Manganese in PDB 6n0t: Trna Ligase

All present enzymatic activity of Trna Ligase:
6.5.1.3;

The structure of Trna Ligase, PDB code: 6n0t was solved by A.Banerjee, Y.Goldgur, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.42 / 2.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.310, 56.688, 172.718, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 24.7

The binding sites of Manganese atom in the Trna Ligase (pdb code 6n0t). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Trna Ligase, PDB code: 6n0t:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Trna Ligase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Trna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:64.1 occ:1.00 O1B A:ATP502 2.3 47.1 1.0 O2G A:ATP502 2.4 64.0 1.0 O A:HOH700 2.6 87.1 1.0 O A:HOH630 2.8 54.1 1.0 O A:HOH724 2.9 74.6 1.0 OD2 A:ASP86 3.2 0.5 1.0 PG A:ATP502 3.4 58.6 1.0 PB A:ATP502 3.5 43.1 1.0 O3B A:ATP502 3.6 64.0 1.0 O3G A:ATP502 3.7 58.1 1.0 O A:HOH692 4.4 34.1 1.0 O3A A:ATP502 4.4 46.5 1.0 CG A:ASP86 4.4 0.6 1.0 CE A:LYS120 4.5 57.0 1.0 O2B A:ATP502 4.6 35.5 1.0 NH2 A:ARG99 4.6 66.1 1.0 O1G A:ATP502 4.7 51.5 1.0 NZ A:LYS120 4.8 54.9 1.0 OD1 A:ASP86 5.0 0.6 1.0

Manganese binding site 2 out of 2 in the Trna Ligase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Trna Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn504 b:45.4 occ:1.00 O A:HOH652 2.2 39.2 1.0 O2A A:ATP502 2.2 48.8 1.0 O A:HOH624 2.2 40.6 1.0 O A:HOH605 2.4 34.2 1.0 O A:HOH601 2.4 25.9 1.0 O A:HOH603 2.6 29.4 1.0 PA A:ATP502 3.7 46.7 1.0 O2 A:SO4501 3.8 50.0 1.0 OE2 A:GLU300 3.9 43.5 1.0 O2B A:ATP502 4.0 35.5 1.0 OE1 A:GLU218 4.1 40.8 1.0 O A:GLY151 4.1 30.7 1.0 O4' A:ATP502 4.2 35.2 1.0 OE1 A:GLU300 4.3 48.5 1.0 O5' A:ATP502 4.4 56.4 1.0 C4' A:ATP502 4.4 36.7 1.0 ND2 A:ASN150 4.4 52.6 1.0 O A:HOH706 4.4 49.0 1.0 CD A:GLU300 4.5 51.2 1.0 O1A A:ATP502 4.6 49.1 1.0 C1' A:ATP502 4.6 31.7 1.0 O A:HOH676 4.6 45.4 1.0 O A:HOH682 4.6 44.9 1.0 O3A A:ATP502 4.7 46.5 1.0 N A:GLY151 4.8 39.3 1.0 O A:GLU149 4.9 37.8 1.0 PB A:ATP502 5.0 43.1 1.0

A.Banerjee, S.Ghosh, Y.Goldgur, S.Shuman. Structure and Two-Metal Mechanism of Fungal Trna Ligase. Nucleic Acids Res. V. 47 1428 2019.
ISSN: ESSN 1362-4962
PubMed: 30590734
DOI: 10.1093/NAR/GKY1275