Chlorine in PDB 8dcb: Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp

All present enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp:
6.5.1.8;

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp, PDB code: 8dcb 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)	49.52 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.241, 137.492, 149.559, 90, 90, 90
R / Rfree (%)	17 / 20.9

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp also contains other interesting chemical elements:

Nickel

(Ni)

5 atoms

The binding sites of Chlorine atom in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ and Gtp (pdb code 8dcb). 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 NI2+ and Gtp, PDB code: 8dcb:
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 NI2+ 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 NI2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl510 b:85.4 occ:1.00 N A:LYS110 3.4 64.7 1.0 CB A:LYS110 3.7 67.1 1.0 N A:GLU109 3.9 57.0 1.0 CB A:GLU109 4.0 53.2 1.0 CB A:THR108 4.0 49.1 1.0 CA A:LYS110 4.2 63.3 1.0 CG A:LYS110 4.2 80.9 1.0 OG1 A:THR108 4.2 54.6 1.0 C A:GLU109 4.2 58.4 1.0 CA A:GLU109 4.3 54.8 1.0 CD A:LYS110 4.4 83.9 1.0 C A:THR108 4.6 56.5 1.0 O A:GLY227 4.7 56.5 1.0 CG A:GLU109 4.7 58.5 1.0 CG2 A:THR108 4.9 45.5 1.0 CA A:THR108 4.9 55.9 1.0

Chlorine binding site 2 out of 2 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with NI2+ 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 NI2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl510 b:95.1 occ:1.00 NE B:ARG190 3.2 82.3 1.0 NE2 B:GLN194 3.3 77.2 1.0 NH2 A:ARG436 3.6 74.7 1.0 NH2 B:ARG190 3.6 76.3 1.0 CZ B:ARG190 3.8 79.9 1.0 CG B:ARG190 4.2 74.6 1.0 CD B:ARG190 4.2 81.6 1.0 CD B:GLN194 4.3 77.8 1.0 OE1 B:GLN194 4.6 77.9 1.0 CE2 A:PHE124 4.6 61.8 1.0 CA B:GLY239 4.6 67.5 1.0 CZ A:ARG436 4.9 89.6 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