Cobalt in PDB 7p3b: Human Rna Ligase Rtcb in Complex with Gmp and Co(II)

All present enzymatic activity of Human Rna Ligase Rtcb in Complex with Gmp and Co(II):
6.5.1.8;

The structure of Human Rna Ligase Rtcb in Complex with Gmp and Co(II), PDB code: 7p3b was solved by A.Kroupova, F.Ackle, M.Jinek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.99 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.906, 96.906, 227.137, 90, 90, 90
R / Rfree (%)	19.2 / 22

The binding sites of Cobalt atom in the Human Rna Ligase Rtcb in Complex with Gmp and Co(II) (pdb code 7p3b). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Human Rna Ligase Rtcb in Complex with Gmp and Co(II), PDB code: 7p3b:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Human Rna Ligase Rtcb in Complex with Gmp and Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Human Rna Ligase Rtcb in Complex with Gmp and Co(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co602 b:27.8 occ:1.00 O1P A:5GP601 2.0 33.2 1.0 NE2 A:HIS259 2.1 32.3 1.0 NE2 A:HIS353 2.2 33.9 1.0 SG A:CYS122 2.3 31.4 1.0 CE1 A:HIS259 2.9 30.0 1.0 HE1 A:HIS259 3.1 36.0 1.0 CE1 A:HIS353 3.1 32.2 1.0 CD2 A:HIS259 3.1 31.8 1.0 HB3 A:CYS122 3.1 35.4 1.0 CD2 A:HIS353 3.1 32.8 1.0 H5'1 A:5GP601 3.1 40.6 1.0 O A:HOH772 3.3 29.2 1.0 HE1 A:HIS353 3.3 38.7 1.0 P A:5GP601 3.3 34.6 1.0 HD2 A:HIS353 3.3 39.4 1.0 HD2 A:HIS259 3.3 38.1 1.0 CB A:CYS122 3.4 29.5 1.0 H5'2 A:5GP601 3.4 40.6 1.0 C5' A:5GP601 3.6 33.8 1.0 O5' A:5GP601 3.7 33.9 1.0 CO A:CO603 3.8 34.1 1.0 O A:HOH822 3.9 36.2 1.0 HB2 A:CYS122 4.0 35.4 1.0 H A:GLY123 4.1 34.0 1.0 ND1 A:HIS259 4.1 30.7 1.0 HD2 A:HIS428 4.1 40.8 1.0 O2P A:5GP601 4.1 36.0 1.0 N A:GLY123 4.1 28.4 1.0 CG A:HIS259 4.2 29.3 1.0 ND1 A:HIS353 4.2 32.1 1.0 C A:CYS122 4.2 29.0 1.0 CG A:HIS353 4.3 31.0 1.0 CA A:CYS122 4.3 30.5 1.0 O3P A:5GP601 4.4 31.2 1.0 OD1 A:ASN354 4.4 34.1 1.0 HA2 A:GLY123 4.5 33.9 1.0 HA A:CYS122 4.6 36.6 1.0 O A:CYS122 4.7 25.9 1.0 HD2 A:HIS227 4.8 44.8 1.0 HD1 A:HIS259 4.8 36.8 1.0 CA A:GLY123 4.8 28.2 1.0 CD2 A:HIS428 4.9 34.0 1.0 NE2 A:HIS227 4.9 39.1 1.0 HD1 A:HIS353 5.0 38.6 1.0

Cobalt binding site 2 out of 4 in the Human Rna Ligase Rtcb in Complex with Gmp and Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Human Rna Ligase Rtcb in Complex with Gmp and Co(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co603 b:34.1 occ:1.00 NE2 A:HIS227 2.1 39.1 1.0 O A:HOH772 2.2 29.2 1.0 O A:HOH765 2.3 49.1 1.0 OD2 A:ASP119 2.3 28.5 1.0 SG A:CYS122 2.4 31.4 1.0 O A:HOH822 2.5 36.2 1.0 CE1 A:HIS227 3.0 37.0 1.0 HB2 A:CYS122 3.1 35.4 1.0 CD2 A:HIS227 3.2 37.3 1.0 HE1 A:HIS227 3.2 44.4 1.0 CG A:ASP119 3.4 30.1 1.0 CB A:CYS122 3.4 29.5 1.0 HD2 A:HIS227 3.4 44.8 1.0 HB3 A:ASP119 3.5 32.2 1.0 CO A:CO602 3.8 27.8 1.0 CB A:ASP119 3.8 26.9 1.0 HB2 A:ASP119 3.8 32.2 1.0 HB3 A:CYS122 3.9 35.4 1.0 ND1 A:HIS227 4.2 38.5 1.0 CG A:HIS227 4.3 35.9 1.0 O1P A:5GP601 4.4 33.2 1.0 HA3 A:GLY261 4.4 33.3 1.0 OD1 A:ASP119 4.4 31.4 1.0 HA A:CYS122 4.5 36.6 1.0 HE1 A:HIS259 4.5 36.0 1.0 NE2 A:HIS259 4.5 32.3 1.0 HB2 A:ASN226 4.5 55.5 1.0 CA A:CYS122 4.6 30.5 1.0 CE1 A:HIS259 4.6 30.0 1.0 O2P A:5GP601 4.7 36.0 1.0 HA A:SER260 4.8 34.9 1.0 H A:GLY261 4.8 32.6 1.0 N A:GLY261 4.9 27.1 1.0 O A:HOH756 4.9 31.0 1.0 HD1 A:HIS227 5.0 46.2 1.0

Cobalt binding site 3 out of 4 in the Human Rna Ligase Rtcb in Complex with Gmp and Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Human Rna Ligase Rtcb in Complex with Gmp and Co(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co602 b:32.4 occ:1.00 O1P B:5GP601 2.0 36.4 1.0 NE2 B:HIS259 2.1 41.4 1.0 NE2 B:HIS353 2.1 40.2 1.0 SG B:CYS122 2.3 32.1 1.0 HB3 B:CYS122 2.9 39.3 1.0 CE1 B:HIS259 3.0 39.1 1.0 CE1 B:HIS353 3.0 39.0 1.0 HE1 B:HIS259 3.1 46.9 1.0 CD2 B:HIS353 3.1 38.1 1.0 O B:HOH701 3.1 41.1 1.0 CD2 B:HIS259 3.1 40.6 1.0 H5'1 B:5GP601 3.1 51.1 1.0 CB B:CYS122 3.2 32.7 1.0 HE1 B:HIS353 3.2 46.8 1.0 P B:5GP601 3.3 38.5 1.0 HD2 B:HIS353 3.3 45.8 1.0 H5'2 B:5GP601 3.3 51.1 1.0 HD2 B:HIS259 3.4 48.7 1.0 C5' B:5GP601 3.6 42.6 1.0 O2P B:5GP601 3.7 38.9 1.0 CO B:CO603 3.7 32.9 1.0 O5' B:5GP601 3.8 40.7 1.0 HB2 B:CYS122 3.8 39.3 1.0 HD2 B:HIS428 4.0 49.8 1.0 ND1 B:HIS259 4.1 39.5 1.0 O B:HOH822 4.1 34.8 1.0 ND1 B:HIS353 4.1 38.2 1.0 CA B:CYS122 4.2 31.9 1.0 CG B:HIS353 4.2 37.9 1.0 C B:CYS122 4.2 31.9 1.0 CG B:HIS259 4.2 39.0 1.0 OD1 B:ASN354 4.3 34.5 1.0 N B:GLY123 4.4 32.3 1.0 H B:GLY123 4.4 38.7 1.0 O3P B:5GP601 4.5 37.0 1.0 HA B:CYS122 4.5 38.3 1.0 HD2 B:HIS227 4.6 50.8 1.0 O B:CYS122 4.6 31.1 1.0 NE2 B:HIS227 4.8 43.3 1.0 HA2 B:GLY123 4.8 37.4 1.0 HD1 B:HIS259 4.8 47.5 1.0 CD2 B:HIS428 4.9 41.5 1.0 HD1 B:HIS353 4.9 45.8 1.0 CD2 B:HIS227 5.0 42.3 1.0

Cobalt binding site 4 out of 4 in the Human Rna Ligase Rtcb in Complex with Gmp and Co(II)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Human Rna Ligase Rtcb in Complex with Gmp and Co(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co603 b:32.9 occ:1.00 NE2 B:HIS227 2.0 43.3 1.0 O B:HOH701 2.1 41.1 1.0 OD2 B:ASP119 2.2 35.6 1.0 SG B:CYS122 2.4 32.1 1.0 O B:HOH779 2.6 49.5 1.0 O B:HOH822 2.6 34.8 1.0 CE1 B:HIS227 2.9 40.8 1.0 HE1 B:HIS227 3.0 49.0 1.0 CD2 B:HIS227 3.1 42.3 1.0 HB2 B:CYS122 3.2 39.3 1.0 CG B:ASP119 3.3 32.9 1.0 HD2 B:HIS227 3.4 50.8 1.0 CB B:CYS122 3.4 32.7 1.0 HB3 B:ASP119 3.6 36.3 1.0 CO B:CO602 3.7 32.4 1.0 HB2 B:ASP119 3.8 36.3 1.0 CB B:ASP119 3.8 30.3 1.0 HB3 B:CYS122 3.9 39.3 1.0 ND1 B:HIS227 4.1 42.2 1.0 O2P B:5GP601 4.1 38.9 1.0 CG B:HIS227 4.2 42.2 1.0 OD1 B:ASP119 4.3 34.4 1.0 HA3 B:GLY261 4.4 34.6 1.0 O B:HOH735 4.5 42.6 1.0 HA B:CYS122 4.5 38.3 1.0 O1P B:5GP601 4.5 36.4 1.0 HE1 B:HIS259 4.6 46.9 1.0 NE2 B:HIS259 4.6 41.4 1.0 HB2 B:ASN226 4.6 48.6 1.0 H B:GLY261 4.6 35.0 1.0 CA B:CYS122 4.7 31.9 1.0 HA B:SER260 4.7 45.0 1.0 CE1 B:HIS259 4.7 39.1 1.0 N B:GLY261 4.8 29.2 1.0 HD1 B:HIS227 4.8 50.6 1.0 O B:HOH750 4.8 45.4 1.0 P B:5GP601 4.9 38.5 1.0

A.Kroupova, F.Ackle, I.Asanovic, S.Weitzer, F.M.Boneberg, M.Faini, A.Leitner, A.Chui, R.Aebersold, J.Martinez, M.Jinek. Molecular Architecture of the Human Trna Ligase Complex. Elife V. 10 2021.
ISSN: ESSN 2050-084X
PubMed: 34854379
DOI: 10.7554/ELIFE.71656