Chlorine in PDB 6d13: Crystal Structure of E.Coli Rpph-Dapf Complex

All present enzymatic activity of Crystal Structure of E.Coli Rpph-Dapf Complex:
5.1.1.7;

The structure of Crystal Structure of E.Coli Rpph-Dapf Complex, PDB code: 6d13 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)	19.99 / 3.06
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.810, 85.810, 177.374, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 26.4

The structure of Crystal Structure of E.Coli Rpph-Dapf Complex also contains other interesting chemical elements:

Iodine

(I)

10 atoms

The binding sites of Chlorine atom in the Crystal Structure of E.Coli Rpph-Dapf Complex (pdb code 6d13). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of E.Coli Rpph-Dapf Complex, PDB code: 6d13:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl309 b:93.9 occ:1.00 O A:MET104 3.6 0.2 1.0 CD A:ARG96 3.8 1.0 1.0 CG A:ARG103 3.9 87.6 1.0 CD2 A:LEU56 4.0 93.0 1.0 NE A:ARG96 4.0 0.9 1.0 CB A:ARG103 4.1 89.5 1.0 CG A:ARG96 4.1 0.4 1.0 CB A:ARG96 4.1 0.2 1.0 N A:MET104 4.2 97.8 1.0 C A:MET104 4.2 97.7 1.0 CD A:ARG103 4.7 97.4 1.0 CA A:ARG96 4.7 0.7 1.0 CA A:MET104 4.7 91.4 1.0 CB A:VAL105 5.0 99.3 1.0 C A:ARG103 5.0 95.3 1.0 CA A:ARG103 5.0 86.6 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl310 b:0.5 occ:1.00 CG1 A:VAL105 3.8 0.2 1.0 ND2 A:ASN117 4.3 98.9 1.0 CB A:VAL105 4.8 99.3 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of E.Coli Rpph-Dapf Complex


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:0.7 occ:1.00 NE2 B:GLN95 2.8 0.6 1.0 CG B:GLN95 3.7 0.7 1.0 CD B:GLN95 3.7 0.6 1.0 SG B:CYS92 3.8 0.0 1.0 CD B:ARG8 4.1 1.0 1.0 CD2 B:LEU79 4.3 90.8 1.0 CD1 B:LEU79 4.5 0.7 1.0 CG B:ARG8 4.6 0.6 1.0 O B:GLY94 4.6 0.4 1.0 OE1 B:GLN95 4.8 0.8 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