Fluorine in PDB 8rap: Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex

Enzymatic activity of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex

All present enzymatic activity of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex:
2.7.7.6;

Other elements in 8rap:

The structure of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 9 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex (pdb code 8rap). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex, PDB code: 8rap:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8rap

Go back to Fluorine Binding Sites List in 8rap
Fluorine binding site 1 out of 3 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:F3003

b:224.7
occ:1.00
 F1 O:BEF3003 0.0 224.7 1.0
BE O:BEF3003 1.5 224.7 1.0
OE2 O:GLU1591 2.1 213.1 1.0
F3 O:BEF3003 2.5 224.7 1.0
F2 O:BEF3003 2.6 224.7 1.0
O1B O:ADP3001 3.1 213.0 1.0
CD O:GLU1591 3.3 213.1 1.0
NZ O:LYS1363 3.3 210.1 1.0
PB O:ADP3001 3.3 213.0 1.0
CA O:GLY1785 3.4 232.1 1.0
O3B O:ADP3001 3.4 213.0 1.0
CD O:LYS1363 3.4 210.1 1.0
O2B O:ADP3001 3.4 213.0 1.0
CE O:LYS1363 3.6 210.1 1.0
N O:GLY1785 3.8 232.1 1.0
OE1 O:GLU1591 3.9 213.1 1.0
MG O:MG3002 3.9 207.3 1.0
NE2 O:GLN1619 3.9 218.5 1.0
NH2 O:ARG1820 4.4 230.3 1.0
CG O:GLU1591 4.4 213.1 1.0
CG O:LYS1363 4.5 210.1 1.0
C O:GLY1785 4.6 232.1 1.0
NH1 O:ARG1820 4.6 230.3 1.0
CG O:GLN1784 4.7 226.0 1.0
O O:GLY1785 4.8 232.1 1.0
C O:GLN1784 4.8 226.0 1.0
CZ O:ARG1820 4.9 230.3 1.0
O3A O:ADP3001 4.9 213.0 1.0
NH1 O:ARG1656 5.0 225.3 1.0

Fluorine binding site 2 out of 3 in 8rap

Go back to Fluorine Binding Sites List in 8rap
Fluorine binding site 2 out of 3 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:F3003

b:224.7
occ:1.00
 F2 O:BEF3003 0.0 224.7 1.0
BE O:BEF3003 1.6 224.7 1.0
F3 O:BEF3003 2.5 224.7 1.0
F1 O:BEF3003 2.6 224.7 1.0
NZ O:LYS1363 2.9 210.1 1.0
NE2 O:GLN1619 3.2 218.5 1.0
CD O:LYS1363 3.2 210.1 1.0
CA O:PRO1359 3.2 220.1 1.0
CG O:PRO1359 3.3 220.1 1.0
N O:PRO1359 3.4 220.1 1.0
O1B O:ADP3001 3.4 213.0 1.0
CB O:PRO1359 3.5 220.1 1.0
CE O:LYS1363 3.6 210.1 1.0
CD O:PRO1359 3.7 220.1 1.0
OE2 O:GLU1591 3.9 213.1 1.0
CD O:GLN1619 3.9 218.5 1.0
C O:PRO1358 3.9 212.2 1.0
O O:GLY1357 4.0 207.8 1.0
CG O:GLN1619 4.2 218.5 1.0
O O:PRO1358 4.2 212.2 1.0
PB O:ADP3001 4.5 213.0 1.0
OE1 O:GLU1591 4.6 213.1 1.0
CB O:ASP1616 4.6 215.8 1.0
CG O:LYS1363 4.6 210.1 1.0
NH2 O:ARG1820 4.6 230.3 1.0
C O:PRO1359 4.6 220.1 1.0
CD O:GLU1591 4.6 213.1 1.0
OE1 O:GLN1619 4.7 218.5 1.0
CA O:PRO1358 4.7 212.2 1.0
O3B O:ADP3001 4.9 213.0 1.0
NH1 O:ARG1656 5.0 225.3 1.0

Fluorine binding site 3 out of 3 in 8rap

Go back to Fluorine Binding Sites List in 8rap
Fluorine binding site 3 out of 3 in the Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of SEN1-Adp.BEF3 Bound Rna Polymerase II Pre-Termination Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:F3003

b:224.7
occ:1.00
 F3 O:BEF3003 0.0 224.7 1.0
BE O:BEF3003 1.5 224.7 1.0
NH2 O:ARG1820 2.3 230.3 1.0
NE2 O:GLN1619 2.3 218.5 1.0
F2 O:BEF3003 2.5 224.7 1.0
F1 O:BEF3003 2.5 224.7 1.0
CZ O:ARG1820 3.2 230.3 1.0
CG O:PRO1359 3.3 220.1 1.0
CB O:PRO1359 3.3 220.1 1.0
CD O:GLN1619 3.6 218.5 1.0
NH1 O:ARG1820 3.6 230.3 1.0
O1B O:ADP3001 3.7 213.0 1.0
O3B O:ADP3001 3.8 213.0 1.0
CA O:PRO1359 4.0 220.1 1.0
NH1 O:ARG1656 4.0 225.3 1.0
N O:GLY1785 4.1 232.1 1.0
NE O:ARG1820 4.3 230.3 1.0
OE1 O:GLN1619 4.3 218.5 1.0
PB O:ADP3001 4.3 213.0 1.0
OG1 O:THR1819 4.3 233.0 1.0
OE2 O:GLU1591 4.3 213.1 1.0
CA O:GLY1785 4.3 232.1 1.0
CD O:PRO1359 4.5 220.1 1.0
CG O:GLN1619 4.6 218.5 1.0
N O:PRO1359 4.6 220.1 1.0
CG O:GLN1784 4.6 226.0 1.0
NZ O:LYS1363 4.9 210.1 1.0
CB O:THR1819 4.9 233.0 1.0

Reference:

S.Rengachari, T.Hainthaler, C.Oberthuer, M.Lidschreiber, P.Cramer. Mechanism of Polyadenylation-Independent Rna Polymerase II Termination. Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
PubMed: 39424994
DOI: 10.1038/S41594-024-01409-0
Page generated: Wed Nov 13 08:16:48 2024

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