Chlorine in PDB 8dcf: Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp

All present enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp:
6.5.1.8;

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp, PDB code: 8dcf 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)	49.56 / 2.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.105, 137.828, 149.755, 90, 90, 90
R / Rfree (%)	16.5 / 20.4

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp also contains other interesting chemical elements:

Copper

(Cu)

6 atoms

The binding sites of Chlorine atom in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ and Gtp (pdb code 8dcf). 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 CU2+ and Gtp, PDB code: 8dcf:
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 CU2+ 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 CU2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl615 b:63.8 occ:0.87 ND1 A:HIS301 2.7 63.3 0.8 O A:HOH756 3.4 67.3 1.0 CD A:ARG304 3.5 51.2 1.0 N A:GLY161 3.5 55.5 1.0 CA A:GLY161 3.6 53.5 0.6 NH1 A:ARG304 3.6 43.8 0.8 CE1 A:HIS301 3.6 60.6 1.0 CG A:HIS301 3.6 58.4 1.0 CA A:HIS301 3.7 49.5 1.0 CB A:HIS301 3.9 52.9 1.0 NE1 A:TRP162 3.9 53.3 0.9 C A:GLY161 4.2 53.2 1.0 CD1 A:TRP162 4.3 57.6 0.9 CB A:ARG304 4.4 52.0 1.0 NE A:ARG304 4.5 55.8 1.0 CZ A:ARG304 4.5 52.7 1.0 C A:TYR160 4.5 51.0 1.0 O A:HIS301 4.5 48.5 1.0 CG A:ARG304 4.6 55.6 1.0 CE2 A:TRP162 4.6 52.7 1.0 N A:HIS301 4.6 49.7 1.0 C A:HIS301 4.7 50.3 0.8 O A:GLY161 4.7 56.5 1.0 NE2 A:HIS301 4.7 61.3 0.7 CD2 A:HIS301 4.8 52.7 1.0 N A:TRP162 4.9 57.2 1.0

Chlorine binding site 2 out of 2 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CU2+ 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 CU2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl516 b:55.3 occ:0.81 ND1 B:HIS301 2.9 60.0 1.0 CA B:GLY161 3.4 58.6 1.0 CD B:ARG304 3.4 44.0 1.0 NH1 B:ARG304 3.5 49.1 1.0 NE1 B:TRP162 3.6 55.9 1.0 N B:GLY161 3.7 58.5 1.0 CE1 B:HIS301 3.9 61.4 1.0 CA B:HIS301 3.9 43.5 1.0 CG B:HIS301 3.9 61.9 1.0 CD1 B:TRP162 4.0 54.8 1.0 CB B:HIS301 4.1 47.5 1.0 C B:GLY161 4.3 54.5 1.0 CB B:ARG304 4.3 45.6 1.0 CE2 B:TRP162 4.3 56.0 1.0 NE B:ARG304 4.4 49.0 1.0 CZ B:ARG304 4.4 49.3 1.0 CG B:ARG304 4.5 51.7 1.0 O B:HIS301 4.5 50.4 1.0 C B:TYR160 4.6 53.9 1.0 C B:HIS301 4.7 54.5 1.0 N B:HIS301 4.8 45.9 1.0 O B:GLY161 4.8 52.6 1.0 N B:TRP162 4.9 56.6 1.0 CZ2 B:TRP162 4.9 55.1 1.0 CG B:TRP162 4.9 58.2 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