Magnesium in PDB 3rr5: Dna Ligase From the Archaeon Thermococcus Sp. 1519

All present enzymatic activity of Dna Ligase From the Archaeon Thermococcus Sp. 1519:
6.5.1.1;

The structure of Dna Ligase From the Archaeon Thermococcus Sp. 1519, PDB code: 3rr5 was solved by T.Petrova, E.Y.Bezsudnova, K.M.Boyko, A.V.Mardanov, V.O.Popov, K.M.Polyakov, N.V.Ravin, I.G.Shabalin, K.G.Skryabin, T.N.Stekhanova, M.V.Kovalchuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.26 / 3.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.950, 85.600, 105.960, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 31

The binding sites of Magnesium atom in the Dna Ligase From the Archaeon Thermococcus Sp. 1519 (pdb code 3rr5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Dna Ligase From the Archaeon Thermococcus Sp. 1519, PDB code: 3rr5:

Magnesium binding site 1 out of 1 in the Dna Ligase From the Archaeon Thermococcus Sp. 1519


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Ligase From the Archaeon Thermococcus Sp. 1519 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:69.3 occ:1.00 CZ A:PHE323 3.6 56.1 1.0 OE2 A:GLU409 3.7 64.0 1.0 CE2 A:PHE323 3.8 56.1 1.0 NH1 A:ARG280 3.9 92.0 1.0 CE1 A:PHE323 4.0 56.1 1.0 O A:GLY263 4.0 51.1 1.0 CD2 A:PHE323 4.3 56.1 1.0 CD1 A:PHE323 4.4 56.1 1.0 CG A:PHE323 4.6 56.1 1.0 CD A:GLU409 4.6 64.0 1.0 CZ A:ARG280 4.6 92.0 1.0 OE1 A:GLU409 4.7 64.0 1.0 NZ A:LYS260 4.8 71.4 1.0 OE2 A:GLU310 5.0 71.2 1.0

T.Petrova, E.Y.Bezsudnova, K.M.Boyko, A.V.Mardanov, K.M.Polyakov, V.V.Volkov, M.Kozin, N.V.Ravin, I.G.Shabalin, K.G.Skryabin, T.N.Stekhanova, M.V.Kovalchuk, V.O.Popov. Atp-Dependent Dna Ligase From Thermococcus Sp. 1519 Displays A New Arrangement of the Ob-Fold Domain. Acta Crystallogr.,Sect.F V. 68 1440 2012.
ISSN: ESSN 1744-3091
PubMed: 23192021
DOI: 10.1107/S1744309112043394