Magnesium in PDB 5co8: Crystal Structure of the Holliday Junction-Resolving Enzyme GEN1 (Wt) in Complex with Product Dna and MG2+ Ion

The structure of Crystal Structure of the Holliday Junction-Resolving Enzyme GEN1 (Wt) in Complex with Product Dna and MG2+ Ion, PDB code: 5co8 was solved by Y.J.Liu, A.D.J.Freeman, A.C.Declais, T.J.Wilson, A.Gartner, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.04 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.072, 98.072, 119.571, 90.00, 90.00, 120.00
R / Rfree (%)	23.9 / 25.5

The binding sites of Magnesium atom in the Crystal Structure of the Holliday Junction-Resolving Enzyme GEN1 (Wt) in Complex with Product Dna and MG2+ Ion (pdb code 5co8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Holliday Junction-Resolving Enzyme GEN1 (Wt) in Complex with Product Dna and MG2+ Ion, PDB code: 5co8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Holliday Junction-Resolving Enzyme GEN1 (Wt) in Complex with Product Dna and MG2+ Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Holliday Junction-Resolving Enzyme GEN1 (Wt) in Complex with Product Dna and MG2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:52.7 occ:0.50 O C:HOH612 2.1 56.9 0.5 OD2 C:ASP143 2.1 58.9 0.5 OD2 C:ASP141 2.2 53.6 0.5 O C:HOH603 2.2 45.0 0.5 OD1 C:ASP141 2.5 53.4 0.5 CG C:ASP141 2.7 50.8 0.5 CG C:ASP143 3.2 55.3 0.5 CB C:ASP143 3.8 46.8 0.5 OP2 X:DG2 4.1 87.3 0.5 CB C:ASP141 4.2 46.6 0.5 OD1 C:ASP143 4.2 55.0 0.5 C5' X:DG2 4.4 81.8 0.5 O C:HOH613 4.5 47.8 0.5 OE1 C:GLU140 4.5 57.0 0.5 CB C:GLU140 4.5 53.6 0.5 O C:GLY2 4.6 65.0 0.5 N C:ASP141 4.6 47.8 0.5 O C:HOH610 4.8 63.0 0.5 O C:HOH606 4.8 61.8 0.5 OE2 C:GLU122 4.9 59.6 0.5 CD C:GLU122 4.9 49.4 0.5 N C:ASP143 5.0 44.7 0.5 CA C:ASP141 5.0 40.5 0.5 CA C:ASP143 5.0 44.9 0.5

Magnesium binding site 2 out of 2 in the Crystal Structure of the Holliday Junction-Resolving Enzyme GEN1 (Wt) in Complex with Product Dna and MG2+ Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Holliday Junction-Resolving Enzyme GEN1 (Wt) in Complex with Product Dna and MG2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:62.3 occ:0.50 O A:HOH611 2.1 54.7 0.5 O A:HOH601 2.2 47.3 0.5 OD2 A:ASP143 2.3 57.9 0.5 O H:HOH601 2.4 68.8 0.5 O H:HOH602 2.7 70.6 0.5 OE2 A:GLU122 2.7 55.3 0.5 OD2 A:ASP141 2.9 51.7 0.5 OE1 A:GLU122 3.0 53.5 0.5 CD A:GLU122 3.2 55.2 0.5 CG A:ASP143 3.4 56.0 0.5 OD1 A:ASP141 3.4 52.4 0.5 CG A:ASP141 3.6 50.6 0.5 CB A:ASP143 3.9 46.3 0.5 O3' H:DT16 4.1 86.3 0.5 O A:HOH602 4.1 51.9 0.5 O A:HOH603 4.2 58.6 0.5 O A:HOH604 4.2 50.7 0.5 OD1 A:ASP143 4.5 59.8 0.5 O A:HOH606 4.6 57.8 0.5 CG A:GLU122 4.7 49.4 0.5 C5' H:DG17 4.8 72.1 0.5 O A:GLY2 4.9 63.1 0.5 OE1 A:GLU140 4.9 55.4 0.5

Y.Liu, A.D.Freeman, A.C.Declais, T.J.Wilson, A.Gartner, D.M.Lilley. Crystal Structure of A Eukaryotic GEN1 Resolving Enzyme Bound to Dna. Cell Rep V. 13 2565 2015.
ISSN: ESSN 2211-1247
PubMed: 26686639
DOI: 10.1016/J.CELREP.2015.11.042