Manganese in PDB 6n0v: Trna Ligase

All present enzymatic activity of Trna Ligase:
6.5.1.3;

The structure of Trna Ligase, PDB code: 6n0v 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)	46.48 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	155.231, 114.071, 68.200, 90.00, 100.36, 90.00
R / Rfree (%)	21.2 / 25.6

The binding sites of Manganese atom in the Trna Ligase (pdb code 6n0v). 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: 6n0v:
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:Mn501 b:0.1 occ:1.00 O A:HOH633 2.2 66.1 1.0 O A:HOH646 2.3 84.5 1.0 O2P A:APK148 2.3 70.8 1.0 O A:HOH645 2.4 0.2 1.0 O A:HOH632 2.4 93.7 1.0 O A:HOH628 2.7 61.3 1.0 P A:APK148 3.7 62.1 1.0 OE1 A:GLU218 3.8 63.3 1.0 O4' A:APK148 3.8 55.4 1.0 NZ A:APK148 3.9 60.5 1.0 O A:GLY151 4.1 57.7 1.0 C4' A:APK148 4.2 53.1 1.0 ND2 A:ASN150 4.3 61.8 1.0 C1' A:APK148 4.5 54.5 1.0 O5' A:APK148 4.6 66.1 1.0 N A:GLY151 4.6 57.4 1.0 OE1 A:GLU300 4.7 81.4 1.0 O A:GLU149 4.7 46.4 1.0 O1P A:APK148 4.7 74.0 1.0 CA A:ASN150 4.9 64.2 1.0 O A:HOH611 4.9 39.0 1.0 CD A:GLU218 4.9 64.4 1.0 C A:GLY151 5.0 59.4 1.0 O2' A:APK148 5.0 43.0 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 B:Mn501 b:55.8 occ:1.00 O2P B:APK148 2.1 69.3 1.0 O B:HOH642 2.3 49.0 1.0 O B:HOH632 2.4 45.9 1.0 O B:HOH618 2.7 35.8 1.0 O B:HOH689 2.8 47.8 1.0 O B:HOH611 3.0 66.3 1.0 P B:APK148 3.5 49.3 1.0 NZ B:APK148 3.9 32.1 1.0 O B:GLY151 4.0 41.4 1.0 O4' B:APK148 4.1 42.1 1.0 OE2 B:GLU218 4.1 50.8 1.0 C4' B:APK148 4.3 40.1 1.0 O5' B:APK148 4.4 55.7 1.0 ND2 B:ASN150 4.4 36.4 1.0 O1P B:APK148 4.5 47.9 1.0 OE2 B:GLU300 4.6 73.8 1.0 O B:HOH602 4.6 26.5 1.0 C1' B:APK148 4.7 41.8 1.0 N B:GLY151 4.7 43.1 1.0 OE1 B:GLU300 4.7 68.9 1.0 O B:GLU149 4.8 40.5 1.0 C5' B:APK148 5.0 42.0 1.0 NZ B:LYS325 5.0 63.2 1.0 CA B:ASN150 5.0 40.3 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