Fluorine in PDB 3rgf: Crystal Structure of Human CDK8/Cycc
Enzymatic activity of Crystal Structure of Human CDK8/Cycc
All present enzymatic activity of Crystal Structure of Human CDK8/Cycc:
2.7.11.22;
2.7.11.23;
Protein crystallography data
The structure of Crystal Structure of Human CDK8/Cycc, PDB code: 3rgf
was solved by
E.V.Schneider,
J.Boettcher,
M.Blaesse,
R.Huber,
K.Maskos,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.57 /
2.20
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.690,
70.610,
79.140,
90.00,
108.31,
90.00
|
R / Rfree (%)
|
18 /
22.1
|
Other elements in 3rgf:
The structure of Crystal Structure of Human CDK8/Cycc also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Human CDK8/Cycc
(pdb code 3rgf). 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 Human CDK8/Cycc, PDB code: 3rgf:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 3rgf
Go back to
Fluorine Binding Sites List in 3rgf
Fluorine binding site 1 out
of 3 in the Crystal Structure of Human CDK8/Cycc
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 CDK8/Cycc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F465
b:40.0
occ:1.00
|
F8
|
A:BAX465
|
0.0
|
40.0
|
1.0
|
C7
|
A:BAX465
|
1.3
|
40.6
|
1.0
|
F9
|
A:BAX465
|
2.2
|
40.3
|
1.0
|
F10
|
A:BAX465
|
2.2
|
41.8
|
1.0
|
C6
|
A:BAX465
|
2.4
|
40.5
|
1.0
|
C1
|
A:BAX465
|
2.8
|
40.5
|
1.0
|
O
|
A:ILE171
|
3.3
|
32.1
|
1.0
|
CG1
|
A:VAL78
|
3.5
|
31.1
|
1.0
|
C5
|
A:BAX465
|
3.7
|
40.5
|
1.0
|
C
|
A:ILE171
|
3.9
|
30.7
|
1.0
|
CA
|
A:ALA172
|
4.0
|
32.4
|
1.0
|
CG2
|
A:ILE171
|
4.2
|
27.6
|
1.0
|
C2
|
A:BAX465
|
4.2
|
33.6
|
1.0
|
C
|
A:ALA172
|
4.3
|
33.0
|
1.0
|
N
|
A:ALA172
|
4.3
|
31.9
|
1.0
|
CL11
|
A:BAX465
|
4.4
|
48.5
|
1.0
|
N
|
A:ASP173
|
4.4
|
36.5
|
1.0
|
O15
|
A:BAX465
|
4.5
|
32.9
|
1.0
|
CG2
|
A:ILE79
|
4.5
|
38.0
|
1.0
|
CD2
|
A:LEU70
|
4.6
|
39.1
|
1.0
|
CB
|
A:ILE171
|
4.6
|
30.3
|
1.0
|
CB
|
A:VAL78
|
4.7
|
33.9
|
1.0
|
N
|
A:ILE79
|
4.8
|
34.1
|
1.0
|
O
|
A:ALA172
|
4.8
|
33.2
|
1.0
|
CD1
|
A:LEU142
|
4.8
|
27.8
|
1.0
|
C4
|
A:BAX465
|
4.8
|
36.1
|
1.0
|
CB
|
A:ASP173
|
4.9
|
42.9
|
1.0
|
CD2
|
A:HIS149
|
4.9
|
29.3
|
1.0
|
CA
|
A:ILE171
|
5.0
|
31.1
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 3rgf
Go back to
Fluorine Binding Sites List in 3rgf
Fluorine binding site 2 out
of 3 in the Crystal Structure of Human CDK8/Cycc
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 CDK8/Cycc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F465
b:40.3
occ:1.00
|
F9
|
A:BAX465
|
0.0
|
40.3
|
1.0
|
C7
|
A:BAX465
|
1.3
|
40.6
|
1.0
|
F8
|
A:BAX465
|
2.2
|
40.0
|
1.0
|
F10
|
A:BAX465
|
2.2
|
41.8
|
1.0
|
C6
|
A:BAX465
|
2.4
|
40.5
|
1.0
|
CL11
|
A:BAX465
|
2.9
|
48.5
|
1.0
|
C5
|
A:BAX465
|
2.9
|
40.5
|
1.0
|
CD2
|
A:LEU142
|
3.4
|
24.6
|
1.0
|
C1
|
A:BAX465
|
3.5
|
40.5
|
1.0
|
CG1
|
A:VAL78
|
3.6
|
31.1
|
1.0
|
CD1
|
A:LEU73
|
3.6
|
41.2
|
1.0
|
CD1
|
A:LEU142
|
3.9
|
27.8
|
1.0
|
CG
|
A:LEU142
|
4.2
|
30.0
|
1.0
|
C4
|
A:BAX465
|
4.2
|
36.1
|
1.0
|
CD2
|
A:LEU70
|
4.6
|
39.1
|
1.0
|
C2
|
A:BAX465
|
4.7
|
33.6
|
1.0
|
CB
|
A:VAL78
|
4.9
|
33.9
|
1.0
|
C3
|
A:BAX465
|
4.9
|
36.6
|
1.0
|
CG
|
A:LEU73
|
5.0
|
38.1
|
1.0
|
CG1
|
A:VAL147
|
5.0
|
33.0
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 3rgf
Go back to
Fluorine Binding Sites List in 3rgf
Fluorine binding site 3 out
of 3 in the Crystal Structure of Human CDK8/Cycc
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 CDK8/Cycc within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F465
b:41.8
occ:1.00
|
F10
|
A:BAX465
|
0.0
|
41.8
|
1.0
|
C7
|
A:BAX465
|
1.4
|
40.6
|
1.0
|
F9
|
A:BAX465
|
2.2
|
40.3
|
1.0
|
F8
|
A:BAX465
|
2.2
|
40.0
|
1.0
|
C6
|
A:BAX465
|
2.3
|
40.5
|
1.0
|
C5
|
A:BAX465
|
2.9
|
40.5
|
1.0
|
CL11
|
A:BAX465
|
3.0
|
48.5
|
1.0
|
CD2
|
A:HIS149
|
3.4
|
29.3
|
1.0
|
C1
|
A:BAX465
|
3.4
|
40.5
|
1.0
|
CD1
|
A:LEU142
|
3.7
|
27.8
|
1.0
|
NE2
|
A:HIS149
|
4.0
|
30.3
|
1.0
|
CG2
|
A:ILE171
|
4.2
|
27.6
|
1.0
|
CB
|
A:ASP173
|
4.2
|
42.9
|
1.0
|
C4
|
A:BAX465
|
4.2
|
36.1
|
1.0
|
CG
|
A:HIS149
|
4.2
|
28.8
|
1.0
|
C2
|
A:BAX465
|
4.5
|
33.6
|
1.0
|
CD2
|
A:LEU142
|
4.6
|
24.6
|
1.0
|
C
|
A:ALA172
|
4.6
|
33.0
|
1.0
|
N
|
A:ASP173
|
4.7
|
36.5
|
1.0
|
CB
|
A:HIS149
|
4.7
|
29.4
|
1.0
|
O
|
A:ALA172
|
4.7
|
33.2
|
1.0
|
CG
|
A:LEU142
|
4.8
|
30.0
|
1.0
|
CA
|
A:HIS149
|
4.8
|
30.1
|
1.0
|
OD2
|
A:ASP173
|
4.9
|
61.7
|
1.0
|
C3
|
A:BAX465
|
4.9
|
36.6
|
1.0
|
O
|
A:ILE171
|
5.0
|
32.1
|
1.0
|
|
Reference:
E.V.Schneider,
J.Bottcher,
M.Blaesse,
L.Neumann,
R.Huber,
K.Maskos.
The Structure of CDK8/Cycc Implicates Specificity in the Cdk/Cyclin Family and Reveals Interaction with A Deep Pocket Binder. J.Mol.Biol. V. 412 251 2011.
ISSN: ISSN 0022-2836
PubMed: 21806996
DOI: 10.1016/J.JMB.2011.07.020
Page generated: Sun Dec 13 11:54:35 2020
|