Chlorine in PDB 8dc9: Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp

All present enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp:
6.5.1.8;

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp, PDB code: 8dc9 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)	49.39 / 2.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.741, 137.284, 150.157, 90, 90, 90
R / Rfree (%)	18.3 / 21.8

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Chlorine atom in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp (pdb code 8dc9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp, PDB code: 8dc9:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ 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 MN2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl515 b:98.8 occ:1.00 N A:ASP340 3.0 74.3 1.0 CA A:ASP340 3.7 75.3 1.0 NZ A:LYS58 3.8 62.1 1.0 OD2 A:ASP340 3.9 92.1 1.0 CE A:LYS58 4.0 55.4 1.0 C A:VAL339 4.1 68.5 1.0 CA A:VAL339 4.2 61.8 1.0 CG A:ASP340 4.4 89.0 1.0 O4 C:FRU2 4.4 78.2 0.8 CB A:ASP340 4.7 80.2 1.0 O A:GLU338 4.8 62.7 1.0 N A:GLY341 4.8 73.8 1.0 C A:ASP340 4.8 75.1 1.0 CG1 A:VAL339 4.8 63.0 1.0

Chlorine binding site 2 out of 3 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ 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 MN2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl512 b:90.2 occ:1.00 NE B:ARG190 3.0 72.7 1.0 NH2 B:ARG190 3.2 64.7 1.0 NE2 B:GLN194 3.4 63.5 1.0 CZ B:ARG190 3.5 71.0 1.0 NH2 A:ARG436 4.1 81.3 1.0 CG B:ARG190 4.1 71.2 1.0 CD B:ARG190 4.1 64.9 1.0 CA B:GLY239 4.3 61.6 1.0 CD B:GLN194 4.5 67.2 1.0 CE2 A:PHE124 4.6 53.9 1.0 NH1 A:ARG436 4.6 75.1 1.0 NH1 B:ARG190 4.8 69.4 1.0 CZ A:ARG436 4.8 74.0 1.0 OE1 B:GLN194 4.9 74.0 1.0 N B:GLY239 5.0 54.9 1.0

Chlorine binding site 3 out of 3 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with MN2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl513 b:78.1 occ:1.00 NZ B:LYS286 3.6 54.8 1.0 CE B:LYS286 3.9 49.2 1.0 CE2 B:PHE282 4.2 52.9 1.0 CZ B:PHE282 4.5 50.8 1.0 CG2 B:VAL334 4.6 50.2 1.0 CB B:VAL334 4.6 51.0 1.0 O B:GLU176 4.8 59.8 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