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Magnesium in PDB 2xo6: Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site

Protein crystallography data

The structure of Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site, PDB code: 2xo6 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 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.308, 86.915, 128.297, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.9

Other elements in 2xo6:

The structure of Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site also contains other interesting chemical elements:

Cadmium (Cd) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site (pdb code 2xo6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site, PDB code: 2xo6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2xo6

Go back to Magnesium Binding Sites List in 2xo6
Magnesium binding site 1 out of 8 in the Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site


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 Y132F Mutant Complexed with Left End Recognition and Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1141

b:16.8
occ:0.60
 CD A:CD1002 0.0 32.3 0.4
O B:HOH2069 2.1 14.1 0.6
OP2 B:DC31 2.1 17.1 1.0
O A:PRO114 2.2 16.3 1.0
O B:HOH2076 2.2 16.4 0.6
O B:HOH2075 2.2 12.4 0.6
O B:HOH2066 2.2 31.8 0.4
O B:HOH2077 2.3 31.3 0.4
O B:HOH2073 2.3 30.4 0.4
O B:HOH2074 2.3 11.9 0.6
O B:HOH2072 2.3 30.6 0.4
C A:PRO114 3.2 15.8 1.0
P B:DC31 3.3 15.8 1.0
O5' B:DC31 3.6 16.8 1.0
CA A:PRO114 3.8 15.4 1.0
CB A:PRO114 3.8 15.0 1.0
OP1 B:DC31 3.9 16.1 1.0
OP2 B:DA32 4.0 14.7 1.0
O4 B:DT33 4.1 22.8 1.0
O A:HOH2081 4.2 22.0 1.0
O B:HOH2068 4.3 18.0 1.0
C5 B:DC31 4.4 15.0 1.0
N A:SER115 4.4 15.9 1.0
O D:GLY15 4.4 17.4 1.0
C6 B:DC31 4.4 15.0 1.0
O3' B:DT30 4.6 15.4 1.0
CA D:GLY15 4.7 18.4 1.0
CA A:SER115 4.7 15.7 1.0
C5' B:DC31 4.9 16.1 1.0
C3' B:DT30 5.0 15.2 1.0
N7 B:DA32 5.0 16.8 1.0

Magnesium binding site 2 out of 8 in 2xo6

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Magnesium binding site 2 out of 8 in the Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site


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 Y132F Mutant Complexed with Left End Recognition and Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1142

b:36.7
occ:0.60
 CD A:CD1004 0.0 22.2 0.4
O A:HOH2030 2.1 26.7 0.4
O A:HOH2034 2.1 39.3 0.6
O A:HOH2035 2.4 40.1 0.6
O A:HOH2032 2.4 26.1 0.4
OD1 A:ASP41 2.4 52.6 1.0
OD2 A:ASP41 2.7 50.9 1.0
CG A:ASP41 2.9 48.3 1.0
OD1 A:ASP45 4.3 49.2 1.0
OD2 A:ASP45 4.3 56.3 1.0
CB A:ASP41 4.4 34.8 1.0
O A:ASP41 4.5 27.1 1.0
CG A:ASP45 4.6 47.9 1.0
O A:HOH2037 4.9 38.7 1.0
C A:ASP41 5.0 26.7 1.0

Magnesium binding site 3 out of 8 in 2xo6

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Magnesium binding site 3 out of 8 in the Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site


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 Y132F Mutant Complexed with Left End Recognition and Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1143

b:27.7
occ:0.60
 CD A:CD1007 0.0 43.6 0.4
OE1 A:GLU123 2.6 82.7 1.0
OE2 A:GLU9 2.7 81.1 1.0
OE1 A:GLU9 2.9 73.1 1.0
CD A:GLU9 3.2 74.3 1.0
O A:PRO7 3.4 75.4 1.0
C A:PRO7 3.4 72.9 1.0
CD A:GLU123 3.5 82.0 1.0
N A:LEU8 3.8 67.9 1.0
OE2 A:GLU123 3.9 94.7 1.0
CA A:PRO7 3.9 73.6 1.0
CA A:LEU8 4.1 64.7 1.0
C A:LEU8 4.5 62.0 1.0
CG A:GLU123 4.7 51.3 1.0
CG A:GLU9 4.7 59.6 1.0
CB A:PRO7 4.8 73.9 1.0
O A:HOH2001 4.8 39.8 1.0
O A:LEU8 4.9 62.1 1.0
N A:GLU9 4.9 56.9 1.0

Magnesium binding site 4 out of 8 in 2xo6

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Magnesium binding site 4 out of 8 in the Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site


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 Y132F Mutant Complexed with Left End Recognition and Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:28.2
occ:1.00
 O B:HOH2009 1.9 29.5 1.0
O B:HOH2026 2.0 34.2 1.0
O B:HOH2006 2.1 33.3 1.0
O B:HOH2083 2.1 27.3 1.0
O B:HOH2082 2.1 28.8 1.0
O B:HOH2081 2.2 35.4 1.0
O B:HOH2014 4.0 31.6 1.0
N7 B:DA35 4.2 27.8 1.0
O4 B:DT37 4.3 32.5 1.0
O B:HOH2012 4.3 34.4 1.0
O6 B:DG36 4.4 28.1 1.0
N7 B:DG36 4.4 31.5 1.0
OP2 B:DA14 4.5 36.7 1.0
C2' B:DA14 4.6 24.2 1.0
C8 B:DA35 4.7 29.1 1.0

Magnesium binding site 5 out of 8 in 2xo6

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Magnesium binding site 5 out of 8 in the Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1137

b:41.1
occ:0.60
 CD D:CD1004 0.1 53.7 0.4
O D:HOH2038 2.3 34.1 0.6
O D:HOH2046 2.3 47.3 0.6
O D:HOH2045 2.3 56.9 0.4
O D:HOH2039 2.3 50.0 0.4
OD2 D:ASP45 2.7 47.1 1.0
OD2 D:ASP49 2.8 54.5 1.0
OD1 D:ASP49 2.8 53.1 1.0
OD1 D:ASP45 2.9 40.2 1.0
CG D:ASP45 3.1 38.5 1.0
CG D:ASP49 3.2 48.1 1.0
O D:ASP45 4.3 20.8 1.0
CB D:ASP45 4.6 23.0 1.0
CB D:ASP49 4.7 29.9 1.0
C D:ASP45 4.9 20.6 1.0
O D:HOH2047 5.0 34.8 1.0

Magnesium binding site 6 out of 8 in 2xo6

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Magnesium binding site 6 out of 8 in the Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1001

b:27.2
occ:1.00
 O E:HOH2074 1.9 28.5 1.0
O E:HOH2078 1.9 30.9 1.0
O E:HOH2075 1.9 26.4 1.0
O E:HOH2022 2.0 30.4 1.0
O E:HOH2003 2.1 33.8 1.0
O E:HOH2072 2.3 32.5 1.0
O4 E:DT37 4.1 35.6 1.0
O E:HOH2071 4.2 32.1 1.0
N7 E:DA35 4.2 28.3 1.0
O E:HOH2009 4.3 35.0 1.0
OP2 E:DA14 4.3 32.4 1.0
O6 E:DG36 4.4 28.1 1.0
N7 E:DG36 4.4 30.5 1.0
C2' E:DA14 4.6 25.5 1.0
O E:HOH2073 4.7 41.7 1.0
C8 E:DA35 4.7 29.3 1.0

Magnesium binding site 7 out of 8 in 2xo6

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Magnesium binding site 7 out of 8 in the Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1038

b:20.6
occ:0.60
 CD D:CD1002 0.0 28.6 0.4
OP2 E:DC31 2.1 16.8 1.0
O E:HOH2057 2.2 19.7 0.6
O E:HOH2056 2.2 28.2 0.4
O D:PRO114 2.2 16.6 1.0
O E:HOH2065 2.3 20.7 0.6
O E:HOH2061 2.3 16.0 0.6
O E:HOH2060 2.3 18.1 0.6
O E:HOH2066 2.3 28.9 0.4
O E:HOH2062 2.3 26.4 0.4
O E:HOH2063 2.3 27.6 0.4
P E:DC31 3.2 16.6 1.0
C D:PRO114 3.3 16.6 1.0
O5' E:DC31 3.5 18.1 1.0
CA D:PRO114 3.8 16.9 1.0
CB D:PRO114 3.9 17.3 1.0
OP1 E:DC31 3.9 16.4 1.0
OP2 E:DA32 4.0 16.8 1.0
O4 E:DT33 4.1 20.2 1.0
O E:HOH2055 4.3 17.6 1.0
C5 E:DC31 4.4 16.8 1.0
O A:GLY15 4.4 16.8 1.0
C6 E:DC31 4.4 16.9 1.0
O E:HOH2010 4.4 21.8 1.0
N D:SER115 4.5 16.4 1.0
O3' E:DT30 4.6 17.1 1.0
CA D:SER115 4.7 16.9 1.0
CA A:GLY15 4.7 18.2 1.0
C5' E:DC31 4.9 17.8 1.0
N7 E:DA32 4.9 18.9 1.0
C3' E:DT30 5.0 16.9 1.0

Magnesium binding site 8 out of 8 in 2xo6

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Magnesium binding site 8 out of 8 in the Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1039

b:34.4
occ:0.60
 CD E:CD1002 0.0 17.6 0.4
O E:HOH2041 2.3 42.1 0.6
O E:HOH2042 2.3 28.1 0.4
OP1 E:DT26 2.3 26.1 1.0
P E:DT26 3.5 24.8 1.0
OP2 E:DT26 3.9 27.1 1.0
O D:HOH2049 4.1 31.8 1.0
O3' E:DT25 4.1 22.8 1.0
O E:HOH2044 4.2 26.2 1.0
O E:HOH2036 4.3 31.1 1.0
C3' E:DT25 4.5 21.9 1.0
O D:HOH2050 4.6 37.5 1.0
O5' E:DT26 4.8 24.1 1.0

Reference:

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
Page generated: Wed Aug 14 07:15:40 2024

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