Magnesium in PDB 2cfm: Atp-Dependent Dna Ligase From Pyrococcus Furiosus

All present enzymatic activity of Atp-Dependent Dna Ligase From Pyrococcus Furiosus:
6.5.1.1;

The structure of Atp-Dependent Dna Ligase From Pyrococcus Furiosus, PDB code: 2cfm was solved by H.Nishida, Y.Ishino, K.Morikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.866, 87.399, 62.648, 90.00, 109.22, 90.00
R / Rfree (%)	20.4 / 23.1

The binding sites of Magnesium atom in the Atp-Dependent Dna Ligase From Pyrococcus Furiosus (pdb code 2cfm). 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 Atp-Dependent Dna Ligase From Pyrococcus Furiosus, PDB code: 2cfm:

Magnesium binding site 1 out of 1 in the Atp-Dependent Dna Ligase From Pyrococcus Furiosus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Atp-Dependent Dna Ligase From Pyrococcus Furiosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1562 b:15.6 occ:1.00 O A:HOH2218 2.1 17.4 1.0 O A:HOH2329 2.1 16.4 1.0 O A:HOH2253 2.2 20.6 1.0 O A:HOH2450 2.2 16.8 1.0 O A:HOH2330 2.2 13.6 1.0 O A:HOH2419 2.4 29.1 1.0 OE2 A:GLU299 3.6 12.3 1.0 O A:HOH2418 3.7 26.3 1.0 O A:GLY252 3.8 12.9 1.0 O A:HOH2402 3.8 24.6 1.0 O A:HOH2221 3.8 19.3 1.0 OE2 A:GLU398 4.1 24.3 1.0 OE1 A:GLU398 4.1 19.9 1.0 OD1 A:ASP251 4.2 18.2 1.0 O2' A:AMP1563 4.2 13.1 1.0 O A:HOH2356 4.2 20.8 1.0 O A:HOH2355 4.3 23.1 1.0 CD A:GLU398 4.4 19.2 1.0 NZ A:LYS249 4.4 18.0 1.0 N A:GLY252 4.5 12.5 1.0 O A:HOH2215 4.5 28.5 1.0 CD A:GLU299 4.6 11.6 1.0 C A:GLY252 4.7 13.1 1.0 O A:TYR250 4.7 12.0 1.0 C1' A:AMP1563 4.8 12.1 1.0 CA A:ASP251 4.9 13.7 1.0 O A:HOH2421 5.0 17.5 1.0

H.Nishida, S.Kiyonari, Y.Ishino, K.Morikawa. The Closed Structure of An Archaeal Dna Ligase From Pyrococcus Furiosus. J.Mol.Biol. V. 360 956 2006.
ISSN: ISSN 0022-2836
PubMed: 16820169
DOI: 10.1016/J.JMB.2006.05.062