Zinc 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:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp, PDB code: 8dcd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn513 b:44.2 occ:0.86 O A:HOH606 2.2 43.1 1.0 O2A A:GTP501 2.2 34.4 0.8 NE2 A:HIS329 2.3 40.9 1.0 NE2 A:HIS234 2.3 34.4 1.0 O1B A:GTP501 2.3 39.9 0.8 SG A:CYS98 2.3 39.5 1.0 CE1 A:HIS234 3.1 36.9 1.0 CE1 A:HIS329 3.2 41.7 1.0 CD2 A:HIS329 3.3 42.6 1.0 CD2 A:HIS234 3.4 40.6 1.0 CB A:CYS98 3.5 38.4 1.0 PB A:GTP501 3.5 40.7 0.8 PA A:GTP501 3.6 42.5 0.8 ZN A:ZN514 3.6 42.4 0.7 O3B A:GTP501 3.8 46.0 0.8 O3A A:GTP501 4.0 49.6 0.8 O1G A:GTP501 4.1 45.5 0.8 O5' A:GTP501 4.3 45.7 0.8 ND1 A:HIS234 4.3 36.4 1.0 ND1 A:HIS329 4.3 44.3 1.0 O A:HOH673 4.4 46.7 0.9 PG A:GTP501 4.4 59.3 0.8 CG A:HIS329 4.4 41.0 1.0 CG A:HIS234 4.5 34.2 1.0 C A:CYS98 4.5 39.3 1.0 O2G A:GTP501 4.5 42.3 0.8 CA A:CYS98 4.5 38.8 1.0 C5' A:GTP501 4.6 45.8 0.8 N A:GLY99 4.6 33.8 1.0 CD2 A:HIS404 4.7 41.9 1.0 O1A A:GTP501 4.7 44.1 0.8 O2B A:GTP501 4.8 42.7 0.8 CD2 A:HIS203 4.9 40.4 1.0 NE2 A:HIS203 4.9 41.0 1.0 O A:CYS98 4.9 36.5 1.0

Zinc binding site 2 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn514 b:42.4 occ:0.73 O1G A:GTP501 1.8 45.5 0.8 OD2 A:ASP95 2.0 42.9 1.0 NE2 A:HIS203 2.2 41.0 1.0 SG A:CYS98 2.3 39.5 1.0 O1B A:GTP501 2.7 39.9 0.8 CG A:ASP95 3.0 40.1 1.0 CB A:CYS98 3.1 38.4 1.0 CE1 A:HIS203 3.2 39.1 1.0 CD2 A:HIS203 3.2 40.4 1.0 PG A:GTP501 3.2 59.3 0.8 CB A:ASP95 3.6 36.0 1.0 ZN A:ZN513 3.6 44.2 0.9 O A:HOH606 3.6 43.1 1.0 PB A:GTP501 3.6 40.7 0.8 O3B A:GTP501 3.9 46.0 0.8 O2B A:GTP501 3.9 42.7 0.8 O2G A:GTP501 3.9 42.3 0.8 OD1 A:ASP95 4.0 41.2 1.0 O3G A:GTP501 4.3 56.4 0.8 O A:HOH652 4.3 36.4 1.0 ND1 A:HIS203 4.3 45.2 1.0 CA A:CYS98 4.3 38.8 1.0 CG A:HIS203 4.4 40.8 1.0 N A:GLY236 4.5 36.4 1.0 O2 A:SO4504 4.5 55.7 0.8 NE2 A:HIS234 4.5 34.4 1.0 CA A:GLY236 4.8 31.1 1.0 C A:THR235 4.8 39.0 1.0 CA A:THR235 5.0 40.7 1.0

Zinc binding site 3 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn509 b:44.4 occ:0.78 O2B B:GTP501 1.8 51.6 0.9 NE2 B:HIS234 2.2 42.2 1.0 NE2 B:HIS329 2.3 39.0 1.0 SG B:CYS98 2.3 38.5 1.0 PB B:GTP501 2.5 71.2 0.9 O1B B:GTP501 2.9 70.4 0.9 O3B B:GTP501 2.9 63.1 0.9 CE1 B:HIS234 3.0 38.3 1.0 CD2 B:HIS329 3.2 38.5 1.0 CD2 B:HIS234 3.3 36.6 1.0 ZN B:ZN510 3.3 42.5 0.7 CE1 B:HIS329 3.3 47.0 1.0 CB B:CYS98 3.3 30.1 1.0 O1G B:GTP501 3.7 45.5 0.9 PG B:GTP501 4.0 63.3 0.9 O3A B:GTP501 4.0 61.0 0.9 O5' B:GTP501 4.1 56.3 0.9 ND1 B:HIS234 4.2 42.1 1.0 C B:CYS98 4.3 39.9 1.0 CG B:HIS329 4.4 42.9 1.0 CG B:HIS234 4.4 40.8 1.0 ND1 B:HIS329 4.4 43.8 1.0 CA B:CYS98 4.4 33.9 1.0 N B:GLY99 4.5 34.2 1.0 CD2 B:HIS203 4.6 41.5 1.0 NE2 B:HIS203 4.6 42.0 1.0 C5' B:GTP501 4.6 48.7 0.9 O B:CYS98 4.7 38.5 1.0 PA B:GTP501 4.7 55.1 0.9 O2G B:GTP501 4.7 69.6 0.9 CD2 B:HIS404 4.8 48.6 1.0 ND2 B:ASN330 4.9 39.6 1.0

Zinc binding site 4 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with ZN2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn510 b:42.5 occ:0.71 O1G B:GTP501 1.9 45.5 0.9 OD2 B:ASP95 2.1 42.5 1.0 NE2 B:HIS203 2.2 42.0 1.0 SG B:CYS98 2.3 38.5 1.0 CG B:ASP95 3.0 41.1 1.0 CB B:CYS98 3.1 30.1 1.0 CE1 B:HIS203 3.2 39.7 1.0 CD2 B:HIS203 3.2 41.5 1.0 PG B:GTP501 3.2 63.3 0.9 ZN B:ZN509 3.3 44.4 0.8 O1B B:GTP501 3.6 70.4 0.9 CB B:ASP95 3.6 38.9 1.0 O3B B:GTP501 3.6 63.1 0.9 OD1 B:ASP95 4.0 38.2 1.0 PB B:GTP501 4.1 71.2 0.9 O2G B:GTP501 4.2 69.6 0.9 O3G B:GTP501 4.2 69.5 0.9 ND1 B:HIS203 4.3 40.8 1.0 CG B:HIS203 4.3 42.5 1.0 O B:HOH648 4.3 37.9 1.0 CA B:CYS98 4.4 33.9 1.0 N B:GLY236 4.4 41.9 1.0 ND2 B:ASN202 4.5 54.8 1.0 NE2 B:HIS234 4.5 42.2 1.0 O2B B:GTP501 4.6 51.6 0.9 O4 B:SO4503 4.6 48.5 0.9 CA B:GLY236 4.7 31.8 1.0 C B:THR235 4.7 37.9 1.0 CE1 B:HIS234 4.9 38.3 1.0 CA B:THR235 4.9 36.7 1.0 ND2 B:ASN330 4.9 39.6 1.0 O B:ASP95 5.0 43.1 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