Iron in PDB 7ud7: Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom

The structure of Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom, PDB code: 7ud7 was solved by A.K.Donkor, 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)	26.36 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.344, 82.031, 53.454, 90, 99.49, 90
R / Rfree (%)	15.1 / 19.1

The binding sites of Iron atom in the Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom (pdb code 7ud7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom, PDB code: 7ud7:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:10.3 occ:1.00 FE A:HEM201 0.0 10.3 1.0 NE2 A:HIS87 2.1 9.4 1.0 NC A:HEM201 2.1 9.8 1.0 NA A:HEM201 2.1 10.2 1.0 ND A:HEM201 2.1 6.4 1.0 NB A:HEM201 2.1 10.9 1.0 CE1 A:HIS87 2.9 10.0 1.0 C1C A:HEM201 3.1 10.4 1.0 C4B A:HEM201 3.1 10.4 1.0 C1A A:HEM201 3.1 8.1 1.0 C4D A:HEM201 3.1 8.0 1.0 C4C A:HEM201 3.1 8.5 1.0 C4A A:HEM201 3.1 10.1 1.0 C1B A:HEM201 3.1 9.8 1.0 C1D A:HEM201 3.2 7.8 1.0 CD2 A:HIS87 3.2 9.8 1.0 CHC A:HEM201 3.4 9.6 1.0 CHA A:HEM201 3.4 9.8 1.0 O A:HOH342 3.4 15.6 1.0 CHB A:HEM201 3.5 9.4 1.0 CHD A:HEM201 3.5 8.0 1.0 ND1 A:HIS87 4.1 11.4 1.0 CG A:HIS87 4.3 10.2 1.0 C2C A:HEM201 4.3 9.1 1.0 C3B A:HEM201 4.3 12.4 1.0 CE1 A:HIS58 4.3 11.4 1.0 C2A A:HEM201 4.3 10.1 1.0 C3D A:HEM201 4.3 8.4 1.0 C3C A:HEM201 4.3 8.1 1.0 C2B A:HEM201 4.3 11.8 1.0 C3A A:HEM201 4.3 10.9 1.0 C2D A:HEM201 4.4 8.9 1.0 CD1 A:LEU91 4.4 9.1 1.0 NE2 A:HIS58 4.5 11.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:9.5 occ:1.00 FE B:HEM201 0.0 9.5 1.0 NC B:HEM201 2.1 7.6 1.0 NE2 B:HIS92 2.1 7.8 1.0 ND B:HEM201 2.1 7.1 1.0 NB B:HEM201 2.1 7.8 1.0 NA B:HEM201 2.1 7.4 1.0 CE1 B:HIS92 3.0 10.9 1.0 C4C B:HEM201 3.1 7.5 1.0 C1D B:HEM201 3.1 7.5 1.0 C1C B:HEM201 3.1 8.5 1.0 C1B B:HEM201 3.1 9.2 1.0 C4B B:HEM201 3.1 9.6 1.0 C1A B:HEM201 3.1 8.0 1.0 C4D B:HEM201 3.1 8.6 1.0 C4A B:HEM201 3.1 7.4 1.0 CD2 B:HIS92 3.2 10.4 1.0 CHD B:HEM201 3.4 8.3 1.0 CHB B:HEM201 3.5 8.5 1.0 CHC B:HEM201 3.5 9.7 1.0 CHA B:HEM201 3.5 11.5 1.0 CG2 B:VAL67 3.9 7.0 1.0 ND1 B:HIS92 4.1 10.5 1.0 CG B:HIS92 4.3 12.7 1.0 NE2 B:HIS63 4.3 11.0 1.0 C2D B:HEM201 4.3 9.1 1.0 C3C B:HEM201 4.3 7.1 1.0 C2B B:HEM201 4.3 9.8 1.0 C2C B:HEM201 4.3 9.0 1.0 C3B B:HEM201 4.3 10.4 1.0 C3D B:HEM201 4.3 8.4 1.0 C2A B:HEM201 4.3 8.8 1.0 C3A B:HEM201 4.3 9.0 1.0 CE1 B:HIS63 4.5 13.6 1.0 CD1 B:LEU96 5.0 10.4 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:8.8 occ:1.00 FE C:HEM201 0.0 8.8 1.0 NB C:HEM201 2.1 7.0 1.0 NE2 C:HIS87 2.1 5.2 1.0 NA C:HEM201 2.1 11.1 1.0 NC C:HEM201 2.1 6.8 1.0 ND C:HEM201 2.1 7.8 1.0 CE1 C:HIS87 2.9 8.6 1.0 C1A C:HEM201 3.1 9.3 1.0 C1B C:HEM201 3.1 6.3 1.0 C4B C:HEM201 3.1 6.9 1.0 C4A C:HEM201 3.1 10.7 1.0 C4D C:HEM201 3.1 8.6 1.0 C4C C:HEM201 3.1 7.0 1.0 C1C C:HEM201 3.1 5.1 1.0 C1D C:HEM201 3.1 4.8 1.0 CD2 C:HIS87 3.2 6.4 1.0 CHA C:HEM201 3.4 10.8 1.0 CHC C:HEM201 3.5 7.2 1.0 CHB C:HEM201 3.5 7.5 1.0 CHD C:HEM201 3.5 5.1 1.0 NE2 C:HIS58 4.0 15.1 1.0 ND1 C:HIS87 4.1 9.8 1.0 CG C:HIS87 4.3 9.2 1.0 C2B C:HEM201 4.3 6.3 1.0 C2A C:HEM201 4.3 8.4 1.0 C3B C:HEM201 4.3 6.2 1.0 C3A C:HEM201 4.3 10.3 1.0 C3D C:HEM201 4.3 10.5 1.0 C3C C:HEM201 4.3 5.2 1.0 C2C C:HEM201 4.3 8.6 1.0 C2D C:HEM201 4.3 11.9 1.0 CD1 C:LEU91 4.5 7.7 1.0 CE1 C:HIS58 4.5 10.2 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Deoxygenated Hemoglobin in Complex with 5HMF-No at 1.8 Angstrom within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:10.3 occ:1.00 FE D:HEM201 0.0 10.3 1.0 NB D:HEM201 2.1 7.9 1.0 NE2 D:HIS92 2.1 9.3 1.0 NC D:HEM201 2.1 7.5 1.0 NA D:HEM201 2.1 9.0 1.0 ND D:HEM201 2.1 8.2 1.0 CE1 D:HIS92 3.0 9.1 1.0 C4B D:HEM201 3.1 7.0 1.0 C4A D:HEM201 3.1 8.6 1.0 C1B D:HEM201 3.1 9.0 1.0 C1C D:HEM201 3.1 9.1 1.0 C4C D:HEM201 3.1 7.9 1.0 C1D D:HEM201 3.1 8.4 1.0 C4D D:HEM201 3.1 9.9 1.0 C1A D:HEM201 3.1 14.1 1.0 CD2 D:HIS92 3.2 7.0 1.0 CHB D:HEM201 3.4 8.7 1.0 CHC D:HEM201 3.4 10.4 1.0 CHD D:HEM201 3.5 8.1 1.0 CHA D:HEM201 3.5 9.4 1.0 ND1 D:HIS92 4.1 8.6 1.0 CG2 D:VAL67 4.2 14.2 1.0 CG D:HIS92 4.2 11.4 1.0 C3B D:HEM201 4.3 8.2 1.0 C2B D:HEM201 4.3 8.3 1.0 C3A D:HEM201 4.3 9.6 1.0 CE1 D:HIS63 4.3 11.8 1.0 C2C D:HEM201 4.3 7.4 1.0 C3C D:HEM201 4.3 7.9 1.0 C2A D:HEM201 4.3 10.8 1.0 C3D D:HEM201 4.3 10.0 1.0 C2D D:HEM201 4.3 11.7 1.0 NE2 D:HIS63 4.6 15.6 1.0 CD1 D:LEU96 4.9 9.7 1.0

R.T.Alhashimi, M.S.Ghatge, A.K.Donkor, T.M.Deshpande, N.Anabaraonye, D.Alramadhani, R.Danso-Danquah, B.Huang, Y.Zhang, F.N.Musayev, O.Abdulmalik, M.K.Safo. Design, Synthesis, and Antisickling Investigation of A Nitric Oxide-Releasing Prodrug of 5HMF For the Treatment of Sickle Cell Disease. Biomolecules V. 12 2022.
ISSN: ESSN 2218-273X
PubMed: 35625623
DOI: 10.3390/BIOM12050696