Chlorine in PDB 8dcd: Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp

All present enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp:
6.5.1.8;

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp, PDB code: 8dcd was solved by A.Jacewicz, S.Dantuluri, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.27 / 2.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.91, 136.473, 150.065, 90, 90, 90
R / Rfree (%)	17 / 19.7

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Chlorine atom in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp (pdb code 8dcd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp, PDB code: 8dcd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl515 b:80.7 occ:1.00 ND1 A:HIS301 2.8 58.7 1.0 O A:HOH676 3.3 56.6 1.0 N A:GLY161 3.6 47.2 1.0 CG A:HIS301 3.7 54.2 1.0 CE1 A:HIS301 3.7 54.8 1.0 CA A:GLY161 3.8 45.9 1.0 CA A:HIS301 3.8 45.4 1.0 CB A:HIS301 3.8 46.3 1.0 C A:TYR160 4.0 52.1 1.0 NH1 A:ARG304 4.0 38.3 1.0 CD A:ARG304 4.1 44.4 1.0 NE1 A:TRP162 4.2 49.7 1.0 O A:TYR160 4.5 58.7 1.0 O A:HIS301 4.5 44.9 1.0 C A:GLY161 4.5 49.1 1.0 CA A:TYR160 4.5 59.2 1.0 CD1 A:TRP162 4.6 52.8 1.0 C A:HIS301 4.6 50.0 1.0 O A:GLY159 4.7 54.4 1.0 N A:HIS301 4.8 40.5 1.0 NE2 A:HIS301 4.8 57.1 1.0 CD2 A:HIS301 4.8 50.1 1.0 CB A:ARG304 4.8 42.6 1.0 O A:GLY161 4.9 51.5 1.0 CZ A:ARG304 5.0 44.4 1.0

Chlorine binding site 2 out of 2 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl516 b:86.6 occ:1.00 NH1 A:ARG23 2.6 61.2 1.0 O A:HOH656 3.0 48.1 1.0 C3 A:GOL502 3.4 61.8 1.0 O3 A:GOL502 3.4 66.0 1.0 N A:GLY55 3.5 51.9 1.0 CZ A:ARG23 3.8 65.2 1.0 CD A:ARG23 3.8 58.8 1.0 CA A:GLY55 4.2 43.1 1.0 NE A:ARG23 4.2 66.1 1.0 CA A:PRO54 4.4 46.8 1.0 C A:PRO54 4.4 46.6 1.0 C2 A:GOL502 4.7 71.7 1.0 CG A:ARG23 4.8 52.5 1.0 NH2 A:ARG23 4.8 63.5 1.0 CB A:PRO54 4.8 44.9 1.0

A.Jacewicz, S.Dantuluri, S.Shuman. Structures of Rna Ligase Rtcb in Complexes with Divalent Cations and Gtp. Rna V. 28 1509 2022.
ISSN: ESSN 1469-9001
PubMed: 36130078
DOI: 10.1261/RNA.079327.122