Fluorine in PDB 8w03: Crystal Structure of the Er-Alpha Ligand-Binding Domain (L372S, L536S) in Complex with K-1154
Protein crystallography data
The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (L372S, L536S) in Complex with K-1154, PDB code: 8w03
was solved by
C.K.Min,
J.C.Nwachukwu,
Y.Hou,
R.J.Russo,
A.Papa,
J.Min,
R.Peng,
S.H.Kim,
Y.Ziegler,
E.S.Rangarajan,
T.Izard,
B.S.Katzenellenbogen,
J.A.Katzenellenbogen,
K.W.Nettles,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.36 /
1.68
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.489,
58.771,
93.208,
86.61,
75.17,
62.96
|
R / Rfree (%)
|
20.1 /
24.5
|
Other elements in 8w03:
The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (L372S, L536S) in Complex with K-1154 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (L372S, L536S) in Complex with K-1154
(pdb code 8w03). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Crystal Structure of the Er-Alpha Ligand-Binding Domain (L372S, L536S) in Complex with K-1154, PDB code: 8w03:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 8w03
Go back to
Fluorine Binding Sites List in 8w03
Fluorine binding site 1 out
of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (L372S, L536S) in Complex with K-1154
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 the Er-Alpha Ligand-Binding Domain (L372S, L536S) in Complex with K-1154 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F600
b:74.0
occ:1.00
|
F1
|
D:OBT600
|
0.0
|
74.0
|
1.0
|
C20
|
D:OBT600
|
1.3
|
78.4
|
1.0
|
F3
|
D:OBT600
|
2.0
|
84.5
|
1.0
|
F2
|
D:OBT600
|
2.1
|
74.2
|
1.0
|
HB3
|
D:HIS524
|
2.2
|
68.2
|
1.0
|
C19
|
D:OBT600
|
2.4
|
78.9
|
1.0
|
H16
|
D:OBT600
|
2.5
|
95.2
|
1.0
|
O05
|
D:OBT600
|
2.6
|
68.1
|
1.0
|
HB2
|
D:HIS524
|
2.6
|
68.2
|
1.0
|
CB
|
D:HIS524
|
2.8
|
56.5
|
1.0
|
HD23
|
D:LEU525
|
3.1
|
61.2
|
1.0
|
N01
|
D:OBT600
|
3.2
|
66.4
|
1.0
|
H17
|
D:OBT600
|
3.2
|
95.2
|
1.0
|
C
|
D:HIS524
|
3.2
|
56.3
|
1.0
|
S01
|
D:OBT600
|
3.2
|
68.3
|
1.0
|
N
|
D:LEU525
|
3.3
|
54.7
|
1.0
|
SD
|
D:MET528
|
3.3
|
107.4
|
1.0
|
HA
|
D:LEU525
|
3.4
|
67.2
|
1.0
|
H
|
D:LEU525
|
3.4
|
66.1
|
1.0
|
O
|
D:HIS524
|
3.6
|
60.1
|
1.0
|
CA
|
D:HIS524
|
3.6
|
53.6
|
1.0
|
HG
|
D:LEU525
|
3.7
|
57.9
|
1.0
|
O
|
D:GLY521
|
3.8
|
38.8
|
1.0
|
CA
|
D:LEU525
|
3.8
|
55.6
|
1.0
|
CD2
|
D:LEU525
|
3.9
|
50.6
|
1.0
|
O04
|
D:OBT600
|
4.0
|
61.3
|
1.0
|
CG
|
D:HIS524
|
4.0
|
63.0
|
1.0
|
H22
|
D:OBT600
|
4.0
|
83.2
|
1.0
|
HB3
|
D:MET528
|
4.1
|
87.0
|
1.0
|
HD2
|
D:HIS524
|
4.2
|
74.1
|
1.0
|
HD21
|
D:LEU525
|
4.2
|
61.2
|
1.0
|
CG
|
D:LEU525
|
4.2
|
47.8
|
1.0
|
C21
|
D:OBT600
|
4.2
|
66.4
|
1.0
|
HA
|
D:HIS524
|
4.3
|
64.8
|
1.0
|
HA2
|
D:GLY521
|
4.3
|
40.0
|
1.0
|
HG2
|
D:MET528
|
4.3
|
96.2
|
1.0
|
HE1
|
D:MET528
|
4.4
|
93.5
|
1.0
|
HD12
|
D:ILE424
|
4.4
|
52.5
|
1.0
|
CE
|
D:MET528
|
4.4
|
77.5
|
1.0
|
CG
|
D:MET528
|
4.4
|
79.8
|
1.0
|
HE3
|
D:MET528
|
4.4
|
93.5
|
1.0
|
CD2
|
D:HIS524
|
4.5
|
61.4
|
1.0
|
H
|
D:HIS524
|
4.5
|
55.4
|
1.0
|
C26
|
D:OBT600
|
4.6
|
68.9
|
1.0
|
CB
|
D:LEU525
|
4.6
|
49.3
|
1.0
|
N
|
D:HIS524
|
4.6
|
45.7
|
1.0
|
HD22
|
D:LEU525
|
4.6
|
61.2
|
1.0
|
CB
|
D:MET528
|
4.8
|
72.1
|
1.0
|
H7
|
D:OBT600
|
4.8
|
63.4
|
1.0
|
C
|
D:GLY521
|
4.8
|
35.1
|
1.0
|
HG
|
D:SER527
|
4.8
|
87.4
|
1.0
|
C17
|
D:OBT600
|
4.9
|
51.4
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 8w03
Go back to
Fluorine Binding Sites List in 8w03
Fluorine binding site 2 out
of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (L372S, L536S) in Complex with K-1154
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 the Er-Alpha Ligand-Binding Domain (L372S, L536S) in Complex with K-1154 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F600
b:74.2
occ:1.00
|
F2
|
D:OBT600
|
0.0
|
74.2
|
1.0
|
C20
|
D:OBT600
|
1.3
|
78.4
|
1.0
|
F1
|
D:OBT600
|
2.1
|
74.0
|
1.0
|
F3
|
D:OBT600
|
2.1
|
84.5
|
1.0
|
C19
|
D:OBT600
|
2.3
|
78.9
|
1.0
|
H17
|
D:OBT600
|
2.3
|
95.2
|
1.0
|
HE1
|
D:MET528
|
2.7
|
93.5
|
1.0
|
HE3
|
D:MET528
|
2.7
|
93.5
|
1.0
|
SD
|
D:MET528
|
2.7
|
107.4
|
1.0
|
H16
|
D:OBT600
|
2.8
|
95.2
|
1.0
|
CE
|
D:MET528
|
2.8
|
77.5
|
1.0
|
HB3
|
D:HIS524
|
2.8
|
68.2
|
1.0
|
HB3
|
D:MET528
|
3.4
|
87.0
|
1.0
|
N01
|
D:OBT600
|
3.5
|
66.4
|
1.0
|
H22
|
D:OBT600
|
3.5
|
83.2
|
1.0
|
CB
|
D:HIS524
|
3.8
|
56.5
|
1.0
|
HE2
|
D:MET528
|
3.8
|
93.5
|
1.0
|
HD2
|
D:HIS524
|
3.8
|
74.1
|
1.0
|
C26
|
D:OBT600
|
4.0
|
68.9
|
1.0
|
HE1
|
D:MET343
|
4.0
|
77.9
|
1.0
|
C21
|
D:OBT600
|
4.0
|
66.4
|
1.0
|
CG
|
D:MET528
|
4.0
|
79.8
|
1.0
|
HB2
|
D:HIS524
|
4.0
|
68.2
|
1.0
|
CB
|
D:MET528
|
4.0
|
72.1
|
1.0
|
HB2
|
D:MET528
|
4.1
|
87.0
|
1.0
|
O05
|
D:OBT600
|
4.2
|
68.1
|
1.0
|
O
|
D:HIS524
|
4.2
|
60.1
|
1.0
|
HA
|
D:MET421
|
4.4
|
62.5
|
1.0
|
HG2
|
D:MET528
|
4.4
|
96.2
|
1.0
|
C
|
D:HIS524
|
4.4
|
56.3
|
1.0
|
S01
|
D:OBT600
|
4.4
|
68.3
|
1.0
|
CD2
|
D:HIS524
|
4.4
|
61.4
|
1.0
|
HD23
|
D:LEU525
|
4.5
|
61.2
|
1.0
|
CG
|
D:HIS524
|
4.5
|
63.0
|
1.0
|
HA
|
D:LEU525
|
4.7
|
67.2
|
1.0
|
CA
|
D:HIS524
|
4.7
|
53.6
|
1.0
|
CB
|
D:MET421
|
4.7
|
54.8
|
1.0
|
HG3
|
D:MET528
|
4.8
|
96.2
|
1.0
|
CE
|
D:MET343
|
4.8
|
64.5
|
1.0
|
HG
|
D:SER527
|
4.8
|
87.4
|
1.0
|
HE3
|
D:MET343
|
4.9
|
77.9
|
1.0
|
CA
|
D:MET421
|
4.9
|
51.7
|
1.0
|
N
|
D:LEU525
|
4.9
|
54.7
|
1.0
|
N
|
D:MET421
|
4.9
|
50.7
|
1.0
|
C25
|
D:OBT600
|
5.0
|
72.4
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 8w03
Go back to
Fluorine Binding Sites List in 8w03
Fluorine binding site 3 out
of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (L372S, L536S) in Complex with K-1154
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 the Er-Alpha Ligand-Binding Domain (L372S, L536S) in Complex with K-1154 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F600
b:84.5
occ:1.00
|
F3
|
D:OBT600
|
0.0
|
84.5
|
1.0
|
C20
|
D:OBT600
|
1.3
|
78.4
|
1.0
|
F1
|
D:OBT600
|
2.0
|
74.0
|
1.0
|
H22
|
D:OBT600
|
2.1
|
83.2
|
1.0
|
F2
|
D:OBT600
|
2.1
|
74.2
|
1.0
|
C19
|
D:OBT600
|
2.3
|
78.9
|
1.0
|
N01
|
D:OBT600
|
2.5
|
66.4
|
1.0
|
O05
|
D:OBT600
|
2.6
|
68.1
|
1.0
|
SD
|
D:MET528
|
2.7
|
107.4
|
1.0
|
C26
|
D:OBT600
|
2.9
|
68.9
|
1.0
|
H17
|
D:OBT600
|
2.9
|
95.2
|
1.0
|
S01
|
D:OBT600
|
3.0
|
68.3
|
1.0
|
C21
|
D:OBT600
|
3.1
|
66.4
|
1.0
|
HE1
|
D:MET343
|
3.1
|
77.9
|
1.0
|
HE1
|
D:MET528
|
3.1
|
93.5
|
1.0
|
H16
|
D:OBT600
|
3.2
|
95.2
|
1.0
|
HD23
|
D:LEU525
|
3.2
|
61.2
|
1.0
|
H7
|
D:OBT600
|
3.3
|
63.4
|
1.0
|
CE
|
D:MET528
|
3.5
|
77.5
|
1.0
|
CE
|
D:MET343
|
3.9
|
64.5
|
1.0
|
HE3
|
D:MET528
|
3.9
|
93.5
|
1.0
|
SD
|
D:MET343
|
4.0
|
62.8
|
1.0
|
HD21
|
D:LEU525
|
4.0
|
61.2
|
1.0
|
CD2
|
D:LEU525
|
4.0
|
50.6
|
1.0
|
C25
|
D:OBT600
|
4.0
|
72.4
|
1.0
|
HB3
|
D:HIS524
|
4.0
|
68.2
|
1.0
|
C11
|
D:OBT600
|
4.2
|
52.4
|
1.0
|
HE2
|
D:MET528
|
4.3
|
93.5
|
1.0
|
C17
|
D:OBT600
|
4.3
|
51.4
|
1.0
|
HE3
|
D:MET343
|
4.3
|
77.9
|
1.0
|
O04
|
D:OBT600
|
4.3
|
61.3
|
1.0
|
CG
|
D:MET528
|
4.4
|
79.8
|
1.0
|
H21
|
D:OBT600
|
4.4
|
87.4
|
1.0
|
HA
|
D:LEU525
|
4.4
|
67.2
|
1.0
|
C22
|
D:OBT600
|
4.4
|
64.6
|
1.0
|
HG2
|
D:MET528
|
4.5
|
96.2
|
1.0
|
HB2
|
D:HIS524
|
4.6
|
68.2
|
1.0
|
HD22
|
D:LEU525
|
4.6
|
61.2
|
1.0
|
HE2
|
D:MET343
|
4.6
|
77.9
|
1.0
|
HB3
|
D:MET528
|
4.6
|
87.0
|
1.0
|
HG
|
D:LEU525
|
4.6
|
57.9
|
1.0
|
CB
|
D:HIS524
|
4.8
|
56.5
|
1.0
|
H13
|
D:OBT600
|
4.8
|
62.1
|
1.0
|
H3
|
D:OBT600
|
4.9
|
52.8
|
1.0
|
O03
|
D:OBT600
|
4.9
|
54.7
|
1.0
|
CG
|
D:LEU525
|
5.0
|
47.8
|
1.0
|
HG3
|
D:MET528
|
5.0
|
96.2
|
1.0
|
N
|
D:LEU525
|
5.0
|
54.7
|
1.0
|
|
Reference:
C.K.Min,
J.C.Nwachukwu,
Y.Hou,
R.J.Russo,
A.Papa,
J.Min,
R.Peng,
S.H.Kim,
Y.Ziegler,
E.S.Rangarajan,
T.Izard,
B.S.Katzenellenbogen,
J.A.Katzenellenbogen,
K.W.Nettles.
Asymmetric Allostery in Estrogen Receptor-Alpha Homodimers Drives Responses to the Ensemble of Estrogens in the Hormonal Milieu. Proc.Natl.Acad.Sci.Usa V. 121 44121 2024.
ISSN: ESSN 1091-6490
PubMed: 38830107
DOI: 10.1073/PNAS.2321344121
Page generated: Sat Aug 3 01:32:50 2024
|