ:1.00
 FE A:HEM202 0.0 26.6 1.0
C A:CMO201 1.9 25.4 1.0
NC A:HEM202 2.0 26.5 1.0
ND A:HEM202 2.0 25.8 1.0
NA A:HEM202 2.1 26.5 1.0
NB A:HEM202 2.1 25.4 1.0
NE2 A:HIS87 2.1 24.5 1.0
O A:CMO201 3.0 28.5 1.0
C4C A:HEM202 3.0 25.8 1.0
C1D A:HEM202 3.0 25.1 1.0
C1C A:HEM202 3.1 24.3 1.0
C4D A:HEM202 3.1 28.3 1.0
CE1 A:HIS87 3.1 23.8 1.0
C1A A:HEM202 3.1 25.3 1.0
C4A A:HEM202 3.1 25.0 1.0
C1B A:HEM202 3.1 23.7 1.0
C4B A:HEM202 3.1 25.7 1.0
CD2 A:HIS87 3.1 21.6 1.0
CHD A:HEM202 3.4 23.8 1.0
CHA A:HEM202 3.4 27.7 1.0
CHC A:HEM202 3.5 24.7 1.0
CHB A:HEM202 3.5 23.4 1.0
ND1 A:HIS87 4.2 22.1 1.0
C3C A:HEM202 4.3 25.6 1.0
CG A:HIS87 4.3 20.1 1.0
C2C A:HEM202 4.3 26.0 1.0
C2D A:HEM202 4.3 26.1 1.0
C3D A:HEM202 4.3 26.6 1.0
C2A A:HEM202 4.3 28.0 1.0
C3A A:HEM202 4.3 26.3 1.0
C2B A:HEM202 4.3 24.2 1.0
C3B A:HEM202 4.3 23.7 1.0
NE2 A:HIS58 4.5 27.6 1.0
CG2 A:VAL62 5.0 24.9 1.0

Iron binding site 2 out of 4 in 6xd9

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Iron binding site 2 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:31.8
occ:1.00
 FE B:HEM202 0.0 31.8 1.0
NE2 B:HIS92 1.8 28.2 1.0
C B:CMO201 1.9 28.2 1.0
NC B:HEM202 2.0 28.9 1.0
NA B:HEM202 2.1 31.5 1.0
ND B:HEM202 2.1 30.5 1.0
NB B:HEM202 2.1 28.1 1.0
CD2 B:HIS92 2.8 28.5 1.0
CE1 B:HIS92 2.8 31.0 1.0
O B:CMO201 3.0 27.3 1.0
C1C B:HEM202 3.1 30.7 1.0
C4C B:HEM202 3.1 29.8 1.0
C4D B:HEM202 3.1 29.1 1.0
C1A B:HEM202 3.1 31.3 1.0
C1D B:HEM202 3.1 33.9 1.0
C4B B:HEM202 3.1 26.8 1.0
C4A B:HEM202 3.1 30.9 1.0
C1B B:HEM202 3.1 26.9 1.0
CHA B:HEM202 3.4 32.1 1.0
CHC B:HEM202 3.4 26.9 1.0
CHD B:HEM202 3.4 29.0 1.0
CHB B:HEM202 3.5 28.1 1.0
ND1 B:HIS92 3.9 29.4 1.0
CG B:HIS92 3.9 29.7 1.0
C2C B:HEM202 4.3 30.0 1.0
C3C B:HEM202 4.3 29.4 1.0
C2A B:HEM202 4.3 32.4 1.0
C3D B:HEM202 4.3 32.5 1.0
C2B B:HEM202 4.3 26.4 1.0
C3A B:HEM202 4.3 30.0 1.0
C2D B:HEM202 4.3 32.1 1.0
C3B B:HEM202 4.3 27.8 1.0
NE2 B:HIS63 4.4 32.1 1.0

Iron binding site 3 out of 4 in 6xd9

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Iron binding site 3 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:24.9
occ:1.00
 FE C:HEM202 0.0 24.9 1.0
C C:CMO201 1.9 24.6 1.0
NE2 C:HIS87 2.0 24.8 1.0
NC C:HEM202 2.0 22.3 1.0
NA C:HEM202 2.1 25.1 1.0
ND C:HEM202 2.1 25.7 1.0
NB C:HEM202 2.1 21.8 1.0
O C:CMO201 2.9 25.8 1.0
CD2 C:HIS87 2.9 23.4 1.0
CE1 C:HIS87 3.0 24.8 1.0
C4C C:HEM202 3.0 24.1 1.0
C1D C:HEM202 3.1 24.9 1.0
C1A C:HEM202 3.1 27.8 1.0
C1C C:HEM202 3.1 24.9 1.0
C4A C:HEM202 3.1 23.2 1.0
C4D C:HEM202 3.1 27.7 1.0
C4B C:HEM202 3.1 23.0 1.0
C1B C:HEM202 3.1 22.1 1.0
CHD C:HEM202 3.4 24.1 1.0
CHA C:HEM202 3.4 25.6 1.0
CHC C:HEM202 3.5 22.3 1.0
CHB C:HEM202 3.5 22.8 1.0
ND1 C:HIS87 4.1 24.3 1.0
CG C:HIS87 4.1 24.8 1.0
C3C C:HEM202 4.3 22.3 1.0
C2C C:HEM202 4.3 24.2 1.0
C2A C:HEM202 4.3 25.0 1.0
C3A C:HEM202 4.3 25.1 1.0
C2D C:HEM202 4.3 24.1 1.0
C3D C:HEM202 4.3 24.5 1.0
C2B C:HEM202 4.3 24.8 1.0
C3B C:HEM202 4.3 23.3 1.0
NE2 C:HIS58 4.4 28.0 1.0

Iron binding site 4 out of 4 in 6xd9

Go back to Iron Binding Sites List in 6xd9
Iron binding site 4 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 2- Hydroxy-6-((6-(Hydroxymethyl)Pyridin-2-Yl)Methoxy)Benzaldehyde (VZHE039) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:27.7
occ:1.00
 FE D:HEM202 0.0 27.7 1.0
C D:CMO201 1.9 25.3 1.0
ND D:HEM202 2.1 25.6 1.0
NC D:HEM202 2.1 26.7 1.0
NA D:HEM202 2.1 23.9 1.0
NB D:HEM202 2.1 21.8 1.0
NE2 D:HIS92 2.1 23.9 1.0
O D:CMO201 3.0 26.9 1.0
CD2 D:HIS92 3.0 25.6 1.0
C1D D:HEM202 3.1 25.0 1.0
C4D D:HEM202 3.1 25.6 1.0
C4C D:HEM202 3.1 26.7 1.0
C1A D:HEM202 3.1 25.0 1.0
C1C D:HEM202 3.1 26.6 1.0
C4A D:HEM202 3.1 27.0 1.0
C1B D:HEM202 3.1 24.6 1.0
C4B D:HEM202 3.1 25.6 1.0
CE1 D:HIS92 3.2 25.9 1.0
CHD D:HEM202 3.4 25.2 1.0
CHA D:HEM202 3.4 24.7 1.0
CHB D:HEM202 3.5 25.9 1.0
CHC D:HEM202 3.5 25.4 1.0
CG D:HIS92 4.2 27.4 1.0
ND1 D:HIS92 4.2 28.0 1.0
C3D D:HEM202 4.3 24.6 1.0
C3C D:HEM202 4.3 25.3 1.0
C2D D:HEM202 4.3 27.1 1.0
C2C D:HEM202 4.3 25.2 1.0
C2A D:HEM202 4.3 26.4 1.0
C3A D:HEM202 4.3 26.9 1.0
C2B D:HEM202 4.3 25.7 1.0
C3B D:HEM202 4.4 26.4 1.0
NE2 D:HIS63 4.4 26.4 1.0
CG2 D:VAL67 4.8 25.5 1.0

Reference:

O.Abdulmalik, P.P.Pagare, B.Huang, G.G.Xu, M.S.Ghatge, X.Xu, Q.Chen, N.Anabaraonye, F.N.Musayev, A.M.Omar, J.Venitz, Y.Zhang, M.K.Safo. Vzhe-039, A Novel Antisickling Agent That Prevents Erythrocyte Sickling Under Both Hypoxic and Anoxic Conditions. Sci Rep V. 10 20277 2020.
ISSN: ESSN 2045-2322
PubMed: 33219275
DOI: 10.1038/S41598-020-77171-2
Page generated: Wed Aug 7 15:20:53 2024

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