Chlorine in PDB 6hbz: Bdellovibrio Bacteriovorus Dgcb Full-Length

The structure of Bdellovibrio Bacteriovorus Dgcb Full-Length, PDB code: 6hbz was solved by A.L.Lovering, R.W.Meek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	153.09 / 1.79
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	176.776, 176.776, 112.117, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 21.6

The binding sites of Chlorine atom in the Bdellovibrio Bacteriovorus Dgcb Full-Length (pdb code 6hbz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Bdellovibrio Bacteriovorus Dgcb Full-Length, PDB code: 6hbz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Bdellovibrio Bacteriovorus Dgcb Full-Length


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bdellovibrio Bacteriovorus Dgcb Full-Length within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:22.4 occ:1.00 O A:HOH728 3.2 32.9 1.0 N A:TRP284 3.5 21.5 1.0 CA A:PRO166 3.6 21.1 1.0 CA A:GLU283 3.7 26.7 1.0 CB A:PRO166 3.7 21.6 1.0 CG A:PRO166 3.7 23.3 1.0 CD1 A:TRP284 3.9 22.8 1.0 O A:THR282 4.0 25.5 1.0 N A:PRO166 4.0 20.2 1.0 CG A:MET169 4.1 23.7 1.0 C A:GLU283 4.1 23.2 1.0 CD A:PRO166 4.3 21.8 1.0 CB A:GLU283 4.3 33.2 1.0 CB A:TRP284 4.4 18.9 1.0 O A:HOH703 4.5 42.0 1.0 CB A:MET169 4.5 22.0 1.0 CA A:TRP284 4.5 20.5 1.0 CG A:TRP284 4.6 21.2 1.0 C A:GLY165 4.6 19.4 1.0 O A:GLY165 4.7 19.3 1.0 N A:GLU283 4.7 24.6 1.0 C A:THR282 4.8 23.2 1.0 CG A:GLU283 4.8 40.4 1.0 C A:PRO166 4.8 20.2 1.0 NE1 A:TRP284 4.9 23.6 1.0 O A:PRO166 5.0 22.6 1.0

Chlorine binding site 2 out of 5 in the Bdellovibrio Bacteriovorus Dgcb Full-Length


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bdellovibrio Bacteriovorus Dgcb Full-Length within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:31.8 occ:1.00 CL B:CL403 3.2 29.9 1.0 N A:ARG76 3.3 20.7 1.0 O A:HOH520 3.3 34.7 1.0 OD1 B:ASP56 3.5 26.8 1.0 NE A:ARG76 3.5 37.5 1.0 O A:HOH704 3.6 46.1 1.0 CB A:ARG76 3.8 21.9 1.0 CG A:ARG76 3.9 24.2 1.0 CB A:SER75 3.9 22.2 1.0 CA A:SER75 4.0 20.8 1.0 CG B:ASP56 4.0 28.2 1.0 CG2 B:VAL58 4.1 24.4 1.0 OD2 B:ASP56 4.1 25.2 1.0 NH2 A:ARG61 4.1 36.4 1.0 C A:SER75 4.1 20.5 1.0 CA A:ARG76 4.1 21.1 1.0 NH2 A:ARG76 4.3 41.0 1.0 CD A:ARG76 4.3 30.6 1.0 CZ A:ARG76 4.4 40.0 1.0 OG A:SER75 4.6 23.3 1.0 OE2 B:GLU64 4.8 47.4 1.0 CZ A:ARG61 4.9 33.0 1.0 O B:ASP56 4.9 34.4 1.0 N A:SER77 5.0 20.7 1.0

Chlorine binding site 3 out of 5 in the Bdellovibrio Bacteriovorus Dgcb Full-Length


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bdellovibrio Bacteriovorus Dgcb Full-Length within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:54.3 occ:1.00 O B:HOH633 3.0 54.8 1.0 O B:HOH630 3.3 34.3 1.0 N B:ARG76 3.5 29.5 1.0 NH1 B:ARG61 3.7 39.2 1.0 CA B:SER75 3.8 26.1 1.0 CB B:SER75 3.9 25.6 1.0 CG B:ARG76 3.9 42.9 1.0 C B:SER75 4.2 26.0 1.0 OG B:SER75 4.2 30.2 1.0 CB B:ARG76 4.2 36.1 1.0 CA B:ARG76 4.5 31.1 1.0 NH2 B:ARG61 4.6 45.4 1.0 CZ B:ARG61 4.6 40.3 1.0 CD B:ARG76 4.6 50.1 1.0

Chlorine binding site 4 out of 5 in the Bdellovibrio Bacteriovorus Dgcb Full-Length


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Bdellovibrio Bacteriovorus Dgcb Full-Length within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:58.1 occ:1.00 NE B:ARG303 3.4 39.8 1.0 N B:HIS188 3.5 37.2 1.0 O B:HOH515 3.6 47.6 1.0 NH2 B:ARG303 3.8 48.6 0.6 CZ B:ARG303 4.0 44.5 0.6 O B:HOH601 4.2 54.5 1.0 CA B:HIS188 4.2 38.6 1.0 CD B:ARG303 4.4 36.7 1.0 CA B:ASP187 4.4 31.3 1.0 C B:ASP187 4.5 34.9 1.0 ND1 B:HIS188 4.5 46.6 1.0 O B:ILE186 4.7 27.8 1.0 CG B:HIS188 4.9 42.7 1.0 CE1 B:HIS188 5.0 50.9 1.0

Chlorine binding site 5 out of 5 in the Bdellovibrio Bacteriovorus Dgcb Full-Length


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Bdellovibrio Bacteriovorus Dgcb Full-Length within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:29.9 occ:1.00 NZ B:LYS80 3.2 21.1 1.0 N A:SER77 3.2 20.7 1.0 CL A:CL404 3.2 31.8 1.0 CE B:LYS80 3.5 21.7 1.0 CD B:LYS80 3.6 22.1 1.0 CB A:ARG76 3.7 21.9 1.0 O A:HOH619 3.7 31.4 1.0 N A:ARG76 3.7 20.7 1.0 CG2 B:VAL58 3.8 24.4 1.0 O A:SER77 3.8 20.7 1.0 OD1 B:ASP56 3.9 26.8 1.0 CA A:ARG76 4.0 21.1 1.0 CA A:SER77 4.0 20.5 1.0 C A:ARG76 4.0 20.9 1.0 CB A:SER77 4.0 22.3 1.0 C A:SER77 4.3 19.0 1.0 CB A:SER75 4.4 22.2 1.0 CD1 B:LEU93 4.5 28.5 1.0 OG A:SER77 4.6 22.4 1.0 C A:SER75 4.6 20.5 1.0 NE A:ARG76 4.7 37.5 1.0 CG A:ARG76 4.8 24.2 1.0 CG B:LYS80 4.9 22.8 1.0 CB B:LYS80 4.9 23.2 1.0 CA A:SER75 5.0 20.8 1.0

R.W.Meek, I.T.Cadby, P.J.Moynihan, A.L.Lovering. Structural Basis For Activation of A Diguanylate Cyclase Required For Bacterial Predation in Bdellovibrio. Nat Commun V. 10 4086 2019.
ISSN: ESSN 2041-1723
PubMed: 31501441
DOI: 10.1038/S41467-019-12051-6