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:
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: Thu Aug 8 05:54:47 2024
|