Fluorine in PDB 7erd: Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)
Enzymatic activity of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)
All present enzymatic activity of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg):
1.3.1.24;
1.5.1.30;
Protein crystallography data
The structure of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg), PDB code: 7erd
was solved by
C.Griesinger,
D.Lee,
K.S.Ryu,
M.Kim,
J.H.Ha,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.59 /
2.00
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.821,
116.996,
41.615,
90,
90,
90
|
R / Rfree (%)
|
18 /
22.9
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)
(pdb code 7erd). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg), PDB code: 7erd:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 7erd
Go back to
Fluorine Binding Sites List in 7erd
Fluorine binding site 1 out
of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:41.0
occ:1.00
|
F01
|
A:JBO402
|
0.0
|
41.0
|
1.0
|
C02
|
A:JBO402
|
1.4
|
41.1
|
1.0
|
F21
|
A:JBO402
|
2.2
|
42.2
|
1.0
|
F03
|
A:JBO402
|
2.2
|
41.9
|
1.0
|
C04
|
A:JBO402
|
2.4
|
38.6
|
1.0
|
C20
|
A:JBO402
|
2.6
|
36.3
|
1.0
|
O
|
A:HOH508
|
3.4
|
32.3
|
1.0
|
O
|
A:HOH535
|
3.6
|
19.9
|
1.0
|
O
|
A:ARG78
|
3.6
|
33.5
|
1.0
|
C05
|
A:JBO402
|
3.7
|
38.0
|
1.0
|
CD2
|
A:LEU81
|
3.9
|
28.0
|
1.0
|
O
|
A:HOH511
|
3.9
|
23.8
|
1.0
|
C19
|
A:JBO402
|
4.0
|
36.0
|
1.0
|
O2D
|
A:NAP401
|
4.1
|
20.6
|
1.0
|
C06
|
A:JBO402
|
4.3
|
38.6
|
1.0
|
OG1
|
A:THR77
|
4.7
|
25.0
|
1.0
|
C07
|
A:JBO402
|
4.8
|
36.8
|
1.0
|
CG1
|
A:VAL128
|
4.8
|
18.7
|
1.0
|
C
|
A:ARG78
|
4.8
|
34.0
|
1.0
|
C2D
|
A:NAP401
|
4.9
|
21.8
|
1.0
|
CD2
|
A:LEU125
|
4.9
|
23.9
|
1.0
|
C18
|
A:JBO402
|
4.9
|
36.3
|
1.0
|
CA
|
A:ASN79
|
4.9
|
39.6
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 7erd
Go back to
Fluorine Binding Sites List in 7erd
Fluorine binding site 2 out
of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:41.9
occ:1.00
|
F03
|
A:JBO402
|
0.0
|
41.9
|
1.0
|
C02
|
A:JBO402
|
1.3
|
41.1
|
1.0
|
F21
|
A:JBO402
|
2.2
|
42.2
|
1.0
|
F01
|
A:JBO402
|
2.2
|
41.0
|
1.0
|
C04
|
A:JBO402
|
2.4
|
38.6
|
1.0
|
C06
|
A:JBO402
|
2.9
|
38.6
|
1.0
|
C05
|
A:JBO402
|
3.0
|
38.0
|
1.0
|
CD2
|
A:LEU81
|
3.4
|
28.0
|
1.0
|
C20
|
A:JBO402
|
3.4
|
36.3
|
1.0
|
CD2
|
A:LEU125
|
3.7
|
23.9
|
1.0
|
C07
|
A:JBO402
|
4.3
|
36.8
|
1.0
|
C19
|
A:JBO402
|
4.6
|
36.0
|
1.0
|
CG
|
A:LEU81
|
4.7
|
28.8
|
1.0
|
C18
|
A:JBO402
|
4.9
|
36.3
|
1.0
|
O
|
A:ARG78
|
5.0
|
33.5
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 7erd
Go back to
Fluorine Binding Sites List in 7erd
Fluorine binding site 3 out
of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:42.2
occ:1.00
|
F21
|
A:JBO402
|
0.0
|
42.2
|
1.0
|
C02
|
A:JBO402
|
1.4
|
41.1
|
1.0
|
F03
|
A:JBO402
|
2.2
|
41.9
|
1.0
|
F01
|
A:JBO402
|
2.2
|
41.0
|
1.0
|
C04
|
A:JBO402
|
2.4
|
38.6
|
1.0
|
O
|
A:HOH511
|
3.0
|
23.8
|
1.0
|
C05
|
A:JBO402
|
3.0
|
38.0
|
1.0
|
C06
|
A:JBO402
|
3.0
|
38.6
|
1.0
|
O7N
|
A:NAP401
|
3.3
|
25.3
|
1.0
|
C20
|
A:JBO402
|
3.5
|
36.3
|
1.0
|
C7N
|
A:NAP401
|
3.8
|
24.3
|
1.0
|
O
|
A:HOH508
|
3.9
|
32.3
|
1.0
|
C2N
|
A:NAP401
|
4.3
|
21.3
|
1.0
|
C07
|
A:JBO402
|
4.3
|
36.8
|
1.0
|
O
|
A:ARG78
|
4.4
|
33.5
|
1.0
|
C3N
|
A:NAP401
|
4.4
|
23.1
|
1.0
|
O
|
A:HOH596
|
4.6
|
34.4
|
1.0
|
N7N
|
A:NAP401
|
4.6
|
24.9
|
1.0
|
C19
|
A:JBO402
|
4.6
|
36.0
|
1.0
|
C18
|
A:JBO402
|
5.0
|
36.3
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 7erd
Go back to
Fluorine Binding Sites List in 7erd
Fluorine binding site 4 out
of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F402
b:45.8
occ:1.00
|
F01
|
B:JBO402
|
0.0
|
45.8
|
1.0
|
C02
|
B:JBO402
|
1.4
|
45.8
|
1.0
|
F03
|
B:JBO402
|
2.2
|
46.4
|
1.0
|
F21
|
B:JBO402
|
2.2
|
46.6
|
1.0
|
C04
|
B:JBO402
|
2.5
|
43.6
|
1.0
|
O
|
B:HOH519
|
2.8
|
31.1
|
1.0
|
C05
|
B:JBO402
|
3.1
|
42.2
|
1.0
|
C06
|
B:JBO402
|
3.2
|
41.1
|
1.0
|
C20
|
B:JBO402
|
3.5
|
43.0
|
1.0
|
N7N
|
B:NAP401
|
3.5
|
25.0
|
1.0
|
CG
|
B:ARG78
|
4.0
|
61.5
|
1.0
|
O
|
B:HOH522
|
4.1
|
38.7
|
1.0
|
C07
|
B:JBO402
|
4.5
|
42.1
|
1.0
|
C7N
|
B:NAP401
|
4.5
|
26.6
|
1.0
|
NH2
|
B:ARG78
|
4.5
|
67.7
|
1.0
|
CB
|
B:ARG78
|
4.6
|
58.4
|
1.0
|
C2N
|
B:NAP401
|
4.6
|
28.0
|
1.0
|
CA
|
B:ARG78
|
4.7
|
55.7
|
1.0
|
C19
|
B:JBO402
|
4.7
|
42.3
|
1.0
|
O
|
B:HOH533
|
4.8
|
29.6
|
1.0
|
C3N
|
B:NAP401
|
4.8
|
27.0
|
1.0
|
O2D
|
B:NAP401
|
4.9
|
30.4
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 7erd
Go back to
Fluorine Binding Sites List in 7erd
Fluorine binding site 5 out
of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F402
b:46.4
occ:1.00
|
F03
|
B:JBO402
|
0.0
|
46.4
|
1.0
|
C02
|
B:JBO402
|
1.3
|
45.8
|
1.0
|
F21
|
B:JBO402
|
2.2
|
46.6
|
1.0
|
F01
|
B:JBO402
|
2.2
|
45.8
|
1.0
|
C04
|
B:JBO402
|
2.4
|
43.6
|
1.0
|
C20
|
B:JBO402
|
2.8
|
43.0
|
1.0
|
O
|
B:HOH533
|
3.6
|
29.6
|
1.0
|
C05
|
B:JBO402
|
3.7
|
42.2
|
1.0
|
CA
|
B:ARG78
|
3.8
|
55.7
|
1.0
|
O
|
B:ARG78
|
3.9
|
57.0
|
1.0
|
CD2
|
B:LEU125
|
4.0
|
25.2
|
1.0
|
O
|
B:HOH522
|
4.1
|
38.7
|
1.0
|
C19
|
B:JBO402
|
4.1
|
42.3
|
1.0
|
CG
|
B:ARG78
|
4.3
|
61.5
|
1.0
|
C
|
B:ARG78
|
4.3
|
57.5
|
1.0
|
O
|
B:HOH519
|
4.3
|
31.1
|
1.0
|
C06
|
B:JBO402
|
4.3
|
41.1
|
1.0
|
O2D
|
B:NAP401
|
4.4
|
30.4
|
1.0
|
CB
|
B:ARG78
|
4.4
|
58.4
|
1.0
|
CG2
|
B:VAL128
|
4.6
|
26.3
|
1.0
|
N
|
B:ARG78
|
4.7
|
52.4
|
1.0
|
O
|
B:THR77
|
4.8
|
50.2
|
1.0
|
C07
|
B:JBO402
|
4.8
|
42.1
|
1.0
|
CG1
|
B:VAL128
|
4.9
|
26.7
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 7erd
Go back to
Fluorine Binding Sites List in 7erd
Fluorine binding site 6 out
of 6 in the Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of Human Biliverdin IX-Beta Reductase B with Flunixin Meglumin (Fmg) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F402
b:46.6
occ:1.00
|
F21
|
B:JBO402
|
0.0
|
46.6
|
1.0
|
C02
|
B:JBO402
|
1.4
|
45.8
|
1.0
|
F03
|
B:JBO402
|
2.2
|
46.4
|
1.0
|
F01
|
B:JBO402
|
2.2
|
45.8
|
1.0
|
C04
|
B:JBO402
|
2.4
|
43.6
|
1.0
|
C06
|
B:JBO402
|
3.0
|
41.1
|
1.0
|
C05
|
B:JBO402
|
3.1
|
42.2
|
1.0
|
CD2
|
B:LEU125
|
3.2
|
25.2
|
1.0
|
O
|
A:HOH615
|
3.4
|
51.7
|
1.0
|
C20
|
B:JBO402
|
3.5
|
43.0
|
1.0
|
CG
|
B:LEU125
|
4.4
|
25.5
|
1.0
|
CD1
|
B:LEU125
|
4.4
|
26.3
|
1.0
|
C07
|
B:JBO402
|
4.4
|
42.1
|
1.0
|
O
|
B:ARG78
|
4.6
|
57.0
|
1.0
|
O
|
A:HOH558
|
4.6
|
36.7
|
1.0
|
C19
|
B:JBO402
|
4.7
|
42.3
|
1.0
|
CG
|
B:ARG78
|
4.8
|
61.5
|
1.0
|
O
|
B:HOH577
|
4.8
|
46.3
|
1.0
|
|
Reference:
M.Kim,
J.H.Ha,
J.Choi,
B.R.Kim,
V.Gapsys,
K.O.Lee,
J.G.Jee,
K.S.Chakrabarti,
B.L.De Groot,
C.Griesinger,
K.S.Ryu,
D.Lee.
Repositioning Food and Drug Administration-Approved Drugs For Inhibiting Biliverdin IX Beta Reductase B As A Novel Thrombocytopenia Therapeutic Target. J.Med.Chem. V. 65 2548 2022.
ISSN: ISSN 0022-2623
PubMed: 34957824
DOI: 10.1021/ACS.JMEDCHEM.1C01664
Page generated: Fri Aug 2 06:45:24 2024
|