Chlorine in PDB 6d1v: Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna

The structure of Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna, PDB code: 6d1v was solved by A.Gao, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.60 / 1.81
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	160.644, 191.986, 51.207, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 22

The structure of Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Chlorine atom in the Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna (pdb code 6d1v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna, PDB code: 6d1v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna


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 Complex, Monomer Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl805 b:40.0 occ:1.00 O A:HOH982 3.0 42.6 1.0 NE A:ARG78 3.2 44.9 1.0 N A:CYS79 3.4 32.3 1.0 N A:ARG78 3.4 34.9 1.0 C A:GLY76 3.5 32.4 1.0 CA A:GLY76 3.5 40.6 1.0 CB A:ARG78 3.6 35.1 1.0 NH2 A:ARG78 3.6 40.3 1.0 SG A:CYS79 3.8 37.5 1.0 O A:GLY76 3.8 35.6 1.0 CZ A:ARG78 3.8 44.9 1.0 N A:ALA77 3.8 32.4 1.0 CA A:ARG78 3.9 35.0 1.0 CA A:GLY8 4.0 50.1 1.0 CE2 A:PHE13 4.0 37.2 1.0 N A:GLY76 4.0 39.3 1.0 C A:GLY8 4.1 55.0 1.0 CB A:CYS79 4.1 31.9 1.0 CD A:ARG78 4.1 43.2 1.0 C A:ARG78 4.1 34.0 1.0 O A:GLY8 4.3 48.4 1.0 CA A:CYS79 4.3 31.6 1.0 CG A:ARG78 4.4 39.6 1.0 C A:ALA77 4.4 32.0 1.0 N A:LEU9 4.5 55.9 1.0 CZ A:PHE13 4.6 35.3 1.0 CD2 A:PHE13 4.7 40.3 1.0 CA A:ALA77 4.7 33.9 1.0 N A:GLY8 4.9 42.5 1.0 CB A:LEU9 4.9 57.1 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna


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 Complex, Monomer Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl806 b:77.0 occ:1.00 N A:ARG142 3.3 82.9 1.0 CA A:MET141 3.5 73.3 1.0 CD A:ARG184 3.6 73.3 1.0 CE1 A:HIS182 3.7 68.3 1.0 CG A:ARG142 3.8 93.6 1.0 NE2 A:HIS182 3.8 71.2 1.0 C A:MET141 3.9 80.0 1.0 NH1 A:ARG184 4.0 66.3 1.0 CB A:MET141 4.0 69.9 1.0 CG A:MET141 4.2 71.4 1.0 O A:ILE140 4.2 62.4 1.0 O A:ARG142 4.3 85.2 1.0 CA A:ARG142 4.3 84.5 1.0 CB A:ARG142 4.4 90.0 1.0 CG A:ARG184 4.5 72.3 1.0 N A:MET141 4.6 64.3 1.0 NE A:ARG184 4.6 71.1 1.0 CZ A:ARG184 4.7 73.1 1.0 C A:ARG142 4.8 83.9 1.0 C A:ILE140 4.8 65.9 1.0 CD A:ARG142 4.9 97.2 1.0 NE A:ARG142 4.9 99.8 1.0 ND1 A:HIS182 5.0 67.6 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl807 b:30.0 occ:1.00 NH2 A:ARG209 3.2 44.1 1.0 ND2 A:ASN157 3.5 48.0 1.0 NE A:ARG209 3.6 41.9 1.0 CB A:ASN157 3.7 47.8 1.0 ND2 A:ASN190 3.8 48.9 1.0 CZ A:ARG209 3.8 41.6 1.0 CG A:ASN157 4.1 52.8 1.0 OD1 A:ASN190 4.2 54.9 1.0 CG A:ASN190 4.5 56.2 1.0 CB A:ARG209 4.6 53.9 1.0 CD A:ARG209 4.9 46.6 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl207 b:60.7 occ:0.50 O B:HOH427 2.9 39.2 1.0 N B:ARG62 3.4 36.1 1.0 CB B:SER61 3.6 36.0 1.0 CG B:ARG62 3.9 44.9 1.0 CA B:SER61 3.9 35.6 1.0 CB B:ARG62 4.0 39.7 1.0 C B:SER61 4.2 35.7 1.0 CD B:ARG62 4.2 45.4 1.0 CA B:ARG62 4.3 39.5 1.0 OG B:SER61 4.5 34.0 1.0 O B:HOH355 4.7 30.6 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of E. Coli Rpph-Dapf Complex, Monomer Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl208 b:87.3 occ:1.00 O A:HOH975 3.5 44.6 1.0 CD A:PRO50 3.9 26.3 1.0 CG A:PRO50 3.9 28.3 1.0 NH1 B:ARG134 4.1 30.6 1.0 CA B:ARG134 4.1 28.2 1.0 CZ B:ARG134 4.3 35.0 1.0 CB B:ARG134 4.3 28.1 1.0 CG B:ARG134 4.4 33.3 1.0 NH2 B:ARG145 4.4 40.1 1.0 NH1 B:ARG145 4.5 35.3 1.0 NH2 B:ARG134 4.6 29.7 1.0 O B:VAL133 4.6 28.5 1.0 CD B:ARG141 4.6 33.6 1.0 N B:ARG134 4.7 26.3 1.0 CB A:PRO50 4.8 23.4 1.0 O B:HOH329 4.8 41.8 1.0 NE B:ARG134 4.8 30.2 1.0 O A:HOH914 4.9 41.2 1.0 C B:VAL133 4.9 27.6 1.0 O A:HOH984 4.9 37.3 1.0 NE B:ARG141 5.0 31.6 1.0 CZ B:ARG145 5.0 45.3 1.0

A.Gao, N.Vasilyev, D.J.Luciano, R.Levenson-Palmer, J.Richards, W.M.Marsiglia, N.J.Traaseth, J.G.Belasco, A.Serganov. Structural and Kinetic Insights Into Stimulation of Rpph-Dependent Rna Degradation By the Metabolic Enzyme Dapf. Nucleic Acids Res. V. 46 6841 2018.
ISSN: ESSN 1362-4962
PubMed: 29733359
DOI: 10.1093/NAR/GKY327