Iron in PDB 5kdq: Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid

The structure of Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid, PDB code: 5kdq was solved by M.H.Ahmed, A.M.Omar, M.K.Safo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.64 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.222, 80.830, 53.397, 90.00, 80.77, 90.00
R / Rfree (%)	19.2 / 25.7

The structure of Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid (pdb code 5kdq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid, PDB code: 5kdq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:25.1 occ:1.00 FE A:HEM201 0.0 25.1 1.0 NB A:HEM201 2.0 20.2 1.0 NA A:HEM201 2.1 25.4 1.0 ND A:HEM201 2.1 23.2 1.0 NC A:HEM201 2.1 22.0 1.0 NE2 A:HIS87 2.2 20.8 1.0 C4B A:HEM201 3.0 24.8 1.0 CE1 A:HIS87 3.0 24.4 1.0 C1B A:HEM201 3.1 22.6 1.0 C1A A:HEM201 3.1 21.0 1.0 C4D A:HEM201 3.1 22.9 1.0 C4A A:HEM201 3.1 22.6 1.0 C1C A:HEM201 3.1 19.9 1.0 C1D A:HEM201 3.2 23.4 1.0 C4C A:HEM201 3.2 20.8 1.0 CD2 A:HIS87 3.3 21.9 1.0 CHA A:HEM201 3.4 19.3 1.0 CHC A:HEM201 3.4 21.1 1.0 O A:HOH331 3.4 21.0 1.0 CHB A:HEM201 3.5 22.3 1.0 CHD A:HEM201 3.6 21.8 1.0 ND1 A:HIS87 4.2 22.4 1.0 C3B A:HEM201 4.2 20.6 1.0 C2B A:HEM201 4.3 22.6 1.0 C2A A:HEM201 4.3 26.2 1.0 CE1 A:HIS58 4.3 28.6 1.0 C3A A:HEM201 4.3 25.3 1.0 C3D A:HEM201 4.3 23.8 1.0 CG A:HIS87 4.4 22.4 1.0 C2C A:HEM201 4.4 21.2 1.0 C2D A:HEM201 4.4 20.6 1.0 C3C A:HEM201 4.4 21.0 1.0 CD1 A:LEU91 4.4 23.3 1.0 NE2 A:HIS58 4.4 26.4 1.0

Iron binding site 2 out of 4 in the Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:31.3 occ:1.00 FE B:HEM201 0.0 31.3 1.0 NC B:HEM201 2.0 25.0 1.0 NB B:HEM201 2.1 31.2 1.0 ND B:HEM201 2.1 30.8 1.0 NA B:HEM201 2.1 37.6 1.0 NE2 B:HIS92 2.2 26.4 1.0 C1C B:HEM201 3.0 26.3 1.0 C4C B:HEM201 3.1 30.0 1.0 C4B B:HEM201 3.1 27.0 1.0 C1D B:HEM201 3.1 27.4 1.0 C4D B:HEM201 3.1 33.5 1.0 C1A B:HEM201 3.1 34.5 1.0 CE1 B:HIS92 3.1 29.8 1.0 C1B B:HEM201 3.2 32.6 1.0 CD2 B:HIS92 3.2 25.6 1.0 C4A B:HEM201 3.2 36.0 1.0 CHC B:HEM201 3.4 27.9 1.0 CHD B:HEM201 3.4 27.6 1.0 CHA B:HEM201 3.5 33.6 1.0 CHB B:HEM201 3.5 29.1 1.0 CG2 B:VAL67 3.7 34.7 1.0 ND1 B:HIS92 4.3 28.1 1.0 C2C B:HEM201 4.3 31.9 1.0 C3C B:HEM201 4.3 26.4 1.0 C3B B:HEM201 4.3 33.0 1.0 CG B:HIS92 4.3 30.6 1.0 C2D B:HEM201 4.3 29.5 1.0 C2B B:HEM201 4.3 31.9 1.0 C2A B:HEM201 4.4 36.6 1.0 NE2 B:HIS63 4.4 34.5 1.0 C3D B:HEM201 4.4 32.3 1.0 C3A B:HEM201 4.4 36.3 1.0 CE1 B:HIS63 4.6 36.4 1.0 CD1 B:LEU96 4.9 22.6 1.0

Iron binding site 3 out of 4 in the Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:22.7 occ:1.00 FE C:HEM201 0.0 22.7 1.0 NC C:HEM201 2.0 19.2 1.0 ND C:HEM201 2.1 22.4 1.0 NB C:HEM201 2.1 18.3 1.0 NA C:HEM201 2.1 24.4 1.0 NE2 C:HIS87 2.2 21.5 1.0 C1C C:HEM201 3.0 19.1 1.0 C4B C:HEM201 3.0 17.8 1.0 C4D C:HEM201 3.0 23.1 1.0 C4C C:HEM201 3.1 24.1 1.0 C1A C:HEM201 3.1 22.2 1.0 C1D C:HEM201 3.1 24.9 1.0 CE1 C:HIS87 3.1 22.9 1.0 C1B C:HEM201 3.2 21.3 1.0 C4A C:HEM201 3.2 22.8 1.0 CD2 C:HIS87 3.2 22.1 1.0 CHC C:HEM201 3.3 16.2 1.0 CHA C:HEM201 3.4 22.4 1.0 CHD C:HEM201 3.5 21.8 1.0 O C:HOH327 3.5 26.8 1.0 CHB C:HEM201 3.6 22.9 1.0 CE1 C:HIS58 4.1 27.1 1.0 C2C C:HEM201 4.2 20.3 1.0 C3C C:HEM201 4.3 22.0 1.0 ND1 C:HIS87 4.3 25.2 1.0 C3D C:HEM201 4.3 24.9 1.0 C3B C:HEM201 4.3 17.9 1.0 C2A C:HEM201 4.3 23.8 1.0 C2D C:HEM201 4.3 21.8 1.0 NE2 C:HIS58 4.4 23.4 1.0 CG C:HIS87 4.4 25.1 1.0 C2B C:HEM201 4.4 18.6 1.0 C3A C:HEM201 4.4 22.9 1.0 CD1 C:LEU91 4.4 28.1 1.0

Iron binding site 4 out of 4 in the Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Deoxyhemoglobin in Complex with An Aryloxyalkanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:25.6 occ:1.00 FE D:HEM201 0.0 25.6 1.0 NB D:HEM201 2.1 23.2 1.0 NC D:HEM201 2.1 22.2 1.0 NA D:HEM201 2.1 23.4 1.0 ND D:HEM201 2.1 25.4 1.0 NE2 D:HIS92 2.2 21.4 1.0 CE1 D:HIS92 2.9 21.3 1.0 C1B D:HEM201 3.1 22.6 1.0 C4B D:HEM201 3.1 19.1 1.0 C4A D:HEM201 3.1 27.5 1.0 C1D D:HEM201 3.1 27.5 1.0 C4C D:HEM201 3.1 22.8 1.0 C1C D:HEM201 3.1 21.6 1.0 C4D D:HEM201 3.1 24.6 1.0 C1A D:HEM201 3.1 26.9 1.0 CD2 D:HIS92 3.3 22.0 1.0 CHB D:HEM201 3.4 24.4 1.0 CHD D:HEM201 3.4 17.9 1.0 CHC D:HEM201 3.5 19.5 1.0 CHA D:HEM201 3.5 26.6 1.0 CG2 D:VAL67 3.9 27.3 1.0 ND1 D:HIS92 4.2 25.9 1.0 C3B D:HEM201 4.3 21.5 1.0 C2B D:HEM201 4.3 21.9 1.0 C3A D:HEM201 4.3 33.5 1.0 C3C D:HEM201 4.3 20.5 1.0 C2C D:HEM201 4.3 24.1 1.0 C2D D:HEM201 4.3 25.0 1.0 C2A D:HEM201 4.3 26.2 1.0 C3D D:HEM201 4.3 23.7 1.0 CE1 D:HIS63 4.4 25.9 1.0 CG D:HIS92 4.4 23.4 1.0 NE2 D:HIS63 4.5 26.4 1.0 CD1 D:LEU96 4.9 25.2 1.0

A.M.Omar, M.A.Mahran, M.S.Ghatge, F.H.Bamane, M.H.Ahmed, M.E.El-Araby, O.Abdulmalik, M.K.Safo. Aryloxyalkanoic Acids As Non-Covalent Modifiers of the Allosteric Properties of Hemoglobin. Molecules V. 21 2016.
ISSN: ESSN 1420-3049
PubMed: 27529207
DOI: 10.3390/MOLECULES21081057