Atomistry » Iron » PDB 6azu-6bpt » 6bnr
Atomistry »
  Iron »
    PDB 6azu-6bpt »
      6bnr »

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

Go back to Iron Binding Sites List in 6bnr
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

Go back to Iron Binding Sites List in 6bnr
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

Go back to Iron Binding Sites List in 6bnr
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

Go back to Iron Binding Sites List in 6bnr
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: Tue Aug 6 14:20:44 2024

Last articles

Ca in 5KVA
Ca in 5KWS
Ca in 5KV9
Ca in 5KV8
Ca in 5KTV
Ca in 5KTY
Ca in 5KTI
Ca in 5KN0
Ca in 5KTH
Ca in 5KSA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy