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Iron in PDB 7jy1: Structure of Hba with Compound 19

Protein crystallography data

The structure of Structure of Hba with Compound 19, PDB code: 7jy1 was solved by J.Jasti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.98 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.72, 81.39, 64.5, 90, 97.27, 90
R / Rfree (%) 17.1 / 19.3

Other elements in 7jy1:

The structure of Structure of Hba with Compound 19 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Hba with Compound 19 (pdb code 7jy1). 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 19, PDB code: 7jy1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7jy1

Go back to Iron Binding Sites List in 7jy1
Iron binding site 1 out of 4 in the Structure of Hba with Compound 19


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 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:14.9
occ:1.00
FE A:HEM201 0.0 14.9 1.0
NC A:HEM201 2.0 14.6 1.0
NA A:HEM201 2.0 15.7 1.0
ND A:HEM201 2.0 15.4 1.0
NB A:HEM201 2.0 14.4 1.0
O A:CMO202 2.0 24.3 1.0
NE2 A:HIS87 2.1 12.9 1.0
C A:CMO202 2.9 26.0 1.0
C4B A:HEM201 3.0 14.5 1.0
C4D A:HEM201 3.0 16.0 1.0
CE1 A:HIS87 3.0 13.0 1.0
C1D A:HEM201 3.0 15.7 1.0
C1C A:HEM201 3.0 14.3 1.0
C1B A:HEM201 3.0 15.0 1.0
C4C A:HEM201 3.0 14.9 1.0
C1A A:HEM201 3.0 16.2 1.0
C4A A:HEM201 3.1 15.8 1.0
CD2 A:HIS87 3.2 13.2 1.0
CHC A:HEM201 3.4 14.9 1.0
CHA A:HEM201 3.4 16.8 1.0
CHB A:HEM201 3.4 15.8 1.0
CHD A:HEM201 3.4 15.9 1.0
ND1 A:HIS87 4.2 14.0 1.0
CG A:HIS87 4.2 13.7 1.0
C3B A:HEM201 4.2 14.9 1.0
C2B A:HEM201 4.2 14.9 1.0
C3C A:HEM201 4.3 15.0 1.0
C2D A:HEM201 4.3 16.3 1.0
C3D A:HEM201 4.3 16.6 1.0
C2C A:HEM201 4.3 14.7 1.0
C3A A:HEM201 4.3 16.8 1.0
C2A A:HEM201 4.3 17.1 1.0
NE2 A:HIS58 4.3 20.5 1.0
CG1 A:VAL62 4.5 18.9 0.5
CE1 A:HIS58 4.6 20.1 1.0
CG2 A:VAL62 4.9 13.9 0.5

Iron binding site 2 out of 4 in 7jy1

Go back to Iron Binding Sites List in 7jy1
Iron binding site 2 out of 4 in the Structure of Hba with Compound 19


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 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:15.9
occ:1.00
FE B:HEM201 0.0 15.9 1.0
ND B:HEM201 1.9 16.6 1.0
NB B:HEM201 2.0 15.4 1.0
NA B:HEM201 2.0 16.6 1.0
NC B:HEM201 2.0 15.6 1.0
O B:CMO202 2.0 22.6 1.0
NE2 B:HIS92 2.1 16.9 1.0
C B:CMO202 2.9 29.4 1.0
C1D B:HEM201 3.0 17.0 1.0
CE1 B:HIS92 3.0 17.0 1.0
C4D B:HEM201 3.0 17.3 1.0
C4B B:HEM201 3.0 15.4 1.0
C4C B:HEM201 3.0 16.1 1.0
C1B B:HEM201 3.0 15.9 1.0
C1C B:HEM201 3.0 15.3 1.0
C1A B:HEM201 3.0 17.2 1.0
C4A B:HEM201 3.0 16.6 1.0
CD2 B:HIS92 3.2 16.8 1.0
CHD B:HEM201 3.4 17.2 1.0
CHB B:HEM201 3.4 16.6 1.0
CHA B:HEM201 3.4 17.9 1.0
CHC B:HEM201 3.4 15.8 1.0
ND1 B:HIS92 4.2 17.7 1.0
NE2 B:HIS63 4.2 20.3 1.0
CG B:HIS92 4.2 16.6 1.0
C2D B:HEM201 4.3 18.0 1.0
C2C B:HEM201 4.3 15.9 1.0
C2B B:HEM201 4.3 15.8 1.0
C3A B:HEM201 4.3 17.6 1.0
C3D B:HEM201 4.3 18.4 1.0
C3C B:HEM201 4.3 16.3 1.0
C2A B:HEM201 4.3 17.9 1.0
C3B B:HEM201 4.3 15.9 1.0
CG2 B:VAL67 4.7 17.4 1.0
CE1 B:HIS63 4.9 20.7 1.0

Iron binding site 3 out of 4 in 7jy1

Go back to Iron Binding Sites List in 7jy1
Iron binding site 3 out of 4 in the Structure of Hba with Compound 19


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 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:17.5
occ:1.00
FE C:HEM202 0.0 17.5 1.0
ND C:HEM202 2.0 18.0 1.0
NC C:HEM202 2.0 16.9 1.0
NA C:HEM202 2.0 18.6 1.0
NB C:HEM202 2.0 17.0 1.0
O C:CMO203 2.0 24.1 1.0
NE2 C:HIS87 2.1 15.3 1.0
C C:CMO203 2.9 27.3 1.0
C4D C:HEM202 3.0 18.9 1.0
C1D C:HEM202 3.0 18.1 1.0
C4B C:HEM202 3.0 16.9 1.0
CE1 C:HIS87 3.0 15.2 1.0
C1C C:HEM202 3.0 16.5 1.0
C1A C:HEM202 3.0 19.3 1.0
C4C C:HEM202 3.0 17.1 1.0
C1B C:HEM202 3.0 17.7 1.0
C4A C:HEM202 3.1 18.9 1.0
CD2 C:HIS87 3.2 14.4 1.0
CHA C:HEM202 3.4 19.8 1.0
CHC C:HEM202 3.4 17.1 1.0
CHD C:HEM202 3.4 18.1 1.0
CHB C:HEM202 3.4 18.7 1.0
ND1 C:HIS87 4.2 16.4 1.0
CG C:HIS87 4.2 15.2 1.0
C2D C:HEM202 4.3 18.9 1.0
C3C C:HEM202 4.3 17.1 1.0
C3D C:HEM202 4.3 19.5 1.0
C3B C:HEM202 4.3 17.3 1.0
C2A C:HEM202 4.3 20.4 1.0
C3A C:HEM202 4.3 20.1 1.0
C2C C:HEM202 4.3 16.8 1.0
C2B C:HEM202 4.3 17.5 1.0
NE2 C:HIS58 4.3 24.1 1.0
CE1 C:HIS58 4.6 23.9 1.0
CG2 C:VAL62 4.9 20.3 1.0

Iron binding site 4 out of 4 in 7jy1

Go back to Iron Binding Sites List in 7jy1
Iron binding site 4 out of 4 in the Structure of Hba with Compound 19


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 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:20.6
occ:1.00
FE D:HEM201 0.0 20.6 1.0
ND D:HEM201 2.0 21.4 1.0
NA D:HEM201 2.0 22.0 1.0
NB D:HEM201 2.0 20.1 1.0
NC D:HEM201 2.0 19.7 1.0
O D:CMO202 2.1 29.5 1.0
NE2 D:HIS92 2.1 19.9 1.0
C D:CMO202 3.0 33.2 1.0
C1D D:HEM201 3.0 21.5 1.0
C4D D:HEM201 3.0 22.6 1.0
C4B D:HEM201 3.0 19.8 1.0
C1C D:HEM201 3.0 19.2 1.0
C4A D:HEM201 3.0 22.3 1.0
C1B D:HEM201 3.0 21.0 1.0
C1A D:HEM201 3.0 23.0 1.0
C4C D:HEM201 3.0 19.9 1.0
CE1 D:HIS92 3.1 21.1 1.0
CD2 D:HIS92 3.1 20.6 1.0
CHA D:HEM201 3.4 23.6 1.0
CHD D:HEM201 3.4 21.2 1.0
CHB D:HEM201 3.4 22.2 1.0
CHC D:HEM201 3.4 19.8 1.0
NE2 D:HIS63 4.2 28.4 1.0
C2D D:HEM201 4.3 22.7 1.0
C3D D:HEM201 4.3 23.6 1.0
C3A D:HEM201 4.3 23.9 1.0
C2C D:HEM201 4.3 19.4 1.0
C2A D:HEM201 4.3 24.3 1.0
ND1 D:HIS92 4.3 22.4 1.0
CG D:HIS92 4.3 21.6 1.0
C3C D:HEM201 4.3 19.8 1.0
C2B D:HEM201 4.3 20.8 1.0
C3B D:HEM201 4.3 20.4 1.0
CG2 D:VAL67 4.8 24.5 1.0
CE1 D:HIS63 4.9 29.4 1.0

Reference:

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
Page generated: Wed Aug 6 22:36:21 2025

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