Iron in PDB 6xdt: Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate

Protein crystallography data

The structure of Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate, PDB code: 6xdt 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) 29.32 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.681, 82.977, 105.025, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23.9

Iron Binding Sites:

The binding sites of Iron atom in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate (pdb code 6xdt). 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 Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate, PDB code: 6xdt:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6xdt

Go back to Iron Binding Sites List in 6xdt
Iron binding site 1 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate


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 Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:31.4
occ:1.00
 FE A:HEM202 0.0 31.4 1.0
C A:CMO201 1.9 26.9 1.0
NE2 A:HIS87 2.0 27.8 1.0
NC A:HEM202 2.0 28.1 1.0
NA A:HEM202 2.0 28.9 1.0
NB A:HEM202 2.1 28.3 1.0
ND A:HEM202 2.1 27.3 1.0
CE1 A:HIS87 2.9 28.4 1.0
O A:CMO201 3.0 28.9 1.0
C1A A:HEM202 3.0 28.3 1.0
C1C A:HEM202 3.0 26.9 1.0
C4C A:HEM202 3.1 28.0 1.0
C4D A:HEM202 3.1 29.3 1.0
C4B A:HEM202 3.1 23.6 1.0
C4A A:HEM202 3.1 27.3 1.0
CD2 A:HIS87 3.1 26.4 1.0
C1D A:HEM202 3.1 27.3 1.0
C1B A:HEM202 3.1 24.6 1.0
CHC A:HEM202 3.4 24.4 1.0
CHA A:HEM202 3.4 30.3 1.0
CHD A:HEM202 3.5 25.8 1.0
CHB A:HEM202 3.5 27.6 1.0
ND1 A:HIS87 4.1 25.6 1.0
CG A:HIS87 4.2 24.0 1.0
C2A A:HEM202 4.3 31.5 1.0
C2C A:HEM202 4.3 24.6 1.0
C3C A:HEM202 4.3 26.8 1.0
C3A A:HEM202 4.3 28.7 1.0
C3D A:HEM202 4.3 30.1 1.0
C3B A:HEM202 4.3 23.4 1.0
C2B A:HEM202 4.3 25.5 1.0
C2D A:HEM202 4.3 28.8 1.0
NE2 A:HIS58 4.4 31.1 1.0
CG2 A:VAL62 4.9 25.4 1.0

Iron binding site 2 out of 4 in 6xdt

Go back to Iron Binding Sites List in 6xdt
Iron binding site 2 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate


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 Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:30.8
occ:1.00
 FE B:HEM202 0.0 30.8 1.0
C B:CMO201 1.9 28.1 1.0
NC B:HEM202 2.0 32.5 1.0
NB B:HEM202 2.1 28.8 1.0
ND B:HEM202 2.1 32.3 1.0
NE2 B:HIS92 2.1 27.2 1.0
NA B:HEM202 2.1 31.9 1.0
O B:CMO201 3.0 29.4 1.0
CD2 B:HIS92 3.0 27.9 1.0
C4C B:HEM202 3.0 31.8 1.0
C1C B:HEM202 3.0 30.8 1.0
C1D B:HEM202 3.1 33.2 1.0
C4B B:HEM202 3.1 28.1 1.0
C1B B:HEM202 3.1 27.6 1.0
C4D B:HEM202 3.1 31.7 1.0
C4A B:HEM202 3.1 29.7 1.0
C1A B:HEM202 3.1 30.4 1.0
CE1 B:HIS92 3.1 28.5 1.0
CHD B:HEM202 3.4 31.2 1.0
CHC B:HEM202 3.4 27.9 1.0
CHB B:HEM202 3.5 27.9 1.0
CHA B:HEM202 3.5 30.5 1.0
CG B:HIS92 4.2 28.7 1.0
ND1 B:HIS92 4.2 27.1 1.0
C2C B:HEM202 4.2 33.4 1.0
C3C B:HEM202 4.2 31.4 1.0
C2B B:HEM202 4.3 27.2 1.0
C3B B:HEM202 4.3 25.0 1.0
NE2 B:HIS63 4.3 30.0 1.0
C2D B:HEM202 4.3 33.2 1.0
C3D B:HEM202 4.3 34.4 1.0
C3A B:HEM202 4.3 31.0 1.0
C2A B:HEM202 4.3 30.1 1.0
CG2 B:VAL67 4.9 24.3 1.0

Iron binding site 3 out of 4 in 6xdt

Go back to Iron Binding Sites List in 6xdt
Iron binding site 3 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate


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 Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:25.8
occ:1.00
 FE C:HEM202 0.0 25.8 1.0
C C:CMO201 1.9 26.5 1.0
ND C:HEM202 2.0 24.5 1.0
NC C:HEM202 2.0 21.9 1.0
NA C:HEM202 2.0 24.5 1.0
NB C:HEM202 2.1 23.4 1.0
NE2 C:HIS87 2.1 24.7 1.0
O C:CMO201 3.0 28.0 1.0
C1A C:HEM202 3.0 27.0 1.0
C4D C:HEM202 3.0 28.6 1.0
C4C C:HEM202 3.0 25.1 1.0
C1D C:HEM202 3.0 26.8 1.0
CD2 C:HIS87 3.1 26.3 1.0
C1C C:HEM202 3.1 26.8 1.0
C4A C:HEM202 3.1 26.3 1.0
C4B C:HEM202 3.1 25.5 1.0
C1B C:HEM202 3.1 25.7 1.0
CE1 C:HIS87 3.1 26.2 1.0
CHA C:HEM202 3.4 26.4 1.0
CHD C:HEM202 3.4 21.2 1.0
CHC C:HEM202 3.4 25.6 1.0
CHB C:HEM202 3.5 24.2 1.0
ND1 C:HIS87 4.2 26.2 1.0
CG C:HIS87 4.2 26.3 1.0
C2A C:HEM202 4.3 28.3 1.0
C3C C:HEM202 4.3 24.4 1.0
C2D C:HEM202 4.3 23.7 1.0
C2C C:HEM202 4.3 25.2 1.0
C3D C:HEM202 4.3 26.1 1.0
C3A C:HEM202 4.3 25.3 1.0
C3B C:HEM202 4.3 24.4 1.0
C2B C:HEM202 4.3 24.3 1.0
NE2 C:HIS58 4.4 26.8 1.0
CG2 C:VAL62 4.9 25.4 1.0

Iron binding site 4 out of 4 in 6xdt

Go back to Iron Binding Sites List in 6xdt
Iron binding site 4 out of 4 in the Carbonmonoxy Hemoglobin in Complex with the Antisickling Agent Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate


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 Methyl 5-((2-Formyl-4-Methoxyphenoxy)Methyl)Picolinate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:26.9
occ:1.00
 FE D:HEM202 0.0 26.9 1.0
C D:CMO201 1.9 27.0 1.0
NC D:HEM202 2.0 26.3 1.0
ND D:HEM202 2.1 25.1 1.0
NA D:HEM202 2.1 25.5 1.0
NB D:HEM202 2.1 24.9 1.0
NE2 D:HIS92 2.1 24.5 1.0
O D:CMO201 2.9 28.8 1.0
C1C D:HEM202 3.1 26.9 1.0
C4C D:HEM202 3.1 24.8 1.0
CE1 D:HIS92 3.1 25.2 1.0
C4D D:HEM202 3.1 24.0 1.0
C1D D:HEM202 3.1 26.3 1.0
C1A D:HEM202 3.1 27.4 1.0
C4A D:HEM202 3.1 25.5 1.0
CD2 D:HIS92 3.1 25.9 1.0
C4B D:HEM202 3.1 25.2 1.0
C1B D:HEM202 3.1 24.9 1.0
CHC D:HEM202 3.4 24.4 1.0
CHD D:HEM202 3.4 25.9 1.0
CHA D:HEM202 3.4 26.0 1.0
CHB D:HEM202 3.5 27.0 1.0
ND1 D:HIS92 4.2 27.7 1.0
CG D:HIS92 4.2 28.2 1.0
C2C D:HEM202 4.3 27.9 1.0
C3C D:HEM202 4.3 26.5 1.0
C3D D:HEM202 4.3 28.3 1.0
C3A D:HEM202 4.3 25.2 1.0
C2D D:HEM202 4.3 31.0 1.0
C2A D:HEM202 4.3 28.0 1.0
C2B D:HEM202 4.3 21.9 1.0
C3B D:HEM202 4.3 25.8 1.0
NE2 D:HIS63 4.4 25.3 1.0
CG2 D:VAL67 4.7 30.7 1.0

Reference:

P.P.Pagare, M.S.Ghatge, Q.Chen, F.N.Musayev, J.Venitz, O.Abdulmalik, Y.Zhang, M.K.Safo. Exploration of Structure-Activity Relationship of Aromatic Aldehydes Bearing Pyridinylmethoxy-Methyl Esters As Novel Antisickling Agents. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33205981
DOI: 10.1021/ACS.JMEDCHEM.0C01287
Page generated: Sun Dec 13 17:28:08 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy