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Fluorine in PDB 6vcl: Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-

Enzymatic activity of Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-

All present enzymatic activity of Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-:
5.1.1.7;

Protein crystallography data

The structure of Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-, PDB code: 6vcl was solved by A.Gao, N.Vasilyev, A.Kaushik, W.Duan, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.06
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 162.444, 190.649, 51.336, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.7

Other elements in 6vcl:

The structure of Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F- also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F- (pdb code 6vcl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-, PDB code: 6vcl:

Fluorine binding site 1 out of 1 in 6vcl

Go back to Fluorine Binding Sites List in 6vcl
Fluorine binding site 1 out of 1 in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-


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 E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F- within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F208

b:32.9
occ:1.00
 MG B:MG204 1.9 34.3 1.0
MG B:MG202 2.0 35.5 1.0
MG B:MG203 2.0 34.7 1.0
OE2 B:GLU57 2.7 35.5 1.0
O B:HOH405 2.7 35.8 1.0
O2G B:0O2209 2.7 38.5 1.0
O B:HOH370 2.8 41.2 1.0
OE1 B:GLU120 2.8 35.3 1.0
OE2 B:GLU120 2.9 32.3 1.0
O B:HOH304 2.9 29.7 1.0
O1G B:0O2209 2.9 33.0 1.0
O B:GLN37 3.0 29.5 1.0
OE1 B:GLU53 3.1 30.9 1.0
CD B:GLU120 3.2 40.2 1.0
CA B:GLY38 3.3 31.9 1.0
PG B:0O2209 3.4 37.7 1.0
MG B:MG201 3.6 38.6 1.0
CD B:GLU53 3.7 34.2 1.0
OE2 B:GLU53 3.9 31.7 1.0
CD B:GLU57 3.9 32.9 1.0
C B:GLN37 4.0 30.0 1.0
O B:HOH325 4.1 34.5 1.0
N B:GLY38 4.2 32.9 1.0
O B:HOH361 4.2 31.5 1.0
O B:HOH425 4.3 42.1 1.0
N B:GLY39 4.4 32.0 1.0
O3B B:0O2209 4.4 41.9 1.0
O3G B:0O2209 4.4 32.3 1.0
C B:GLY38 4.4 30.6 1.0
CG B:GLU120 4.7 42.6 1.0
OE1 B:GLU57 4.7 32.8 1.0
O B:HOH306 4.7 45.8 1.0
CG B:GLU57 4.8 32.3 1.0
NH2 B:ARG8 4.9 40.3 1.0
O B:HOH446 5.0 39.4 1.0
CG B:GLU53 5.0 30.3 1.0

Reference:

A.Gao, N.Vasilyev, A.Kaushik, W.Duan, A.Serganov. Principles of Rna and Nucleotide Discrimination By the Rna Processing Enzyme Rpph. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
PubMed: 31960065
DOI: 10.1093/NAR/GKAA024
Page generated: Tue Jul 15 16:36:31 2025

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