Iron in PDB 7jy0: Structure of Hba with Compound 9

The structure of Structure of Hba with Compound 9, PDB code: 7jy0 was solved by J.Jasti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.75 / 1.63
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.23, 82.52, 63.75, 90, 100.17, 90
R / Rfree (%)	17 / 19.7

The structure of Structure of Hba with Compound 9 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Iron atom in the Structure of Hba with Compound 9 (pdb code 7jy0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Hba with Compound 9, PDB code: 7jy0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Hba with Compound 9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Hba with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:18.5 occ:1.00 FE A:HEM201 0.0 18.5 1.0 ND A:HEM201 2.0 18.9 1.0 NC A:HEM201 2.0 18.0 1.0 NA A:HEM201 2.0 19.2 1.0 NB A:HEM201 2.0 18.0 1.0 O A:CMO202 2.0 32.4 1.0 NE2 A:HIS87 2.1 18.2 1.0 C A:CMO202 2.9 36.6 1.0 C1D A:HEM201 3.0 19.1 1.0 C1C A:HEM201 3.0 17.7 1.0 C4B A:HEM201 3.0 18.0 1.0 C4D A:HEM201 3.0 19.5 1.0 C4C A:HEM201 3.0 18.4 1.0 C1A A:HEM201 3.1 19.7 1.0 C1B A:HEM201 3.1 18.5 1.0 CE1 A:HIS87 3.1 18.5 1.0 C4A A:HEM201 3.1 19.2 1.0 CD2 A:HIS87 3.2 19.0 1.0 CHC A:HEM201 3.3 18.3 1.0 CHD A:HEM201 3.4 19.4 1.0 CHA A:HEM201 3.4 20.3 1.0 CHB A:HEM201 3.4 19.3 1.0 ND1 A:HIS87 4.2 19.2 1.0 C3D A:HEM201 4.3 20.2 1.0 C3C A:HEM201 4.3 18.5 1.0 C2C A:HEM201 4.3 18.2 1.0 C2D A:HEM201 4.3 19.9 1.0 NE2 A:HIS58 4.3 25.0 1.0 C3A A:HEM201 4.3 20.2 1.0 CG A:HIS87 4.3 17.2 1.0 C2A A:HEM201 4.3 20.6 1.0 C3B A:HEM201 4.3 18.4 1.0 C2B A:HEM201 4.3 18.4 1.0 CG1 A:VAL62 4.6 21.2 0.5 CE1 A:HIS58 4.6 25.2 1.0 CG2 A:VAL62 4.8 15.1 0.5

Iron binding site 2 out of 4 in the Structure of Hba with Compound 9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Hba with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:18.5 occ:1.00 FE B:HEM201 0.0 18.5 1.0 ND B:HEM201 2.0 19.0 1.0 NC B:HEM201 2.0 18.0 1.0 NA B:HEM201 2.0 19.1 1.0 O B:CMO202 2.0 26.1 1.0 NB B:HEM201 2.0 17.8 1.0 NE2 B:HIS92 2.1 19.3 1.0 C B:CMO202 2.9 30.3 1.0 C1D B:HEM201 3.0 19.4 1.0 C4C B:HEM201 3.0 18.4 1.0 C4B B:HEM201 3.0 17.9 1.0 C1B B:HEM201 3.0 18.4 1.0 C4D B:HEM201 3.0 19.8 1.0 C1C B:HEM201 3.0 17.7 1.0 C1A B:HEM201 3.0 19.8 1.0 C4A B:HEM201 3.1 19.2 1.0 CD2 B:HIS92 3.1 20.2 1.0 CE1 B:HIS92 3.1 19.3 1.0 CHD B:HEM201 3.4 19.5 1.0 CHC B:HEM201 3.4 18.2 1.0 CHA B:HEM201 3.4 20.5 1.0 CHB B:HEM201 3.4 19.2 1.0 CG B:HIS92 4.2 19.5 1.0 ND1 B:HIS92 4.2 21.1 1.0 NE2 B:HIS63 4.2 26.2 1.0 C3C B:HEM201 4.2 18.5 1.0 C2C B:HEM201 4.3 18.1 1.0 C2D B:HEM201 4.3 20.3 1.0 C3D B:HEM201 4.3 20.8 1.0 C3A B:HEM201 4.3 20.2 1.0 C2B B:HEM201 4.3 18.4 1.0 C2A B:HEM201 4.3 20.6 1.0 C3B B:HEM201 4.3 18.3 1.0 CG2 B:VAL67 4.8 19.5 1.0 CE1 B:HIS63 4.9 26.5 1.0

Iron binding site 3 out of 4 in the Structure of Hba with Compound 9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Hba with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:18.1 occ:1.00 FE C:HEM202 0.0 18.1 1.0 NC C:HEM202 2.0 17.4 1.0 ND C:HEM202 2.0 18.3 1.0 NA C:HEM202 2.0 19.1 1.0 O C:CMO203 2.0 29.5 1.0 NB C:HEM202 2.0 18.0 1.0 NE2 C:HIS87 2.1 15.7 1.0 C C:CMO203 2.9 32.6 1.0 C1C C:HEM202 3.0 17.1 1.0 C1D C:HEM202 3.0 18.4 1.0 C4B C:HEM202 3.0 17.9 1.0 C4D C:HEM202 3.0 19.1 1.0 CE1 C:HIS87 3.0 16.1 1.0 C1B C:HEM202 3.0 18.8 1.0 C4C C:HEM202 3.0 17.5 1.0 C1A C:HEM202 3.1 19.7 1.0 C4A C:HEM202 3.1 19.6 1.0 CD2 C:HIS87 3.2 16.1 1.0 CHC C:HEM202 3.3 17.9 1.0 CHD C:HEM202 3.4 18.5 1.0 CHB C:HEM202 3.4 19.8 1.0 CHA C:HEM202 3.4 20.0 1.0 ND1 C:HIS87 4.2 17.9 1.0 C3C C:HEM202 4.3 17.5 1.0 C2C C:HEM202 4.3 17.3 1.0 CG C:HIS87 4.3 15.7 1.0 C3D C:HEM202 4.3 19.7 1.0 C2D C:HEM202 4.3 19.2 1.0 C3B C:HEM202 4.3 18.6 1.0 NE2 C:HIS58 4.3 27.2 1.0 C3A C:HEM202 4.3 20.8 1.0 C2B C:HEM202 4.3 18.9 1.0 C2A C:HEM202 4.3 20.9 1.0 CE1 C:HIS58 4.6 27.7 1.0 CG2 C:VAL62 4.8 19.6 1.0

Iron binding site 4 out of 4 in the Structure of Hba with Compound 9


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Hba with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:20.7 occ:1.00 FE D:HEM201 0.0 20.7 1.0 NA D:HEM201 2.0 21.5 1.0 ND D:HEM201 2.0 21.3 1.0 NB D:HEM201 2.0 20.1 1.0 NC D:HEM201 2.0 20.2 1.0 O D:CMO202 2.0 28.4 1.0 NE2 D:HIS92 2.1 21.1 1.0 C D:CMO202 2.9 33.3 1.0 C1B D:HEM201 3.0 20.7 1.0 C1D D:HEM201 3.0 21.6 1.0 C4B D:HEM201 3.0 20.1 1.0 C4A D:HEM201 3.0 21.6 1.0 C4D D:HEM201 3.0 22.2 1.0 C4C D:HEM201 3.0 20.6 1.0 C1A D:HEM201 3.0 22.2 1.0 C1C D:HEM201 3.0 19.8 1.0 CE1 D:HIS92 3.0 20.9 1.0 CD2 D:HIS92 3.2 21.9 1.0 CHB D:HEM201 3.4 21.6 1.0 CHD D:HEM201 3.4 21.7 1.0 CHC D:HEM201 3.4 20.4 1.0 CHA D:HEM201 3.4 22.8 1.0 ND1 D:HIS92 4.2 22.3 1.0 C3A D:HEM201 4.2 22.7 1.0 NE2 D:HIS63 4.2 26.2 1.0 C2A D:HEM201 4.3 23.1 1.0 C2B D:HEM201 4.3 20.7 1.0 CG D:HIS92 4.3 21.4 1.0 C3C D:HEM201 4.3 20.6 1.0 C3D D:HEM201 4.3 23.1 1.0 C2D D:HEM201 4.3 22.6 1.0 C2C D:HEM201 4.3 20.3 1.0 C3B D:HEM201 4.3 20.6 1.0 CG2 D:VAL67 4.8 21.8 1.0 CE1 D:HIS63 4.9 26.6 1.0

A.Gopalsamy, A.E.Aulabaugh, A.Barakat, K.C.Beaumont, S.Cabral, D.P.Canterbury, A.Casimiro-Garcia, J.S.Chang, M.Z.Chen, C.Choi, R.L.Dow, O.O.Fadeyi, X.Feng, S.P.France, R.M.Howard, J.M.Janz, J.Jasti, R.Jasuja, L.H.Jones, A.King-Ahmad, K.M.Knee, J.T.Kohrt, C.Limberakis, S.Liras, C.A.Martinez, K.F.Mcclure, A.Narayanan, J.Narula, J.J.Novak, T.N.O'connell, M.D.Parikh, D.W.Piotrowski, O.Plotnikova, R.P.Robinson, P.V.Sahasrabudhe, R.Sharma, B.A.Thuma, D.Vasa, L.Wei, A.Z.Wenzel, J.M.Withka, J.Xiao, H.G.Yayla. Pf-07059013: A Noncovalent Modulator of Hemoglobin For Treatment of Sickle Cell Disease. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33356244
DOI: 10.1021/ACS.JMEDCHEM.0C01518