Fluorine in PDB 8qyq: Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten
Protein crystallography data
The structure of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten, PDB code: 8qyq
was solved by
J.Robert-Paganin,
C.Kikuti,
D.Auguin,
S.Rety,
A.David,
A.Houdusse,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
91.64 /
2.61
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.801,
147.977,
116.751,
90,
91.62,
90
|
R / Rfree (%)
|
17.8 /
21.7
|
Other elements in 8qyq:
The structure of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten
(pdb code 8qyq). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten, PDB code: 8qyq:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 8qyq
Go back to
Fluorine Binding Sites List in 8qyq
Fluorine binding site 1 out
of 6 in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1002
b:38.6
occ:1.00
|
F1
|
A:BEF1002
|
0.0
|
38.6
|
1.0
|
BE
|
A:BEF1002
|
1.5
|
34.0
|
1.0
|
O1B
|
A:ADP1001
|
2.4
|
35.3
|
1.0
|
F3
|
A:BEF1002
|
2.5
|
31.1
|
1.0
|
F2
|
A:BEF1002
|
2.5
|
32.4
|
1.0
|
OG
|
A:SER180
|
2.7
|
33.4
|
1.0
|
ND2
|
A:ASN238
|
3.0
|
27.1
|
1.0
|
OG
|
A:SER241
|
3.1
|
35.5
|
1.0
|
N
|
A:GLY181
|
3.3
|
34.7
|
1.0
|
CA
|
A:SER180
|
3.4
|
32.9
|
1.0
|
CB
|
A:SER180
|
3.4
|
33.8
|
1.0
|
CB
|
A:ASN238
|
3.6
|
29.6
|
1.0
|
CB
|
A:SER241
|
3.6
|
27.0
|
1.0
|
CA
|
A:SER241
|
3.6
|
24.5
|
1.0
|
C
|
A:SER180
|
3.7
|
39.7
|
1.0
|
CG
|
A:ASN238
|
3.8
|
42.9
|
1.0
|
PB
|
A:ADP1001
|
3.9
|
37.6
|
1.0
|
O
|
A:HOH1229
|
4.0
|
44.4
|
1.0
|
N
|
A:SER242
|
4.2
|
27.2
|
1.0
|
O3B
|
A:ADP1001
|
4.3
|
37.0
|
1.0
|
CA
|
A:GLY181
|
4.3
|
34.8
|
1.0
|
C
|
A:SER241
|
4.5
|
29.2
|
1.0
|
O3A
|
A:ADP1001
|
4.5
|
35.7
|
1.0
|
O
|
A:HOH1107
|
4.6
|
39.6
|
1.0
|
N
|
A:SER241
|
4.6
|
26.4
|
1.0
|
MG
|
A:MG1003
|
4.7
|
27.6
|
1.0
|
N
|
A:SER180
|
4.8
|
33.7
|
1.0
|
O
|
A:SER180
|
4.8
|
42.8
|
1.0
|
O2B
|
A:ADP1001
|
4.9
|
35.3
|
1.0
|
OD1
|
A:ASN238
|
5.0
|
40.2
|
1.0
|
O
|
A:HOH1115
|
5.0
|
42.2
|
1.0
|
N
|
A:GLY464
|
5.0
|
32.5
|
1.0
|
NZ
|
A:LYS184
|
5.0
|
27.3
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 8qyq
Go back to
Fluorine Binding Sites List in 8qyq
Fluorine binding site 2 out
of 6 in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1002
b:32.4
occ:1.00
|
F2
|
A:BEF1002
|
0.0
|
32.4
|
1.0
|
BE
|
A:BEF1002
|
1.5
|
34.0
|
1.0
|
MG
|
A:MG1003
|
2.3
|
27.6
|
1.0
|
F3
|
A:BEF1002
|
2.5
|
31.1
|
1.0
|
F1
|
A:BEF1002
|
2.5
|
38.6
|
1.0
|
O1B
|
A:ADP1001
|
2.6
|
35.3
|
1.0
|
O
|
A:HOH1107
|
2.7
|
39.6
|
1.0
|
O3B
|
A:ADP1001
|
2.7
|
37.0
|
1.0
|
N
|
A:SER242
|
2.8
|
27.2
|
1.0
|
O
|
A:HOH1109
|
3.0
|
31.0
|
1.0
|
OG
|
A:SER242
|
3.1
|
40.1
|
1.0
|
PB
|
A:ADP1001
|
3.3
|
37.6
|
1.0
|
CB
|
A:SER242
|
3.4
|
29.1
|
1.0
|
ND2
|
A:ASN238
|
3.6
|
27.1
|
1.0
|
CA
|
A:SER242
|
3.7
|
26.8
|
1.0
|
CA
|
A:SER241
|
3.7
|
24.5
|
1.0
|
C
|
A:SER241
|
3.7
|
29.2
|
1.0
|
OG
|
A:SER241
|
3.9
|
35.5
|
1.0
|
OG1
|
A:THR185
|
4.1
|
30.8
|
1.0
|
O
|
A:ASN240
|
4.2
|
32.5
|
1.0
|
O3A
|
A:ADP1001
|
4.2
|
35.7
|
1.0
|
O
|
A:SER242
|
4.3
|
31.7
|
1.0
|
CB
|
A:SER241
|
4.4
|
27.0
|
1.0
|
O2B
|
A:ADP1001
|
4.5
|
35.3
|
1.0
|
O1A
|
A:ADP1001
|
4.5
|
37.9
|
1.0
|
C
|
A:SER242
|
4.5
|
31.9
|
1.0
|
O
|
A:HOH1229
|
4.7
|
44.4
|
1.0
|
N
|
A:SER241
|
4.8
|
26.4
|
1.0
|
NZ
|
A:LYS184
|
4.8
|
27.3
|
1.0
|
CG
|
A:ASN238
|
4.8
|
42.9
|
1.0
|
N
|
A:GLY464
|
4.8
|
32.5
|
1.0
|
O
|
A:SER241
|
4.9
|
29.4
|
1.0
|
C
|
A:ASN240
|
4.9
|
32.4
|
1.0
|
CE
|
A:LYS184
|
5.0
|
25.6
|
1.0
|
O
|
A:ILE462
|
5.0
|
34.3
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 8qyq
Go back to
Fluorine Binding Sites List in 8qyq
Fluorine binding site 3 out
of 6 in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1002
b:31.1
occ:1.00
|
F3
|
A:BEF1002
|
0.0
|
31.1
|
1.0
|
BE
|
A:BEF1002
|
1.5
|
34.0
|
1.0
|
O1B
|
A:ADP1001
|
2.5
|
35.3
|
1.0
|
F2
|
A:BEF1002
|
2.5
|
32.4
|
1.0
|
F1
|
A:BEF1002
|
2.5
|
38.6
|
1.0
|
N
|
A:GLY464
|
2.8
|
32.5
|
1.0
|
NZ
|
A:LYS184
|
3.0
|
27.3
|
1.0
|
CA
|
A:GLY464
|
3.3
|
31.4
|
1.0
|
CA
|
A:SER180
|
3.5
|
32.9
|
1.0
|
CE
|
A:LYS184
|
3.5
|
25.6
|
1.0
|
O
|
A:HOH1109
|
3.5
|
31.0
|
1.0
|
O
|
A:HOH1229
|
3.6
|
44.4
|
1.0
|
PB
|
A:ADP1001
|
3.6
|
37.6
|
1.0
|
O3B
|
A:ADP1001
|
3.8
|
37.0
|
1.0
|
C
|
A:ALA463
|
3.9
|
40.5
|
1.0
|
CB
|
A:SER180
|
3.9
|
33.8
|
1.0
|
O2B
|
A:ADP1001
|
4.0
|
35.3
|
1.0
|
MG
|
A:MG1003
|
4.1
|
27.6
|
1.0
|
OG
|
A:SER180
|
4.1
|
33.4
|
1.0
|
O
|
A:ILE462
|
4.2
|
34.3
|
1.0
|
CA
|
A:ALA463
|
4.2
|
32.3
|
1.0
|
N
|
A:GLY181
|
4.2
|
34.7
|
1.0
|
N
|
A:SER180
|
4.2
|
33.7
|
1.0
|
C
|
A:GLY464
|
4.3
|
34.0
|
1.0
|
C
|
A:SER180
|
4.4
|
39.7
|
1.0
|
O
|
A:GLU179
|
4.5
|
35.7
|
1.0
|
OG
|
A:SER241
|
4.5
|
35.5
|
1.0
|
O
|
A:GLY464
|
4.6
|
30.3
|
1.0
|
C
|
A:GLU179
|
4.7
|
37.3
|
1.0
|
N
|
A:SER242
|
4.8
|
27.2
|
1.0
|
O
|
A:SER242
|
4.9
|
31.7
|
1.0
|
O3A
|
A:ADP1001
|
4.9
|
35.7
|
1.0
|
ND2
|
A:ASN238
|
5.0
|
27.1
|
1.0
|
CB
|
A:SER242
|
5.0
|
29.1
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 8qyq
Go back to
Fluorine Binding Sites List in 8qyq
Fluorine binding site 4 out
of 6 in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1002
b:38.0
occ:1.00
|
F1
|
B:BEF1002
|
0.0
|
38.0
|
1.0
|
BE
|
B:BEF1002
|
1.5
|
38.4
|
1.0
|
MG
|
B:MG1006
|
2.2
|
35.4
|
1.0
|
O1B
|
B:ADP1001
|
2.5
|
39.2
|
1.0
|
F3
|
B:BEF1002
|
2.5
|
34.3
|
1.0
|
F2
|
B:BEF1002
|
2.5
|
42.0
|
1.0
|
O
|
B:HOH1129
|
2.7
|
50.2
|
1.0
|
O
|
B:HOH1120
|
2.9
|
36.0
|
1.0
|
O3B
|
B:ADP1001
|
2.9
|
39.9
|
1.0
|
N
|
B:SER242
|
3.1
|
31.9
|
1.0
|
OG
|
B:SER242
|
3.1
|
38.0
|
1.0
|
PB
|
B:ADP1001
|
3.3
|
39.2
|
1.0
|
CB
|
B:SER242
|
3.3
|
32.2
|
1.0
|
CA
|
B:SER242
|
3.8
|
30.6
|
1.0
|
ND2
|
B:ASN238
|
4.0
|
27.3
|
1.0
|
C
|
B:SER241
|
4.0
|
35.7
|
1.0
|
OG
|
B:SER241
|
4.0
|
51.2
|
1.0
|
CA
|
B:SER241
|
4.1
|
31.6
|
1.0
|
OG1
|
B:THR185
|
4.1
|
35.0
|
1.0
|
O
|
B:SER242
|
4.2
|
38.5
|
1.0
|
O2B
|
B:ADP1001
|
4.3
|
40.9
|
1.0
|
O3A
|
B:ADP1001
|
4.4
|
36.0
|
1.0
|
NZ
|
B:LYS184
|
4.5
|
13.7
|
1.0
|
N
|
B:GLY464
|
4.5
|
33.2
|
1.0
|
C
|
B:SER242
|
4.5
|
35.5
|
1.0
|
CE
|
B:LYS184
|
4.6
|
11.2
|
1.0
|
O
|
B:ILE462
|
4.6
|
30.8
|
1.0
|
O
|
B:ASN240
|
4.6
|
28.8
|
1.0
|
CB
|
B:SER241
|
4.7
|
37.2
|
1.0
|
O1A
|
B:ADP1001
|
4.8
|
38.7
|
1.0
|
CA
|
B:ALA463
|
4.9
|
30.4
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 8qyq
Go back to
Fluorine Binding Sites List in 8qyq
Fluorine binding site 5 out
of 6 in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1002
b:42.0
occ:1.00
|
F2
|
B:BEF1002
|
0.0
|
42.0
|
1.0
|
BE
|
B:BEF1002
|
1.5
|
38.4
|
1.0
|
O1B
|
B:ADP1001
|
2.5
|
39.2
|
1.0
|
F3
|
B:BEF1002
|
2.5
|
34.3
|
1.0
|
F1
|
B:BEF1002
|
2.5
|
38.0
|
1.0
|
NZ
|
B:LYS184
|
2.7
|
13.7
|
1.0
|
N
|
B:GLY464
|
2.8
|
33.2
|
1.0
|
CA
|
B:GLY464
|
3.1
|
33.6
|
1.0
|
CA
|
B:SER180
|
3.2
|
34.9
|
1.0
|
CE
|
B:LYS184
|
3.4
|
11.2
|
1.0
|
PB
|
B:ADP1001
|
3.6
|
39.2
|
1.0
|
O
|
B:HOH1129
|
3.7
|
50.2
|
1.0
|
CB
|
B:SER180
|
3.7
|
36.7
|
1.0
|
N
|
B:SER180
|
3.9
|
36.6
|
1.0
|
O2B
|
B:ADP1001
|
4.0
|
40.9
|
1.0
|
C
|
B:ALA463
|
4.0
|
36.6
|
1.0
|
OG
|
B:SER180
|
4.0
|
44.2
|
1.0
|
O
|
B:GLU179
|
4.1
|
37.4
|
1.0
|
C
|
B:GLY464
|
4.1
|
37.7
|
1.0
|
O3B
|
B:ADP1001
|
4.1
|
39.9
|
1.0
|
N
|
B:GLY181
|
4.1
|
35.5
|
1.0
|
C
|
B:SER180
|
4.2
|
39.2
|
1.0
|
MG
|
B:MG1006
|
4.2
|
35.4
|
1.0
|
C
|
B:GLU179
|
4.2
|
38.6
|
1.0
|
O
|
B:HOH1126
|
4.3
|
37.8
|
1.0
|
O
|
B:ILE462
|
4.3
|
30.8
|
1.0
|
CA
|
B:ALA463
|
4.4
|
30.4
|
1.0
|
O
|
B:GLY464
|
4.4
|
36.2
|
1.0
|
O
|
B:GLY178
|
4.7
|
38.0
|
1.0
|
OG
|
B:SER241
|
4.8
|
51.2
|
1.0
|
CD
|
B:LYS184
|
4.9
|
17.8
|
1.0
|
O3A
|
B:ADP1001
|
4.9
|
36.0
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 8qyq
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Fluorine Binding Sites List in 8qyq
Fluorine binding site 6 out
of 6 in the Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Beta-Cardiac Myosin S1 Fragment in the Pre-Powerstroke State Complexed to Mavacamten within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1002
b:34.3
occ:1.00
|
F3
|
B:BEF1002
|
0.0
|
34.3
|
1.0
|
BE
|
B:BEF1002
|
1.5
|
38.4
|
1.0
|
F1
|
B:BEF1002
|
2.5
|
38.0
|
1.0
|
F2
|
B:BEF1002
|
2.5
|
42.0
|
1.0
|
O1B
|
B:ADP1001
|
2.6
|
39.2
|
1.0
|
OG
|
B:SER180
|
2.7
|
44.2
|
1.0
|
OG
|
B:SER241
|
2.9
|
51.2
|
1.0
|
ND2
|
B:ASN238
|
3.3
|
27.3
|
1.0
|
CB
|
B:SER180
|
3.3
|
36.7
|
1.0
|
CA
|
B:SER180
|
3.4
|
34.9
|
1.0
|
CB
|
B:SER241
|
3.5
|
37.2
|
1.0
|
N
|
B:GLY181
|
3.6
|
35.5
|
1.0
|
CA
|
B:SER241
|
3.7
|
31.6
|
1.0
|
CB
|
B:ASN238
|
3.8
|
37.4
|
1.0
|
C
|
B:SER180
|
3.9
|
39.2
|
1.0
|
CG
|
B:ASN238
|
4.0
|
46.9
|
1.0
|
PB
|
B:ADP1001
|
4.0
|
39.2
|
1.0
|
N
|
B:SER242
|
4.1
|
31.9
|
1.0
|
O
|
B:HOH1126
|
4.3
|
37.8
|
1.0
|
C
|
B:SER241
|
4.4
|
35.7
|
1.0
|
O
|
B:HOH1120
|
4.5
|
36.0
|
1.0
|
MG
|
B:MG1006
|
4.6
|
35.4
|
1.0
|
O3B
|
B:ADP1001
|
4.6
|
39.9
|
1.0
|
O
|
B:HOH1108
|
4.6
|
33.0
|
1.0
|
CA
|
B:GLY181
|
4.7
|
35.0
|
1.0
|
N
|
B:SER180
|
4.7
|
36.6
|
1.0
|
O3A
|
B:ADP1001
|
4.7
|
36.0
|
1.0
|
N
|
B:SER241
|
4.7
|
30.0
|
1.0
|
N
|
B:GLY464
|
4.8
|
33.2
|
1.0
|
O
|
B:SER242
|
5.0
|
38.5
|
1.0
|
O
|
B:SER180
|
5.0
|
38.7
|
1.0
|
NZ
|
B:LYS184
|
5.0
|
13.7
|
1.0
|
|
Reference:
D.Auguin,
J.Robert-Paganin,
S.Rety,
C.Kikuti,
A.David,
G.Theumer,
A.W.Schmidt,
H.J.Knolker,
A.Houdusse.
Omecamtiv Mecarbil and Mavacamten Target the Same Myosin Pocket Despite Antagonistic Effects in Heart Contraction. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 38014327
DOI: 10.1101/2023.11.15.567213
Page generated: Fri Aug 2 22:33:38 2024
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