Iron in PDB 6bnr: Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310)

Protein crystallography data

The structure of Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310), PDB code: 6bnr was solved by P.P.Pagare, F.N.Musayev, M.K.Safo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.40 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.817, 83.550, 104.915, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26.4

Iron Binding Sites:

The binding sites of Iron atom in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310) (pdb code 6bnr). 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 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310), PDB code: 6bnr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6bnr

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Iron binding site 1 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310)


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 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:29.7
occ:1.00
 FE A:HEM202 0.0 29.7 1.0
C A:CMO201 1.8 27.8 1.0
ND A:HEM202 2.0 29.5 1.0
NC A:HEM202 2.0 28.3 1.0
NB A:HEM202 2.0 27.7 1.0
NE2 A:HIS87 2.0 28.2 1.0
NA A:HEM202 2.1 29.3 1.0
CE1 A:HIS87 3.0 28.9 1.0
C1D A:HEM202 3.0 29.8 1.0
C1C A:HEM202 3.1 26.4 1.0
C4B A:HEM202 3.1 27.9 1.0
O A:CMO201 3.1 33.7 1.0
C4D A:HEM202 3.1 30.2 1.0
C4C A:HEM202 3.1 29.1 1.0
CD2 A:HIS87 3.1 28.6 1.0
C1B A:HEM202 3.1 30.1 1.0
C1A A:HEM202 3.1 28.7 1.0
C4A A:HEM202 3.1 28.9 1.0
CHC A:HEM202 3.4 27.9 1.0
CHD A:HEM202 3.4 27.4 1.0
CHA A:HEM202 3.5 29.4 1.0
CHB A:HEM202 3.5 28.6 1.0
ND1 A:HIS87 4.2 29.7 1.0
CG A:HIS87 4.2 29.6 1.0
C3D A:HEM202 4.3 31.6 1.0
C2D A:HEM202 4.3 30.9 1.0
C3B A:HEM202 4.3 30.4 1.0
C2B A:HEM202 4.3 29.8 1.0
C2C A:HEM202 4.3 28.1 1.0
C3C A:HEM202 4.3 29.0 1.0
C3A A:HEM202 4.3 30.4 1.0
C2A A:HEM202 4.3 32.5 1.0
NE2 A:HIS58 4.4 33.0 1.0
CG2 A:VAL62 5.0 29.1 1.0

Iron binding site 2 out of 4 in 6bnr

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Iron binding site 2 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310)


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 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:35.5
occ:1.00
 FE B:HEM202 0.0 35.5 1.0
C B:CMO201 1.9 35.4 1.0
ND B:HEM202 2.0 37.9 1.0
NA B:HEM202 2.0 36.2 1.0
NC B:HEM202 2.0 36.6 1.0
NB B:HEM202 2.0 34.5 1.0
NE2 B:HIS92 2.0 33.5 1.0
CE1 B:HIS92 3.0 34.1 1.0
C1A B:HEM202 3.0 34.8 1.0
C4D B:HEM202 3.1 38.9 1.0
C1C B:HEM202 3.1 37.0 1.0
C4B B:HEM202 3.1 35.3 1.0
C1D B:HEM202 3.1 39.6 1.0
C4A B:HEM202 3.1 36.0 1.0
CD2 B:HIS92 3.1 35.0 1.0
C1B B:HEM202 3.1 33.2 1.0
C4C B:HEM202 3.1 37.4 1.0
O B:CMO201 3.1 37.2 1.0
CHA B:HEM202 3.4 35.8 1.0
CHC B:HEM202 3.4 33.7 1.0
CHD B:HEM202 3.5 38.9 1.0
CHB B:HEM202 3.5 33.9 1.0
ND1 B:HIS92 4.2 34.9 1.0
CG B:HIS92 4.2 35.6 1.0
C2A B:HEM202 4.3 36.9 1.0
C2C B:HEM202 4.3 37.5 1.0
C3D B:HEM202 4.3 41.3 1.0
C3A B:HEM202 4.3 34.9 1.0
C2B B:HEM202 4.3 34.2 1.0
C2D B:HEM202 4.3 40.5 1.0
C3B B:HEM202 4.3 34.5 1.0
C3C B:HEM202 4.3 38.3 1.0
NE2 B:HIS63 4.4 38.8 1.0

Iron binding site 3 out of 4 in 6bnr

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Iron binding site 3 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310)


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 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:29.2
occ:1.00
 FE C:HEM202 0.0 29.2 1.0
C C:CMO201 1.9 28.8 1.0
NA C:HEM202 2.0 29.4 1.0
ND C:HEM202 2.0 30.5 1.0
NB C:HEM202 2.0 27.9 1.0
NC C:HEM202 2.0 28.8 1.0
NE2 C:HIS87 2.0 27.5 1.0
CE1 C:HIS87 3.0 29.2 1.0
C4D C:HEM202 3.0 28.0 1.0
C4A C:HEM202 3.0 27.1 1.0
C1A C:HEM202 3.0 28.6 1.0
C1D C:HEM202 3.1 29.2 1.0
C1B C:HEM202 3.1 26.2 1.0
C4C C:HEM202 3.1 27.4 1.0
C1C C:HEM202 3.1 27.4 1.0
C4B C:HEM202 3.1 25.3 1.0
CD2 C:HIS87 3.1 28.3 1.0
O C:CMO201 3.1 33.1 1.0
CHA C:HEM202 3.4 28.7 1.0
CHB C:HEM202 3.4 26.8 1.0
CHD C:HEM202 3.4 27.7 1.0
CHC C:HEM202 3.5 25.7 1.0
ND1 C:HIS87 4.2 26.8 1.0
CG C:HIS87 4.2 27.6 1.0
C3D C:HEM202 4.3 30.6 1.0
C3A C:HEM202 4.3 30.2 1.0
C2A C:HEM202 4.3 30.2 1.0
C2D C:HEM202 4.3 28.5 1.0
C2B C:HEM202 4.3 26.6 1.0
C3B C:HEM202 4.3 26.2 1.0
C2C C:HEM202 4.3 28.0 1.0
C3C C:HEM202 4.3 29.2 1.0
NE2 C:HIS58 4.4 35.1 1.0
CG2 C:VAL62 4.8 26.8 1.0

Iron binding site 4 out of 4 in 6bnr

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Iron binding site 4 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310)


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 5- Methoxy-2-(Pyridin-2-Ylmethoxy)Benzaldehyde (INN310) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:34.0
occ:1.00
 FE D:HEM202 0.0 34.0 1.0
C D:CMO201 1.9 33.1 1.0
ND D:HEM202 2.0 32.1 1.0
NC D:HEM202 2.0 33.1 1.0
NB D:HEM202 2.0 33.1 1.0
NA D:HEM202 2.0 32.6 1.0
NE2 D:HIS92 2.0 33.8 1.0
C4D D:HEM202 3.0 30.8 1.0
CE1 D:HIS92 3.0 34.7 1.0
C1B D:HEM202 3.0 33.3 1.0
C1D D:HEM202 3.0 33.4 1.0
C1C D:HEM202 3.1 33.8 1.0
C4A D:HEM202 3.1 30.9 1.0
C4C D:HEM202 3.1 32.8 1.0
C4B D:HEM202 3.1 32.3 1.0
O D:CMO201 3.1 36.5 1.0
CD2 D:HIS92 3.1 35.4 1.0
C1A D:HEM202 3.1 31.4 1.0
CHB D:HEM202 3.4 33.5 1.0
CHD D:HEM202 3.4 33.1 1.0
CHC D:HEM202 3.4 31.8 1.0
CHA D:HEM202 3.5 31.8 1.0
ND1 D:HIS92 4.2 35.4 1.0
CG D:HIS92 4.2 33.9 1.0
C3D D:HEM202 4.3 34.5 1.0
C2B D:HEM202 4.3 35.4 1.0
C2C D:HEM202 4.3 32.5 1.0
C3C D:HEM202 4.3 33.1 1.0
C2D D:HEM202 4.3 33.9 1.0
C3A D:HEM202 4.3 31.2 1.0
C2A D:HEM202 4.3 32.1 1.0
C3B D:HEM202 4.3 34.5 1.0
NE2 D:HIS63 4.5 37.2 1.0
CG2 D:VAL67 4.8 33.5 1.0

Reference:

P.P.Pagare, M.S.Ghatge, F.N.Musayev, T.M.Deshpande, Q.Chen, C.Braxton, S.Kim, J.Venitz, Y.Zhang, O.Abdulmalik, M.K.Safo. Rational Design of Pyridyl Derivatives of Vanillin For the Treatment of Sickle Cell Disease. Bioorg. Med. Chem. V. 26 2530 2018.
ISSN: ESSN 1464-3391
PubMed: 29655608
DOI: 10.1016/J.BMC.2018.04.015
Page generated: Sun Dec 13 16:21:41 2020

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