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Bromine in PDB 8bud: Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K

Enzymatic activity of Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K

All present enzymatic activity of Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K:
2.7.11.22; 2.7.11.23;

Protein crystallography data

The structure of Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K, PDB code: 8bud was solved by Z.Kozicka, G.Kempf, G.Petzold, N.H.Thoma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.35 / 3.20
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 249.626, 249.626, 218.222, 90, 90, 120
R / Rfree (%) 18.9 / 22

Bromine Binding Sites:

The binding sites of Bromine atom in the Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K (pdb code 8bud). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K, PDB code: 8bud:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in 8bud

Go back to Bromine Binding Sites List in 8bud
Bromine binding site 1 out of 3 in the Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1101

b:350.1
occ:1.00
BR1 B:RP91101 0.0 350.1 1.0
C14 B:RP91101 1.9 130.3 1.0
HB2 B:PHE813 2.8 158.4 0.0
C13 B:RP91101 2.8 130.7 1.0
C15 B:RP91101 2.8 126.1 1.0
H131 B:RP91101 2.9 156.8 0.0
H151 B:RP91101 2.9 151.3 0.0
HB3 B:PHE813 3.0 158.4 0.0
CB B:PHE813 3.2 132.0 1.0
CG B:PHE813 3.4 133.1 1.0
HB3 B:ALA754 3.4 133.9 0.0
CD2 B:PHE813 3.6 131.1 1.0
HD2 B:LYS756 3.6 140.3 0.0
HD2 B:PHE813 3.6 157.3 0.0
HG21 B:VAL787 3.6 142.2 0.0
CD1 B:PHE813 4.0 137.0 1.0
HB1 B:ALA754 4.1 133.9 0.0
N4 B:RP91101 4.1 125.7 1.0
C16 B:RP91101 4.1 122.3 1.0
CB B:ALA754 4.2 111.6 1.0
HG3 B:LYS756 4.3 136.2 0.0
HD11 B:LEU866 4.3 143.2 0.0
HD1 B:PHE813 4.3 164.5 0.0
HB1 B:ALA876 4.3 156.4 0.0
CE2 B:PHE813 4.5 129.4 1.0
HG11 B:VAL741 4.5 126.1 0.0
HB2 B:ALA754 4.5 133.9 0.0
CD B:LYS756 4.5 116.9 1.0
CG2 B:VAL787 4.6 118.5 1.0
C12 B:RP91101 4.6 123.9 1.0
O B:GLU814 4.6 130.8 1.0
CA B:PHE813 4.7 127.3 1.0
HG11 B:VAL787 4.7 135.6 0.0
HD13 B:LEU866 4.7 143.2 0.0
HG22 B:VAL787 4.7 142.2 0.0
CE1 B:PHE813 4.8 139.0 1.0
CD1 B:LEU866 4.8 119.3 1.0
HD12 B:LEU866 4.8 143.2 0.0
CG B:LYS756 4.8 113.5 1.0
H161 B:RP91101 4.8 146.8 0.0
HE2 B:PHE813 5.0 155.3 0.0
HG2 B:LYS756 5.0 136.2 0.0

Bromine binding site 2 out of 3 in 8bud

Go back to Bromine Binding Sites List in 8bud
Bromine binding site 2 out of 3 in the Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br1201

b:437.6
occ:1.00
BR1 D:RP91201 0.0 437.6 1.0
C14 D:RP91201 1.9 133.3 1.0
C13 D:RP91201 2.8 128.8 1.0
C15 D:RP91201 2.8 127.5 1.0
H131 D:RP91201 2.9 154.6 0.0
H151 D:RP91201 2.9 153.0 0.0
HB2 E:PHE813 3.0 136.7 0.0
HB3 E:PHE813 3.0 136.7 0.0
CB E:PHE813 3.3 113.9 1.0
HG21 E:VAL787 3.4 143.6 0.0
HB3 E:ALA754 3.4 132.3 0.0
CG E:PHE813 3.5 113.2 1.0
HE3 E:LYS756 3.5 154.2 0.0
CD2 E:PHE813 3.8 110.8 1.0
HD11 E:LEU866 3.8 128.4 0.0
HD2 E:PHE813 3.8 132.9 0.0
CD1 E:PHE813 4.0 114.2 1.0
N4 D:RP91201 4.1 123.3 1.0
C16 D:RP91201 4.1 122.3 1.0
HB1 E:ALA754 4.1 132.3 0.0
CB E:ALA754 4.2 110.2 1.0
CG2 E:VAL787 4.3 119.6 1.0
HD1 E:PHE813 4.3 137.1 0.0
HB2 E:ALA754 4.4 132.3 0.0
HD13 E:LEU866 4.4 128.4 0.0
HB1 E:ALA876 4.4 138.2 0.0
CE E:LYS756 4.5 128.5 1.0
CD1 E:LEU866 4.5 107.0 1.0
HG22 E:VAL787 4.5 143.6 0.0
HG23 E:VAL787 4.5 143.6 0.0
HG3 E:LYS756 4.5 138.5 0.0
CE2 E:PHE813 4.6 111.1 1.0
C12 D:RP91201 4.6 121.5 1.0
O E:GLU814 4.6 137.6 1.0
HE2 E:LYS756 4.7 154.2 0.0
HG11 E:VAL741 4.7 127.9 0.0
HD12 E:LEU866 4.7 128.4 0.0
CE1 E:PHE813 4.8 114.4 1.0
CA E:PHE813 4.8 111.3 1.0
H161 D:RP91201 4.9 146.8 0.0
HZ1 E:LYS756 4.9 158.0 0.0
HG11 E:VAL787 5.0 135.9 0.0

Bromine binding site 3 out of 3 in 8bud

Go back to Bromine Binding Sites List in 8bud
Bromine binding site 3 out of 3 in the Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of DDB1 Bound to Z7-Engaged CDK12-Cyclin K within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Br1101

b:351.3
occ:1.00
BR1 H:RP91101 0.0 351.3 1.0
C14 H:RP91101 1.9 122.0 1.0
C13 H:RP91101 2.8 122.7 1.0
C15 H:RP91101 2.8 122.0 1.0
H131 H:RP91101 2.9 147.3 0.0
H151 H:RP91101 2.9 146.5 0.0
HB2 H:PHE813 3.0 140.5 0.0
HB3 H:PHE813 3.0 140.5 0.0
CB H:PHE813 3.3 117.0 1.0
HE3 H:LYS756 3.3 154.8 0.0
HG21 H:VAL787 3.4 119.4 0.0
HB3 H:ALA754 3.4 132.4 0.0
CG H:PHE813 3.4 117.1 1.0
CD2 H:PHE813 3.7 115.7 1.0
HD2 H:PHE813 3.8 138.9 0.0
HD11 H:LEU866 3.9 125.8 0.0
CD1 H:PHE813 4.0 115.7 1.0
HB1 H:ALA754 4.1 132.4 0.0
N4 H:RP91101 4.1 117.2 1.0
C16 H:RP91101 4.1 118.9 1.0
CB H:ALA754 4.1 110.3 1.0
HD1 H:PHE813 4.2 138.9 0.0
CE H:LYS756 4.2 129.0 1.0
CG2 H:VAL787 4.2 99.5 1.0
HD13 H:LEU866 4.4 125.8 0.0
HE2 H:LYS756 4.4 154.8 0.0
HG22 H:VAL787 4.4 119.4 0.0
O H:GLU814 4.4 125.8 1.0
CD1 H:LEU866 4.4 104.8 1.0
HB2 H:ALA754 4.5 132.4 0.0
HG3 H:LYS756 4.5 139.8 0.0
CE2 H:PHE813 4.5 116.2 1.0
HZ1 H:LYS756 4.5 154.5 0.0
HD12 H:LEU866 4.6 125.8 0.0
C12 H:RP91101 4.6 116.5 1.0
HG23 H:VAL787 4.6 119.4 0.0
HB1 H:ALA876 4.7 139.3 0.0
CE1 H:PHE813 4.7 116.9 1.0
HG11 H:VAL741 4.7 130.4 0.0
HG11 H:VAL787 4.8 114.2 0.0
CA H:PHE813 4.8 112.9 1.0
NZ H:LYS756 4.9 128.8 1.0
H161 H:RP91101 4.9 142.7 0.0
CZ H:PHE813 5.0 120.2 1.0
HZ2 H:LYS756 5.0 154.5 0.0

Reference:

Z.Kozicka, G.Kempf, G.Petzold, N.H.Thoma. Structure of DDB1 Bound to DS17-Engaged CDK12-Cyclin K To Be Published.
Page generated: Thu Jul 11 04:55:27 2024

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