Fluorine in PDB 7q2y: Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II)
Other elements in 7q2y:
The structure of Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II) also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II)
(pdb code 7q2y). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II), PDB code: 7q2y:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 7q2y
Go back to
Fluorine Binding Sites List in 7q2y
Fluorine binding site 1 out
of 6 in the Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2002
b:46.5
occ:1.00
|
F1
|
A:BEF2002
|
0.0
|
46.5
|
1.0
|
BE
|
A:BEF2002
|
1.5
|
46.5
|
1.0
|
N
|
B:GLY1326
|
2.5
|
37.9
|
1.0
|
F3
|
A:BEF2002
|
2.5
|
46.5
|
1.0
|
F2
|
A:BEF2002
|
2.6
|
46.5
|
1.0
|
ND2
|
A:ASN34
|
3.1
|
39.2
|
1.0
|
CA
|
B:GLY1326
|
3.2
|
37.9
|
1.0
|
OG
|
B:SER1324
|
3.4
|
43.7
|
1.0
|
O2B
|
A:ADP2001
|
3.5
|
56.4
|
1.0
|
N
|
B:GLY1325
|
3.5
|
38.8
|
1.0
|
C
|
B:GLY1325
|
3.6
|
38.8
|
1.0
|
O3B
|
A:ADP2001
|
3.6
|
56.4
|
1.0
|
CB
|
B:SER1324
|
3.7
|
43.7
|
1.0
|
CA
|
B:GLY1325
|
3.8
|
38.8
|
1.0
|
O
|
B:ALA1356
|
3.8
|
40.6
|
1.0
|
NE2
|
A:GLN147
|
3.9
|
37.4
|
1.0
|
CG
|
A:ASN34
|
3.9
|
39.2
|
1.0
|
PB
|
A:ADP2001
|
4.0
|
56.4
|
1.0
|
CB
|
A:ASN34
|
4.1
|
39.2
|
1.0
|
C
|
B:SER1324
|
4.1
|
43.7
|
1.0
|
CA
|
A:ASN34
|
4.3
|
39.2
|
1.0
|
C
|
B:GLY1326
|
4.4
|
37.9
|
1.0
|
O3A
|
A:ADP2001
|
4.5
|
56.4
|
1.0
|
N
|
B:GLU1327
|
4.5
|
41.4
|
1.0
|
CA
|
B:SER1324
|
4.5
|
43.7
|
1.0
|
MG
|
A:MG2003
|
4.6
|
42.4
|
1.0
|
OE1
|
A:GLN147
|
4.6
|
37.4
|
1.0
|
O
|
B:GLY1325
|
4.7
|
38.8
|
1.0
|
N
|
A:GLY35
|
4.7
|
42.0
|
1.0
|
CD
|
A:GLN147
|
4.7
|
37.4
|
1.0
|
C
|
B:ALA1356
|
4.8
|
40.6
|
1.0
|
O
|
B:SER1324
|
4.8
|
43.7
|
1.0
|
OD1
|
A:ASN34
|
4.9
|
39.2
|
1.0
|
CB
|
B:ALA1356
|
4.9
|
40.6
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 7q2y
Go back to
Fluorine Binding Sites List in 7q2y
Fluorine binding site 2 out
of 6 in the Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2002
b:46.5
occ:1.00
|
F2
|
A:BEF2002
|
0.0
|
46.5
|
1.0
|
BE
|
A:BEF2002
|
1.6
|
46.5
|
1.0
|
F3
|
A:BEF2002
|
2.5
|
46.5
|
1.0
|
O3B
|
A:ADP2001
|
2.5
|
56.4
|
1.0
|
ND2
|
A:ASN34
|
2.6
|
39.2
|
1.0
|
F1
|
A:BEF2002
|
2.6
|
46.5
|
1.0
|
CD1
|
A:LEU1144
|
3.3
|
36.9
|
1.0
|
OE2
|
A:GLU1113
|
3.5
|
40.4
|
1.0
|
PB
|
A:ADP2001
|
3.6
|
56.4
|
1.0
|
O2B
|
A:ADP2001
|
3.6
|
56.4
|
1.0
|
NZ
|
A:LYS38
|
3.8
|
31.9
|
1.0
|
CG
|
A:ASN34
|
3.8
|
39.2
|
1.0
|
CG
|
A:LEU1144
|
3.9
|
36.9
|
1.0
|
CD2
|
A:LEU1144
|
3.9
|
36.9
|
1.0
|
CA
|
A:ASN34
|
4.0
|
39.2
|
1.0
|
CE
|
A:LYS38
|
4.1
|
31.9
|
1.0
|
CB
|
A:ASN34
|
4.3
|
39.2
|
1.0
|
O
|
B:ALA1356
|
4.4
|
40.6
|
1.0
|
CD
|
A:GLU1113
|
4.4
|
40.4
|
1.0
|
N
|
A:ASN34
|
4.6
|
39.2
|
1.0
|
O1B
|
A:ADP2001
|
4.6
|
56.4
|
1.0
|
O
|
A:LEU33
|
4.6
|
39.3
|
1.0
|
O3A
|
A:ADP2001
|
4.7
|
56.4
|
1.0
|
C
|
B:ALA1356
|
4.8
|
40.6
|
1.0
|
OD1
|
A:ASN34
|
4.8
|
39.2
|
1.0
|
NE2
|
A:GLN147
|
4.9
|
37.4
|
1.0
|
C
|
A:LEU33
|
4.9
|
39.3
|
1.0
|
N
|
B:GLY1326
|
4.9
|
37.9
|
1.0
|
N
|
A:GLY35
|
4.9
|
42.0
|
1.0
|
OE1
|
A:GLU1113
|
5.0
|
40.4
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 7q2y
Go back to
Fluorine Binding Sites List in 7q2y
Fluorine binding site 3 out
of 6 in the Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2002
b:46.5
occ:1.00
|
F3
|
A:BEF2002
|
0.0
|
46.5
|
1.0
|
BE
|
A:BEF2002
|
1.5
|
46.5
|
1.0
|
O2B
|
A:ADP2001
|
2.3
|
56.4
|
1.0
|
F2
|
A:BEF2002
|
2.5
|
46.5
|
1.0
|
F1
|
A:BEF2002
|
2.5
|
46.5
|
1.0
|
OE1
|
A:GLN147
|
2.7
|
37.4
|
1.0
|
NE2
|
A:GLN147
|
2.7
|
37.4
|
1.0
|
CD
|
A:GLN147
|
3.1
|
37.4
|
1.0
|
MG
|
A:MG2003
|
3.2
|
42.4
|
1.0
|
PB
|
A:ADP2001
|
3.3
|
56.4
|
1.0
|
OE2
|
A:GLU1113
|
3.3
|
40.4
|
1.0
|
O3B
|
A:ADP2001
|
3.4
|
56.4
|
1.0
|
CG
|
A:GLU1113
|
3.7
|
40.4
|
1.0
|
CD
|
A:GLU1113
|
3.7
|
40.4
|
1.0
|
OG
|
A:SER39
|
4.2
|
40.0
|
1.0
|
O1B
|
A:ADP2001
|
4.3
|
56.4
|
1.0
|
O3A
|
A:ADP2001
|
4.5
|
56.4
|
1.0
|
N
|
B:GLY1325
|
4.5
|
38.8
|
1.0
|
CG
|
A:GLN147
|
4.5
|
37.4
|
1.0
|
N
|
B:GLY1326
|
4.6
|
37.9
|
1.0
|
OE1
|
A:GLU1113
|
4.6
|
40.4
|
1.0
|
ND2
|
A:ASN34
|
4.6
|
39.2
|
1.0
|
CB
|
B:ALA1356
|
4.8
|
40.6
|
1.0
|
CA
|
B:GLY1325
|
4.9
|
38.8
|
1.0
|
O
|
B:ALA1356
|
4.9
|
40.6
|
1.0
|
CB
|
B:SER1324
|
5.0
|
43.7
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 7q2y
Go back to
Fluorine Binding Sites List in 7q2y
Fluorine binding site 4 out
of 6 in the Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F2002
b:44.7
occ:1.00
|
F1
|
B:BEF2002
|
0.0
|
44.7
|
1.0
|
BE
|
B:BEF2002
|
1.5
|
44.7
|
1.0
|
OG
|
A:SER1085
|
2.3
|
43.0
|
1.0
|
ND2
|
B:ASN187
|
2.5
|
38.7
|
1.0
|
F3
|
B:BEF2002
|
2.5
|
44.7
|
1.0
|
F2
|
B:BEF2002
|
2.6
|
44.7
|
1.0
|
N
|
A:GLY1087
|
2.9
|
35.7
|
1.0
|
CG
|
B:ASN187
|
3.4
|
38.7
|
1.0
|
CA
|
A:GLY1087
|
3.4
|
35.7
|
1.0
|
O1B
|
B:ADP2001
|
3.5
|
56.4
|
1.0
|
CB
|
B:ASN187
|
3.5
|
38.7
|
1.0
|
CB
|
A:SER1085
|
3.7
|
43.0
|
1.0
|
CA
|
B:ASN187
|
3.8
|
38.7
|
1.0
|
O
|
A:ALA1117
|
4.0
|
36.3
|
1.0
|
O3B
|
B:ADP2001
|
4.0
|
56.4
|
1.0
|
N
|
A:GLY1086
|
4.0
|
35.7
|
1.0
|
N
|
B:GLY188
|
4.0
|
41.9
|
1.0
|
C
|
A:GLY1086
|
4.1
|
35.7
|
1.0
|
NE2
|
B:GLN302
|
4.3
|
39.6
|
1.0
|
PB
|
B:ADP2001
|
4.3
|
56.4
|
1.0
|
C
|
B:ASN187
|
4.4
|
38.7
|
1.0
|
MG
|
B:MG2003
|
4.4
|
38.2
|
1.0
|
C
|
A:GLY1087
|
4.4
|
35.7
|
1.0
|
CA
|
A:GLY1086
|
4.5
|
35.7
|
1.0
|
N
|
A:GLN1088
|
4.5
|
34.8
|
1.0
|
OD1
|
B:ASN187
|
4.5
|
38.7
|
1.0
|
C
|
A:SER1085
|
4.5
|
43.0
|
1.0
|
CA
|
A:SER1085
|
4.6
|
43.0
|
1.0
|
NZ
|
B:LYS191
|
4.9
|
39.9
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 7q2y
Go back to
Fluorine Binding Sites List in 7q2y
Fluorine binding site 5 out
of 6 in the Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F2002
b:44.7
occ:1.00
|
F2
|
B:BEF2002
|
0.0
|
44.7
|
1.0
|
BE
|
B:BEF2002
|
1.6
|
44.7
|
1.0
|
F3
|
B:BEF2002
|
2.5
|
44.7
|
1.0
|
F1
|
B:BEF2002
|
2.6
|
44.7
|
1.0
|
ND2
|
B:ASN187
|
2.8
|
38.7
|
1.0
|
CE
|
B:LYS191
|
3.3
|
39.9
|
1.0
|
NZ
|
B:LYS191
|
3.5
|
39.9
|
1.0
|
CD1
|
B:LEU1383
|
3.6
|
38.6
|
1.0
|
O1B
|
B:ADP2001
|
3.6
|
56.4
|
1.0
|
MG
|
B:MG2003
|
3.9
|
38.2
|
1.0
|
NE2
|
B:GLN302
|
4.0
|
39.6
|
1.0
|
CG
|
B:ASN187
|
4.0
|
38.7
|
1.0
|
O3B
|
B:ADP2001
|
4.1
|
56.4
|
1.0
|
PB
|
B:ADP2001
|
4.4
|
56.4
|
1.0
|
CG
|
B:LEU1383
|
4.4
|
38.6
|
1.0
|
O
|
A:ALA1117
|
4.4
|
36.3
|
1.0
|
OG
|
A:SER1085
|
4.5
|
43.0
|
1.0
|
CD2
|
B:LEU1383
|
4.6
|
38.6
|
1.0
|
CA
|
B:ASN187
|
4.6
|
38.7
|
1.0
|
CD
|
B:LYS191
|
4.6
|
39.9
|
1.0
|
CB
|
B:ASN187
|
4.7
|
38.7
|
1.0
|
OD1
|
B:ASN187
|
4.9
|
38.7
|
1.0
|
CG
|
B:LYS191
|
5.0
|
39.9
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 7q2y
Go back to
Fluorine Binding Sites List in 7q2y
Fluorine binding site 6 out
of 6 in the Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Cryo-Em Structure of Clamped S.Cerevisiae Condensin-Dna Complex (Form II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F2002
b:44.7
occ:1.00
|
F3
|
B:BEF2002
|
0.0
|
44.7
|
1.0
|
BE
|
B:BEF2002
|
1.5
|
44.7
|
1.0
|
MG
|
B:MG2003
|
2.0
|
38.2
|
1.0
|
O1B
|
B:ADP2001
|
2.3
|
56.4
|
1.0
|
F2
|
B:BEF2002
|
2.5
|
44.7
|
1.0
|
F1
|
B:BEF2002
|
2.5
|
44.7
|
1.0
|
NE2
|
B:GLN302
|
2.6
|
39.6
|
1.0
|
OG
|
A:SER1085
|
3.2
|
43.0
|
1.0
|
CD
|
B:GLN302
|
3.3
|
39.6
|
1.0
|
OE1
|
B:GLN302
|
3.4
|
39.6
|
1.0
|
PB
|
B:ADP2001
|
3.6
|
56.4
|
1.0
|
N
|
A:GLY1086
|
3.9
|
35.7
|
1.0
|
OG
|
B:SER192
|
4.1
|
46.5
|
1.0
|
O3B
|
B:ADP2001
|
4.2
|
56.4
|
1.0
|
CB
|
A:SER1085
|
4.3
|
43.0
|
1.0
|
N
|
A:GLY1087
|
4.3
|
35.7
|
1.0
|
ND2
|
B:ASN187
|
4.4
|
38.7
|
1.0
|
CA
|
A:GLY1086
|
4.5
|
35.7
|
1.0
|
O2B
|
B:ADP2001
|
4.6
|
56.4
|
1.0
|
CG
|
B:GLN302
|
4.6
|
39.6
|
1.0
|
O3A
|
B:ADP2001
|
4.6
|
56.4
|
1.0
|
CA
|
A:SER1085
|
4.8
|
43.0
|
1.0
|
C
|
A:SER1085
|
4.8
|
43.0
|
1.0
|
CE
|
B:LYS191
|
5.0
|
39.9
|
1.0
|
O1A
|
B:ADP2001
|
5.0
|
56.4
|
1.0
|
C
|
A:GLY1086
|
5.0
|
35.7
|
1.0
|
|
Reference:
B.G.Lee,
J.Rhodes,
J.Lowe.
Clamping of Dna Shuts the Condensin Neck Gate. Proc.Natl.Acad.Sci.Usa V. 119 06119 2022.
ISSN: ESSN 1091-6490
PubMed: 35349345
DOI: 10.1073/PNAS.2120006119
Page generated: Fri Aug 2 11:15:04 2024
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