Chlorine in PDB 8dgl: Crystal Structure of the Rdfs Excisionase

The structure of Crystal Structure of the Rdfs Excisionase, PDB code: 8dgl was solved by C.J.Verdonk, J.P.Ramsay, A.C.Marshall, C.S.Bond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.87 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.251, 119.204, 123.397, 90, 90, 90
R / Rfree (%)	19.9 / 24.6

The binding sites of Chlorine atom in the Crystal Structure of the Rdfs Excisionase (pdb code 8dgl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Rdfs Excisionase, PDB code: 8dgl:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Rdfs Excisionase


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 Rdfs Excisionase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:70.5 occ:1.00 OG1 A:THR33 3.2 46.5 1.0 N A:SER30 3.5 43.3 1.0 CD2 A:LEU29 3.8 46.5 1.0 OG A:SER30 3.8 46.4 1.0 CB A:SER30 4.0 41.9 1.0 CB A:THR33 4.1 42.6 1.0 CA A:LEU29 4.2 39.2 1.0 C A:LEU29 4.4 43.6 1.0 CA A:SER30 4.4 38.9 1.0 CG2 A:THR33 4.4 38.7 1.0 CB A:LEU29 4.6 39.0 1.0 CG A:LEU29 4.8 45.8 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Rdfs Excisionase


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 Rdfs Excisionase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl101 b:70.5 occ:1.00 OG1 B:THR33 3.8 42.5 1.0 N B:SER30 3.9 38.1 1.0 CZ A:TYR52 4.1 47.3 1.0 OG B:SER30 4.2 39.2 1.0 CD2 B:LEU29 4.2 29.2 1.0 CE2 A:TYR52 4.3 45.6 1.0 OH A:TYR52 4.3 49.6 1.0 CE1 A:TYR52 4.4 47.5 1.0 CA B:LEU29 4.4 34.4 1.0 CB B:SER30 4.5 34.9 1.0 CB B:THR33 4.6 39.2 1.0 C B:LEU29 4.6 37.3 1.0 CD2 A:TYR52 4.7 45.3 1.0 NH2 A:ARG54 4.7 37.5 1.0 CB B:LEU29 4.8 35.8 1.0 CD1 A:TYR52 4.8 44.2 1.0 CA B:SER30 4.8 35.5 1.0 CG2 B:THR33 4.8 29.1 1.0 CG A:TYR52 4.9 44.1 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Rdfs Excisionase


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 Rdfs Excisionase within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl101 b:63.3 occ:1.00 OG1 C:THR33 2.9 44.6 1.0 N C:SER30 3.3 44.5 1.0 CB C:SER30 3.4 41.5 1.0 CB C:THR33 3.7 44.5 1.0 OG C:SER30 3.7 43.8 1.0 CA C:SER30 4.0 46.0 1.0 CG2 C:THR33 4.1 40.0 1.0 CZ B:TYR52 4.2 52.3 1.0 C C:LEU29 4.3 41.9 1.0 CD2 C:LEU29 4.3 39.1 1.0 OH B:TYR52 4.4 55.7 1.0 CA C:LEU29 4.4 37.2 1.0 O C:HOH222 4.4 51.8 1.0 CE1 B:TYR52 4.4 50.2 1.0 CE2 B:TYR52 4.5 51.4 1.0 CB C:LEU29 4.6 34.6 1.0 CD1 B:TYR52 4.9 46.6 1.0 O C:SER30 5.0 41.4 1.0 CD2 B:TYR52 5.0 49.4 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Rdfs Excisionase


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 the Rdfs Excisionase within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl101 b:67.6 occ:1.00 O D:HOH235 3.2 55.2 1.0 N D:GLU4 3.3 44.9 1.0 CB D:ASP3 3.6 34.4 1.0 CG D:GLU4 3.7 43.5 1.0 CA D:ASP3 3.8 44.1 1.0 CB D:GLU4 4.0 34.9 1.0 C D:ASP3 4.0 39.8 1.0 CA D:GLU4 4.2 33.9 1.0 CD D:GLU4 4.3 48.6 1.0 NH2 D:ARG7 4.3 32.0 1.0 OE1 D:GLU4 4.7 44.6 1.0 CG D:ASP3 4.8 40.9 1.0 OE2 D:GLU4 4.8 44.6 1.0 NH1 D:ARG7 5.0 45.9 1.0

C.J.Verdonk, A.C.Marshall, J.P.Ramsay, C.S.Bond. Crystallographic and X-Ray Scattering Study of Rdfs, A Recombination Directionality Factor From An Integrative and Conjugative Element. Acta Crystallogr D Struct V. 78 1210 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 36189741
DOI: 10.1107/S2059798322008579