Magnesium in PDB 2vjv: Crystal Structure of the IS608 Transposase in Complex with Left End 26-Mer Dna Hairpin and A 6-Mer Dna Representing the Left End Cleavage Site

The structure of Crystal Structure of the IS608 Transposase in Complex with Left End 26-Mer Dna Hairpin and A 6-Mer Dna Representing the Left End Cleavage Site, PDB code: 2vjv was solved by O.Barabas, D.R.Ronning, C.Guynet, A.B.Hickman, B.Ton-Hoang, M.Chandler, F.Dyda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.61 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.292, 72.407, 110.174, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.7

The binding sites of Magnesium atom in the Crystal Structure of the IS608 Transposase in Complex with Left End 26-Mer Dna Hairpin and A 6-Mer Dna Representing the Left End Cleavage Site (pdb code 2vjv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the IS608 Transposase in Complex with Left End 26-Mer Dna Hairpin and A 6-Mer Dna Representing the Left End Cleavage Site, PDB code: 2vjv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the IS608 Transposase in Complex with Left End 26-Mer Dna Hairpin and A 6-Mer Dna Representing the Left End Cleavage Site


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 IS608 Transposase in Complex with Left End 26-Mer Dna Hairpin and A 6-Mer Dna Representing the Left End Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1042 b:20.4 occ:1.00 O B:HOH2009 2.1 16.9 1.0 O C:HOH2050 2.1 15.1 1.0 O C:HOH2044 2.1 17.0 1.0 O C:HOH2045 2.1 18.2 1.0 O C:HOH2047 2.1 18.4 1.0 O6 C:DG39 2.3 22.1 1.0 C6 C:DG39 3.3 19.6 1.0 N7 C:DG39 3.9 20.2 1.0 C5 C:DG39 4.0 20.2 1.0 OD1 B:ASN12 4.0 23.9 1.0 OP1 C:DG19 4.0 16.1 1.0 O C:HOH2015 4.1 22.0 1.0 O6 C:DG38 4.1 20.9 1.0 O C:HOH2023 4.1 27.4 1.0 O C:HOH2049 4.2 23.0 1.0 O6 C:DG40 4.2 24.4 1.0 O C:HOH2012 4.2 17.6 1.0 N4 C:DC22 4.3 18.4 1.0 O B:HIS11 4.4 17.4 1.0 ND2 A:ASN109 4.4 16.4 1.0 N1 C:DG39 4.5 19.5 1.0 N4 C:DC21 4.8 17.6 1.0 O B:HOH2008 4.8 22.7 1.0 CB B:HIS11 4.9 20.8 1.0 CG B:ASN12 4.9 20.7 1.0 C6 C:DG38 4.9 20.7 1.0 C B:HIS11 5.0 19.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the IS608 Transposase in Complex with Left End 26-Mer Dna Hairpin and A 6-Mer Dna Representing the Left End Cleavage Site


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 IS608 Transposase in Complex with Left End 26-Mer Dna Hairpin and A 6-Mer Dna Representing the Left End Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1042 b:16.6 occ:1.00 O D:HOH2045 2.1 19.8 1.0 O D:HOH2049 2.1 18.9 1.0 O D:HOH2012 2.1 17.0 1.0 O D:HOH2056 2.1 16.6 1.0 O D:HOH2052 2.1 17.0 1.0 O6 D:DG39 2.2 23.7 1.0 C6 D:DG39 3.3 21.8 1.0 N7 D:DG39 3.8 26.5 1.0 C5 D:DG39 3.9 23.7 1.0 O D:HOH2013 3.9 17.0 1.0 OD1 A:ASN12 4.0 18.6 1.0 O6 D:DG38 4.0 16.7 1.0 OP1 D:DG19 4.1 22.0 1.0 O D:HOH2055 4.1 25.6 1.0 O6 D:DG40 4.1 25.2 1.0 O D:HOH2015 4.2 18.6 1.0 N4 D:DC22 4.3 18.0 1.0 ND2 B:ASN109 4.3 11.3 1.0 O A:HIS11 4.3 22.4 1.0 O D:HOH2024 4.3 40.9 1.0 N1 D:DG39 4.5 20.9 1.0 CB A:HIS11 4.8 23.4 1.0 O A:HOH2005 4.8 17.7 1.0 N4 D:DC21 4.8 17.0 1.0 C6 D:DG38 4.9 19.1 1.0 CG A:ASN12 4.9 17.8 1.0 C A:HIS11 5.0 22.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the IS608 Transposase in Complex with Left End 26-Mer Dna Hairpin and A 6-Mer Dna Representing the Left End Cleavage Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the IS608 Transposase in Complex with Left End 26-Mer Dna Hairpin and A 6-Mer Dna Representing the Left End Cleavage Site within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1042 b:41.6 occ:1.00 O E:HOH2013 2.1 33.6 1.0 O E:HOH2014 2.1 40.6 1.0 O E:HOH2018 2.1 44.8 1.0 O E:HOH2015 2.1 44.4 1.0 OP2 E:DT-4 4.1 35.5 1.0 OP1 E:DT-4 4.2 33.2 1.0 O E:HOH2011 4.7 39.5 1.0 P E:DT-4 4.7 33.7 1.0

O.Barabas, D.R.Ronning, C.Guynet, A.B.Hickman, B.Ton-Hoang, M.Chandler, F.Dyda. Mechanism of IS200/IS605 Family Dna Transposases: Activation and Transposon-Directed Target Site Selection. Cell(Cambridge,Mass.) V. 132 208 2008.
ISSN: ISSN 0092-8674
PubMed: 18243097
DOI: 10.1016/J.CELL.2007.12.029