Cobalt in PDB 8dca: Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp

All present enzymatic activity of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp:
6.5.1.8;

The structure of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp, PDB code: 8dca 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)	49.77 / 2.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.161, 138.864, 149.877, 90, 90, 90
R / Rfree (%)	17.7 / 20.3

The binding sites of Cobalt atom in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp (pdb code 8dca). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp, PDB code: 8dca:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Co510 b:71.2 occ:0.77 O2A A:GTP501 2.0 52.3 1.0 O A:HOH605 2.2 62.2 1.0 NE2 A:HIS329 2.2 64.6 1.0 NE2 A:HIS234 2.2 63.1 1.0 SG A:CYS98 2.3 71.0 1.0 O1B A:GTP501 2.5 56.4 1.0 CE1 A:HIS234 3.1 61.4 1.0 CE1 A:HIS329 3.2 66.0 1.0 CD2 A:HIS329 3.2 68.7 1.0 CD2 A:HIS234 3.3 60.1 1.0 PA A:GTP501 3.4 60.1 0.7 CB A:CYS98 3.5 65.1 1.0 PB A:GTP501 3.5 60.4 0.8 CO A:CO511 3.6 70.5 0.7 O3B A:GTP501 3.8 67.2 0.9 O3A A:GTP501 3.9 65.4 0.6 O3G A:GTP501 4.1 59.2 1.0 O5' A:GTP501 4.3 66.7 0.6 ND1 A:HIS234 4.3 65.7 1.0 ND1 A:HIS329 4.3 63.5 1.0 CG A:HIS329 4.3 66.4 1.0 PG A:GTP501 4.3 61.9 0.5 C5' A:GTP501 4.4 69.2 0.9 O2G A:GTP501 4.4 67.9 0.9 CG A:HIS234 4.4 61.8 1.0 O1A A:GTP501 4.5 63.5 1.0 C A:CYS98 4.5 63.7 1.0 CA A:CYS98 4.6 65.9 1.0 N A:GLY99 4.6 69.8 1.0 CD2 A:HIS404 4.6 64.3 1.0 NE2 A:HIS203 4.7 73.6 1.0 CD2 A:HIS203 4.8 65.1 1.0 O A:CYS98 4.9 65.9 1.0 O2B A:GTP501 4.9 76.4 0.7 NE2 A:HIS404 5.0 64.2 1.0

Cobalt binding site 2 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Co511 b:70.5 occ:0.66 OD2 A:ASP95 1.9 67.2 0.9 O3G A:GTP501 2.0 59.2 1.0 NE2 A:HIS203 2.1 73.6 1.0 SG A:CYS98 2.4 71.0 1.0 O1B A:GTP501 2.6 56.4 1.0 CG A:ASP95 3.0 68.0 0.9 CB A:CYS98 3.0 65.1 1.0 CE1 A:HIS203 3.0 66.7 1.0 CD2 A:HIS203 3.2 65.1 1.0 PG A:GTP501 3.3 61.9 0.5 CB A:ASP95 3.6 64.5 0.9 CO A:CO510 3.6 71.2 0.8 PB A:GTP501 3.7 60.4 0.8 O2G A:GTP501 3.9 67.9 0.9 O3B A:GTP501 3.9 67.2 0.9 OD1 A:ASP95 4.0 64.5 0.9 O A:HOH605 4.1 62.2 1.0 O2B A:GTP501 4.1 76.4 0.7 ND1 A:HIS203 4.2 73.7 1.0 CA A:CYS98 4.2 65.9 1.0 CG A:HIS203 4.3 75.2 1.0 O1G A:GTP501 4.4 50.0 0.9 NE2 A:HIS234 4.5 63.1 1.0 N A:GLY236 4.5 67.4 1.0 C A:THR235 4.7 65.3 1.0 CA A:GLY236 4.7 64.5 1.0 O2 A:SO4504 4.9 84.0 0.7 O2A A:GTP501 4.9 52.3 1.0 O A:ASP95 5.0 67.0 0.9

Cobalt binding site 3 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Co507 b:72.6 occ:0.79 OD2 B:ASP95 2.2 74.0 1.0 NE2 B:HIS203 2.3 69.3 1.0 O1G B:GTP501 2.3 53.7 1.0 SG B:CYS98 2.4 63.4 1.0 O1B B:GTP501 2.5 54.1 1.0 CG B:ASP95 3.1 65.7 1.0 O3G B:GTP501 3.1 64.8 1.0 CE1 B:HIS203 3.2 66.8 1.0 CB B:CYS98 3.2 59.4 1.0 PG B:GTP501 3.3 61.4 0.4 CD2 B:HIS203 3.4 68.8 1.0 CB B:ASP95 3.4 55.8 1.0 CO B:CO508 3.7 77.8 1.0 PB B:GTP501 3.7 55.1 0.8 O3B B:GTP501 4.0 57.5 0.6 OD1 B:ASP95 4.1 61.9 1.0 O2B B:GTP501 4.2 68.4 0.6 O B:HOH602 4.2 65.1 1.0 ND1 B:HIS203 4.4 72.5 1.0 CA B:CYS98 4.4 60.3 1.0 CG B:HIS203 4.5 75.2 1.0 NE2 B:HIS234 4.5 63.6 1.0 O2G B:GTP501 4.6 83.5 0.9 O3 B:SO4503 4.6 69.0 1.0 O2A B:GTP501 4.8 66.6 0.0 N B:GLY236 4.8 60.6 1.0 CA B:ASP95 4.9 63.9 1.0 ND2 B:ASN330 4.9 58.8 1.0 O B:ASP95 5.0 62.8 1.0

Cobalt binding site 4 out of 4 in the Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Rna Ligase Rtcb From Pyrococcus Horikoshii in Complex with CO2+ and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Co508 b:77.8 occ:0.97 O2A B:GTP501 2.0 66.6 0.0 NE2 B:HIS329 2.3 63.7 1.0 NE2 B:HIS234 2.4 63.6 1.0 O1B B:GTP501 2.5 54.1 1.0 SG B:CYS98 2.6 63.4 1.0 O3G B:GTP501 2.9 64.8 1.0 PA B:GTP501 3.0 66.7 1.0 CE1 B:HIS234 3.0 63.9 1.0 CE1 B:HIS329 3.2 65.2 1.0 CD2 B:HIS329 3.2 59.1 1.0 PB B:GTP501 3.4 55.1 0.8 O5' B:GTP501 3.5 69.2 0.7 O3A B:GTP501 3.5 69.3 0.6 CD2 B:HIS234 3.6 60.0 1.0 CB B:CYS98 3.6 59.4 1.0 CO B:CO507 3.7 72.6 0.8 O3B B:GTP501 3.7 57.5 0.6 PG B:GTP501 3.8 61.4 0.4 ND1 B:HIS234 4.3 63.9 1.0 ND1 B:HIS329 4.3 73.2 1.0 O1G B:GTP501 4.3 53.7 1.0 CG B:HIS329 4.3 66.9 1.0 O1A B:GTP501 4.4 70.2 0.9 CD2 B:HIS404 4.5 74.8 1.0 CG B:HIS234 4.6 65.6 1.0 C5' B:GTP501 4.7 68.1 0.9 NE2 B:HIS404 4.7 70.5 1.0 O2B B:GTP501 4.8 68.4 0.6 C B:CYS98 4.8 65.9 1.0 CA B:CYS98 4.8 60.3 1.0 NE2 B:HIS203 4.9 69.3 1.0 CD2 B:HIS203 4.9 68.8 1.0 ND2 B:ASN330 4.9 58.8 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