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Cadmium 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:

Magnesium (Mg) 8 atoms

Cadmium Binding Sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Deinococcus Radiodurans ISDRA2 Transposase Y132F Mutant Complexed with Left End Recognition and Cleavage Site, PDB code: 2xo6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 2xo6

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Cadmium binding site 1 out of 9 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 Cadmium with other atoms in the Cd 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:Cd1001

b:26.2
occ:1.00
 OE1 D:GLN136 2.1 62.0 1.0
NE2 A:HIS67 2.3 17.1 1.0
NE2 A:HIS69 2.3 18.5 1.0
OP1 C:DG6 2.3 28.0 1.0
O D:HOH2106 2.5 24.2 1.0
CD D:GLN136 2.7 73.9 1.0
NE2 D:GLN136 2.7 81.0 1.0
O3' C:DT5 3.0 26.7 1.0
CD2 A:HIS69 3.2 18.1 1.0
CD2 A:HIS67 3.2 17.0 1.0
P C:DG6 3.3 27.9 1.0
CE1 A:HIS67 3.3 17.2 1.0
CE1 A:HIS69 3.3 18.4 1.0
CG D:GLN136 4.0 84.4 1.0
O5' C:DG6 4.1 29.2 1.0
CG A:MET64 4.1 38.6 1.0
C3' C:DT5 4.3 24.7 1.0
CG A:HIS69 4.4 17.5 1.0
CG A:HIS67 4.4 17.4 1.0
ND1 A:HIS67 4.4 17.6 1.0
ND1 A:HIS69 4.4 18.1 1.0
OP2 C:DG6 4.5 28.2 1.0
C4' C:DT5 4.6 24.1 1.0
CB D:GLN136 4.6 87.4 1.0

Cadmium binding site 2 out of 9 in 2xo6

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Cadmium binding site 2 out of 9 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 Cadmium with other atoms in the Cd 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:Cd1002

b:32.3
occ:0.40
 MG A:MG1141 0.0 16.8 0.6
O B:HOH2069 2.1 14.1 0.6
OP2 B:DC31 2.2 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 2.2 31.3 0.4
O B:HOH2074 2.3 11.9 0.6
O B:HOH2073 2.3 30.4 0.4
O B:HOH2072 2.3 30.6 0.4
C A:PRO114 3.3 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

Cadmium binding site 3 out of 9 in 2xo6

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Cadmium binding site 3 out of 9 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 Cadmium with other atoms in the Cd 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:Cd1004

b:22.2
occ:0.40
 MG A:MG1142 0.0 36.7 0.6
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 2.6 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 4.6 27.1 1.0
CG A:ASP45 4.6 47.9 1.0
O A:HOH2037 4.8 38.7 1.0
C A:ASP41 5.0 26.7 1.0

Cadmium binding site 4 out of 9 in 2xo6

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Cadmium binding site 4 out of 9 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 Cadmium with other atoms in the Cd 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
A:Cd1006

b:0.8
occ:1.00
 O A:HOH2017 2.3 0.4 1.0
OD1 A:ASP66 2.6 39.1 1.0
OD2 A:ASP66 2.8 39.2 1.0
CG A:ASP66 3.1 35.0 1.0
CE1 A:HIS67 4.1 17.2 1.0
ND1 A:HIS67 4.1 17.6 1.0
CB A:ASP66 4.5 21.5 1.0
NH2 A:ARG31 4.6 26.1 1.0
N A:ASP66 4.8 21.2 1.0
NE A:ARG31 4.9 26.4 1.0

Cadmium binding site 5 out of 9 in 2xo6

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Cadmium binding site 5 out of 9 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 Cadmium with other atoms in the Cd 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
A:Cd1007

b:43.6
occ:0.40
 MG A:MG1143 0.0 27.7 0.6
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 3.8 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

Cadmium binding site 6 out of 9 in 2xo6

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Cadmium binding site 6 out of 9 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 Cadmium with other atoms in the Cd 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
D:Cd1001

b:25.6
occ:1.00
 OP1 F:DG6 2.3 27.6 1.0
NE2 D:HIS67 2.3 19.0 1.0
NE2 D:HIS69 2.3 18.2 1.0
OE1 A:GLN136 2.4 42.8 1.0
O F:HOH2010 2.4 24.0 1.0
SD D:MET64 2.9 31.5 1.0
CD2 D:HIS69 3.2 17.7 1.0
CE1 D:HIS69 3.3 18.1 1.0
CD2 D:HIS67 3.3 19.2 1.0
CE1 D:HIS67 3.3 18.8 1.0
CD A:GLN136 3.3 44.8 1.0
O3' F:DT5 3.5 26.7 1.0
P F:DG6 3.5 26.7 1.0
NE2 A:GLN136 3.6 44.0 1.0
CE D:MET64 3.9 31.3 1.0
CG D:MET64 3.9 28.4 1.0
O5' F:DG6 4.3 27.4 1.0
CG D:HIS69 4.4 17.3 1.0
ND1 D:HIS69 4.4 17.7 1.0
ND1 D:HIS67 4.5 18.7 1.0
CG D:HIS67 4.5 18.8 1.0
O F:HOH2014 4.5 48.6 1.0
OP2 F:DG6 4.7 27.1 1.0
CG A:GLN136 4.7 37.5 1.0
CB D:MET64 4.8 25.8 1.0
C3' F:DT5 4.8 25.6 1.0
C4' F:DT5 5.0 25.2 1.0

Cadmium binding site 7 out of 9 in 2xo6

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Cadmium binding site 7 out of 9 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 Cadmium with other atoms in the Cd 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
D:Cd1002

b:28.6
occ:0.40
 MG E:MG1038 0.0 20.6 0.6
OP2 E:DC31 2.1 16.8 1.0
O E:HOH2057 2.1 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:HOH2060 2.3 18.1 0.6
O E:HOH2061 2.3 16.0 0.6
O E:HOH2066 2.3 28.9 0.4
O E:HOH2063 2.3 27.6 0.4
O E:HOH2062 2.3 26.4 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
C6 E:DC31 4.4 16.9 1.0
O A:GLY15 4.4 16.8 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

Cadmium binding site 8 out of 9 in 2xo6

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Cadmium binding site 8 out of 9 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 Cadmium with other atoms in the Cd 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
D:Cd1004

b:53.7
occ:0.40
 MG D:MG1137 0.1 41.1 0.6
O D:HOH2046 2.3 47.3 0.6
O D:HOH2045 2.3 56.9 0.4
O D:HOH2038 2.3 34.1 0.6
O D:HOH2039 2.4 50.0 0.4
OD2 D:ASP45 2.7 47.1 1.0
OD2 D:ASP49 2.7 54.5 1.0
OD1 D:ASP49 2.8 53.1 1.0
OD1 D:ASP45 2.9 40.2 1.0
CG D:ASP49 3.1 48.1 1.0
CG D:ASP45 3.1 38.5 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
O D:HOH2047 4.9 34.8 1.0
C D:ASP45 4.9 20.6 1.0

Cadmium binding site 9 out of 9 in 2xo6

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Cadmium binding site 9 out of 9 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 Cadmium with other atoms in the Cd binding site number 9 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:Cd1002

b:17.6
occ:0.40
 MG E:MG1039 0.0 34.4 0.6
O E:HOH2041 2.2 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 4.4 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: Fri Jul 19 15:27:25 2024

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