Magnesium in PDB 5tt6: T4 Rna Ligase 1 (K99M)

All present enzymatic activity of T4 Rna Ligase 1 (K99M):
6.5.1.3;

The structure of T4 Rna Ligase 1 (K99M), PDB code: 5tt6 was solved by Y.Goldgur, M.-C.Unciuleac, S.H.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.51 / 2.19
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.293, 39.960, 108.268, 90.00, 116.36, 90.00
R / Rfree (%)	18.9 / 25.9

The binding sites of Magnesium atom in the T4 Rna Ligase 1 (K99M) (pdb code 5tt6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the T4 Rna Ligase 1 (K99M), PDB code: 5tt6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the T4 Rna Ligase 1 (K99M)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T4 Rna Ligase 1 (K99M) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:32.0 occ:1.00 O2G A:ATP403 1.8 28.3 1.0 O A:HOH531 1.8 27.8 1.0 O A:HOH522 2.0 31.4 1.0 O1B A:ATP403 2.1 30.2 1.0 O A:HOH536 2.2 21.1 1.0 OD2 A:ASP272 2.3 36.2 1.0 PG A:ATP403 3.1 36.7 1.0 PB A:ATP403 3.2 29.1 1.0 CG A:ASP272 3.2 38.1 1.0 OD1 A:ASP272 3.5 31.5 1.0 O3B A:ATP403 3.5 31.8 1.0 O A:HOH525 3.7 28.6 1.0 O3A A:ATP403 3.8 26.5 1.0 O A:GLY269 3.9 30.7 1.0 O1G A:ATP403 3.9 33.3 1.0 O A:HOH547 3.9 25.5 1.0 O1A A:ATP403 4.1 41.3 1.0 O A:HOH587 4.2 45.8 1.0 O3G A:ATP403 4.2 37.1 1.0 OD1 A:ASP273 4.3 32.8 1.0 NZ A:LYS240 4.3 44.5 1.0 OD2 A:ASP273 4.4 30.1 1.0 O2B A:ATP403 4.5 31.0 1.0 PA A:ATP403 4.6 33.0 1.0 CB A:ASP272 4.6 30.4 1.0 CG A:ASP273 4.7 35.5 1.0 O A:HOH534 4.7 30.9 1.0

Magnesium binding site 2 out of 2 in the T4 Rna Ligase 1 (K99M)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T4 Rna Ligase 1 (K99M) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:40.6 occ:1.00 O A:HOH535 2.0 33.0 1.0 O A:HOH507 2.1 31.2 1.0 O2A A:ATP403 2.2 30.8 1.0 O A:HOH509 2.2 26.2 1.0 O A:HOH508 2.3 27.8 1.0 O A:HOH561 2.4 33.1 1.0 PA A:ATP403 3.7 33.0 1.0 OE1 A:GLU159 3.9 39.3 1.0 O A:GLY102 3.9 39.6 1.0 OE2 A:GLU227 4.0 37.5 1.0 OE1 A:GLU227 4.1 35.3 1.0 OD1 A:ASP101 4.2 31.9 1.0 O2B A:ATP403 4.2 31.0 1.0 O A:HOH525 4.2 28.6 1.0 O4' A:ATP403 4.3 26.8 1.0 O1A A:ATP403 4.4 41.3 1.0 C4' A:ATP403 4.4 34.1 1.0 CD A:GLU227 4.5 36.3 1.0 O A:GLU100 4.5 40.6 1.0 O3A A:ATP403 4.5 26.5 1.0 C1' A:ATP403 4.6 35.7 1.0 O5' A:ATP403 4.6 28.2 1.0 OH A:TYR246 4.6 36.2 1.0 N A:GLY102 4.7 31.0 1.0 PB A:ATP403 4.8 29.1 1.0 CA A:ASP101 4.8 33.0 1.0 CE A:MET99 4.9 37.7 1.0 C A:GLY102 5.0 31.6 1.0

M.C.Unciuleac, Y.Goldgur, S.Shuman. Two-Metal Versus One-Metal Mechanisms of Lysine Adenylylation By Atp-Dependent and Nad(+)-Dependent Polynucleotide Ligases. Proc. Natl. Acad. Sci. V. 114 2592 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28223499
DOI: 10.1073/PNAS.1619220114