Chlorine in PDB 3dkx: Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Trigonal Form, to 2.7 Ang Resolution

The structure of Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Trigonal Form, to 2.7 Ang Resolution, PDB code: 3dkx was solved by D.R.Boer, J.A.Ruiz-Maso, A.G.Blanco, M.Vives-Llacer, I.Uson, F.X.Gomis-Ruth, M.Espinosa, G.Del Solar, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.95 / 2.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.611, 85.611, 245.530, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 27.6

The structure of Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Trigonal Form, to 2.7 Ang Resolution also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Manganese	(Mn)	3 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Trigonal Form, to 2.7 Ang Resolution (pdb code 3dkx). 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 the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Trigonal Form, to 2.7 Ang Resolution, PDB code: 3dkx:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Trigonal Form, to 2.7 Ang Resolution


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 the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Trigonal Form, to 2.7 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl211 b:42.5 occ:1.00 NZ A:LYS186 3.0 30.1 1.0 CE A:LYS186 3.5 28.8 1.0 CD2 A:PHE189 3.6 29.5 1.0 CB A:PHE189 4.1 30.8 1.0 CG A:LYS186 4.3 27.8 1.0 CG A:PHE189 4.3 29.6 1.0 CD A:LYS186 4.5 28.4 1.0 CB A:LYS186 4.6 27.1 1.0 CE2 A:PHE189 4.6 31.2 1.0 CA A:LYS186 4.7 27.2 1.0 O A:GLY185 4.8 30.3 1.0 O A:HOH310 4.8 45.4 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Trigonal Form, to 2.7 Ang Resolution


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 the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Trigonal Form, to 2.7 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl212 b:47.0 occ:1.00 N A:GLY185 3.2 30.9 1.0 CE B:LYS186 3.2 29.6 1.0 O B:HOH358 3.5 67.1 1.0 NZ B:LYS186 3.6 31.2 1.0 CA A:ALA184 3.7 31.2 1.0 CD2 B:PHE189 3.9 29.4 1.0 C A:ALA184 3.9 31.2 1.0 O A:HOH305 4.0 17.9 1.0 CG2 A:THR187 4.0 25.5 1.0 CB A:ALA184 4.1 31.4 1.0 CA A:GLY185 4.1 30.3 1.0 CB B:PHE189 4.2 31.3 1.0 O B:HOH320 4.2 43.3 1.0 CG B:LYS186 4.4 27.9 1.0 CD B:LYS186 4.5 28.8 1.0 CG B:PHE189 4.5 30.2 1.0 CA B:LYS186 4.5 28.1 1.0 O B:GLY185 4.5 30.4 1.0 CB B:LYS186 4.6 28.0 1.0 O A:ILE183 4.8 32.8 1.0 CE2 B:PHE189 4.9 31.1 1.0 N A:ALA184 4.9 31.9 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Trigonal Form, to 2.7 Ang Resolution


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 the Replication Initiator Protein Encoded on Plasmid PMV158 (Repb), Trigonal Form, to 2.7 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl211 b:46.9 occ:1.00 O C:HOH320 3.1 40.2 1.0 N B:GLY185 3.1 31.5 1.0 NZ C:LYS186 3.2 30.1 1.0 CA B:ALA184 3.6 32.0 1.0 O B:HOH305 3.7 29.1 1.0 CE C:LYS186 3.7 28.8 1.0 CD2 C:PHE189 3.9 28.6 1.0 C B:ALA184 3.9 31.7 1.0 CG2 B:THR187 4.1 26.7 1.0 CB B:ALA184 4.1 32.2 1.0 CA B:GLY185 4.1 30.4 1.0 CB C:PHE189 4.2 30.5 1.0 CG C:LYS186 4.4 27.2 1.0 CG C:PHE189 4.5 29.4 1.0 O C:GLY185 4.6 28.5 1.0 CA C:LYS186 4.6 26.8 1.0 CB C:LYS186 4.6 27.2 1.0 O C:HOH317 4.6 47.2 1.0 CD C:LYS186 4.6 28.5 1.0 N B:ALA184 4.8 33.0 1.0 O B:ILE183 4.9 33.9 1.0 CE2 C:PHE189 4.9 30.6 1.0

D.R.Boer, J.A.Ruiz-Maso, J.R.Lopez-Blanco, A.G.Blanco, M.Vives-Llacer, P.Chacon, I.Uson, F.X.Gomis-Ruth, M.Espinosa, O.Llorca, G.Del Solar, M.Coll. Plasmid Replication Initiator Repb Forms A Hexamer Reminiscent of Ring Helicases and Has Mobile Nuclease Domains Embo J. V. 28 1666 2009.
ISSN: ISSN 0261-4189
PubMed: 19440202
DOI: 10.1038/EMBOJ.2009.125