Chlorine in PDB 6vcl: 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;

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

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

Fluorine	(F)	1 atom
Magnesium	(Mg)	4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of E.Coli Rpph-Dapf in Complex with Pppgpp, MG2+ and F-, PDB code: 6vcl:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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 A:Cl301 b:58.4 occ:1.00 O A:HOH490 2.7 62.1 1.0 N A:VAL105 3.4 40.8 1.0 O A:HOH429 3.7 48.9 1.0 CA A:MET104 3.8 43.4 1.0 C A:MET104 4.1 43.7 1.0 CB A:ASN117 4.2 54.7 1.0 O A:HOH519 4.3 47.1 1.0 CB A:VAL105 4.4 41.9 1.0 CA A:VAL105 4.4 38.3 1.0 O A:VAL105 4.5 45.4 1.0 O A:ARG103 4.5 42.7 1.0 CB A:MET104 4.6 38.2 1.0 CG2 A:VAL105 4.6 42.5 1.0 O A:ASN117 4.6 50.7 1.0 CG A:ASN117 4.8 53.1 1.0 C A:VAL105 4.9 39.8 1.0 N A:MET104 4.9 39.4 1.0

Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl binding site number 2 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:Cl207 b:29.8 occ:0.51 N B:ARG62 3.7 35.7 1.0 CB B:SER61 3.7 37.2 1.0 CA B:SER61 4.0 32.5 1.0 CG B:ARG62 4.2 39.9 1.0 C B:SER61 4.4 33.9 1.0 CB B:ARG62 4.4 36.1 1.0 CD B:ARG62 4.6 37.6 1.0 O B:HOH345 4.6 51.3 1.0 OG B:SER61 4.6 36.5 1.0 CA B:ARG62 4.7 35.9 1.0 O B:HOH338 4.8 25.2 1.0

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