Atomistry » Iron » PDB 6xai-6xyv » 6xd9
Atomistry »
  Iron »
    PDB 6xai-6xyv »
      6xd9 »

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

Go back to Iron Binding Sites List in 6xd9
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

Go back to Iron Binding Sites List in 6xd9
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

Go back to Iron Binding Sites List in 6xd9
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy