Magnesium in PDB 2xma: Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex

The structure of Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex, PDB code: 2xma was solved by A.B.Hickman, J.A.James, O.Barabas, C.Pasternak, B.Ton-Hoang, M.Chandler, S.Sommer, F.Dyda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.827, 89.288, 90.104, 90.00, 111.23, 90.00
R / Rfree (%)	21.5 / 23.8

The binding sites of Magnesium atom in the Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex (pdb code 2xma). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex, PDB code: 2xma:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1045 b:41.5 occ:1.00 O C:HOH2026 2.1 40.7 1.0 O C:HOH2027 2.1 43.0 1.0 O C:HOH2022 2.1 43.6 1.0 O A:HOH2038 2.1 41.6 1.0 OP2 C:DC31 2.2 41.2 1.0 O A:PRO114 2.2 39.4 1.0 P C:DC31 3.2 37.0 1.0 C A:PRO114 3.3 39.9 1.0 O5' C:DC31 3.4 37.1 1.0 OP1 C:DC31 3.9 36.9 1.0 OP2 C:DG32 3.9 41.2 1.0 CA A:PRO114 4.0 39.3 1.0 CB A:PRO114 4.1 38.8 1.0 O C:HOH2025 4.2 52.1 1.0 O A:HOH2040 4.2 54.6 1.0 O4 C:DT33 4.2 51.8 1.0 C5 C:DC31 4.3 43.7 1.0 C6 C:DC31 4.3 41.8 1.0 O C:HOH2020 4.4 39.4 1.0 O B:GLY15 4.4 41.3 1.0 N A:SER115 4.4 39.8 1.0 O3' C:DT30 4.6 33.8 1.0 CA A:SER115 4.7 40.3 1.0 C5' C:DC31 4.8 34.8 1.0 CA B:GLY15 4.8 43.0 1.0 N7 C:DG32 4.8 47.7 1.0 C3' C:DT30 4.9 31.2 1.0 C7 C:DT33 4.9 51.2 1.0 C3' C:DC31 5.0 35.0 1.0

Magnesium binding site 2 out of 4 in the Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1045 b:35.1 occ:1.00 O D:HOH2018 2.1 35.1 1.0 O D:HOH2014 2.1 37.8 1.0 O D:HOH2016 2.1 34.8 1.0 O A:HOH2004 2.1 35.2 1.0 O B:PRO114 2.2 30.9 1.0 OP2 D:DC31 2.2 32.5 1.0 C B:PRO114 3.3 31.7 1.0 P D:DC31 3.3 31.2 1.0 O5' D:DC31 3.6 32.1 1.0 OP2 D:DG32 3.9 34.2 1.0 CA B:PRO114 4.0 32.2 1.0 OP1 D:DC31 4.0 31.1 1.0 CB B:PRO114 4.0 31.8 1.0 O4 D:DT33 4.1 38.0 1.0 O D:HOH2017 4.2 39.7 1.0 O B:HOH2040 4.3 41.5 1.0 O A:GLY15 4.3 36.5 1.0 C5 D:DC31 4.4 36.9 1.0 N B:SER115 4.4 30.2 1.0 C6 D:DC31 4.5 36.0 1.0 O B:HOH2015 4.5 32.7 1.0 CA A:GLY15 4.6 36.7 1.0 CA B:SER115 4.7 29.1 1.0 O3' D:DT30 4.7 31.7 1.0 N7 D:DG32 4.8 44.6 1.0 C7 D:DT33 4.9 41.5 1.0 C5' D:DC31 4.9 31.1 1.0 C A:GLY15 4.9 35.5 1.0

Magnesium binding site 3 out of 4 in the Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1139 b:51.9 occ:1.00 O G:HOH2009 2.1 52.3 1.0 O E:HOH2021 2.1 48.4 1.0 O G:HOH2010 2.1 52.5 1.0 O G:HOH2006 2.1 53.8 1.0 O E:PRO114 2.2 49.2 1.0 OP2 G:DC31 2.4 52.5 1.0 C E:PRO114 3.3 48.9 1.0 P G:DC31 3.4 54.1 1.0 O5' G:DC31 3.6 50.8 1.0 CA E:PRO114 3.9 49.2 1.0 CB E:PRO114 4.0 49.1 1.0 OP2 G:DG32 4.0 47.8 1.0 OP1 G:DC31 4.1 56.0 1.0 O4 G:DT33 4.1 72.6 1.0 O E:HOH2022 4.1 60.7 1.0 C5 G:DC31 4.2 63.2 1.0 C6 G:DC31 4.4 62.7 1.0 N E:SER115 4.4 47.4 1.0 O F:GLY15 4.4 56.3 1.0 O G:HOH2007 4.5 41.4 1.0 N7 G:DG32 4.7 71.1 1.0 O3' G:DT30 4.7 58.6 1.0 CA E:SER115 4.8 46.5 1.0 CA F:GLY15 4.8 55.6 1.0 C7 G:DT33 4.8 70.0 1.0 C4 G:DT33 4.9 71.9 1.0 C5' G:DC31 5.0 50.1 1.0

Magnesium binding site 4 out of 4 in the Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Deinococcus Radiodurans ISDRA2 Transposase Right End Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg1045 b:50.8 occ:1.00 O H:HOH2007 2.1 49.6 1.0 O H:HOH2008 2.1 52.5 1.0 O H:HOH2009 2.1 50.2 1.0 O H:HOH2006 2.1 55.6 1.0 O F:PRO114 2.2 54.4 1.0 OP2 H:DC31 2.3 63.9 1.0 P H:DC31 3.2 60.6 1.0 C F:PRO114 3.3 56.2 1.0 O5' H:DC31 3.4 56.3 1.0 OP2 H:DG32 3.8 46.1 1.0 OP1 H:DC31 3.9 57.6 1.0 CA F:PRO114 3.9 57.6 1.0 CB F:PRO114 4.1 57.9 1.0 O4 H:DT33 4.2 88.0 1.0 C5 H:DC31 4.2 71.2 1.0 O F:HOH2019 4.3 50.5 1.0 O E:GLY15 4.3 58.9 1.0 C6 H:DC31 4.4 72.8 1.0 N F:SER115 4.4 55.4 1.0 CA E:GLY15 4.6 58.5 1.0 O3' H:DT30 4.6 65.9 1.0 CA F:SER115 4.7 54.5 1.0 C5' H:DC31 4.8 56.8 1.0 N7 H:DG32 4.8 67.0 1.0 C7 H:DT33 4.8 88.4 1.0 C E:GLY15 4.9 57.5 1.0 C3' H:DC31 4.9 64.2 1.0 C3' H:DT30 5.0 69.1 1.0

A.B.Hickman, J.A.James, O.Barabas, C.Pasternak, B.Ton-Hoang, M.Chandler, S.Sommer, F.Dyda. Dna Recognition and the Precleavage State During Single-Stranded Dna Transposition in D. Radiodurans. Embo J. V. 29 3840 2010.
ISSN: ISSN 0261-4189
PubMed: 20890269
DOI: 10.1038/EMBOJ.2010.241