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Magnesium in PDB 2xm3: Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex

Protein crystallography data

The structure of Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex, PDB code: 2xm3 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 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.583, 128.384, 140.222, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 24.9

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex (pdb code 2xm3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex, PDB code: 2xm3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 2xm3

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Magnesium binding site 1 out of 12 in the Deinococcus Radiodurans ISDRA2 Transposase Left 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 Left End Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1135

b:35.7
occ:1.00
 O O:HOH2019 2.1 34.7 1.0
O E:HOH2034 2.1 34.5 1.0
O O:HOH2017 2.1 36.6 1.0
O O:HOH2020 2.1 37.3 1.0
OP2 O:DC31 2.2 36.3 1.0
O E:PRO114 2.7 40.8 1.0
P O:DC31 3.2 37.4 1.0
C E:PRO114 3.2 38.2 1.0
O5' O:DC31 3.5 39.8 1.0
CA E:PRO114 3.7 36.5 1.0
OP1 O:DC31 3.8 38.4 1.0
CB E:PRO114 3.8 36.4 1.0
O4 O:DT33 4.0 48.8 1.0
OP2 O:DA32 4.1 37.3 1.0
N E:SER115 4.1 37.1 1.0
O F:GLY15 4.3 33.2 1.0
O E:HOH2033 4.4 36.2 1.0
O O:HOH2018 4.4 34.0 1.0
O3' O:DT30 4.5 37.2 1.0
CA E:SER115 4.5 31.8 1.0
C6 O:DC31 4.6 44.2 1.0
C5 O:DC31 4.6 44.2 1.0
C3' O:DT30 4.8 38.0 1.0
CA F:GLY15 4.9 35.5 1.0
C5' O:DC31 4.9 39.9 1.0
C3' O:DC31 5.0 38.0 1.0

Magnesium binding site 2 out of 12 in 2xm3

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Magnesium binding site 2 out of 12 in the Deinococcus Radiodurans ISDRA2 Transposase Left 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 Left End Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1135

b:39.4
occ:1.00
 O Q:HOH2019 2.1 38.9 1.0
O Q:HOH2020 2.1 39.4 1.0
O Q:HOH2018 2.1 39.6 1.0
O F:HOH2023 2.1 39.1 1.0
OP2 Q:DC31 2.2 36.7 1.0
O F:PRO114 2.3 34.1 1.0
P Q:DC31 3.3 35.9 1.0
C F:PRO114 3.4 32.5 1.0
O5' Q:DC31 3.5 33.9 1.0
CA F:PRO114 4.0 30.6 1.0
CB F:PRO114 4.1 30.2 1.0
OP1 Q:DC31 4.1 36.8 1.0
OP2 Q:DA32 4.1 35.3 1.0
O4 Q:DT33 4.2 38.4 1.0
O F:HOH2025 4.2 28.2 1.0
C5 Q:DC31 4.4 44.0 1.0
O E:GLY15 4.5 27.3 1.0
N F:SER115 4.5 30.9 1.0
C6 Q:DC31 4.5 43.2 1.0
O3' Q:DT30 4.7 36.6 1.0
N7 Q:DA32 4.7 39.6 1.0
CA E:GLY15 4.7 26.6 1.0
CA F:SER115 4.8 28.3 1.0
C5' Q:DC31 4.9 34.1 1.0
C3' Q:DC31 4.9 36.2 1.0
C3' Q:DT30 5.0 37.9 1.0

Magnesium binding site 3 out of 12 in 2xm3

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Magnesium binding site 3 out of 12 in the Deinococcus Radiodurans ISDRA2 Transposase Left 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 Left End Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1039

b:23.0
occ:1.00
 O G:HOH2028 2.0 22.9 1.0
O G:HOH2024 2.1 24.3 1.0
O B:HOH2003 2.1 23.3 1.0
O G:HOH2026 2.1 21.6 1.0
O A:PRO114 2.1 25.5 1.0
OP2 G:DC31 2.2 25.4 1.0
C A:PRO114 3.3 23.0 1.0
P G:DC31 3.3 24.2 1.0
O5' G:DC31 3.5 24.9 1.0
OP2 G:DA32 3.9 23.3 1.0
OP1 G:DC31 3.9 22.7 1.0
CA A:PRO114 3.9 21.1 1.0
CB A:PRO114 4.0 20.1 1.0
O4 G:DT33 4.1 28.0 1.0
O A:HOH2053 4.1 24.7 1.0
O G:HOH2025 4.2 15.2 1.0
O B:GLY15 4.3 24.7 1.0
N A:SER115 4.3 21.8 1.0
C6 G:DC31 4.4 23.6 1.0
C5 G:DC31 4.4 23.8 1.0
CA B:GLY15 4.6 20.9 1.0
CA A:SER115 4.6 20.9 1.0
O3' G:DT30 4.7 24.9 1.0
C5' G:DC31 4.7 23.5 1.0
C B:GLY15 4.9 22.9 1.0
N7 G:DA32 4.9 26.6 1.0
C3' G:DC31 4.9 22.5 1.0

Magnesium binding site 4 out of 12 in 2xm3

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Magnesium binding site 4 out of 12 in the Deinococcus Radiodurans ISDRA2 Transposase Left 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 Left End Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1114

b:36.7
occ:1.00
 O G:HOH2034 2.1 37.4 1.0
O G:HOH2013 2.1 36.2 1.0
O G:HOH2033 2.1 35.6 1.0
O G:HOH2032 2.1 36.8 1.0
O G:HOH2012 2.1 38.8 1.0
O G:HOH2030 2.1 36.9 1.0
O4 G:DT37 4.1 46.1 1.0
N7 G:DA35 4.1 36.9 1.0
O G:HOH2004 4.3 30.4 1.0
N7 G:DG36 4.4 43.3 1.0
O6 G:DG36 4.5 42.6 1.0
C2' G:DA14 4.5 33.4 1.0
O G:HOH2031 4.5 38.2 1.0
OP2 G:DA14 4.6 40.3 1.0
C8 G:DA35 4.6 38.0 1.0
C5 G:DA35 4.9 36.0 1.0

Magnesium binding site 5 out of 12 in 2xm3

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Magnesium binding site 5 out of 12 in the Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex


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 Left End Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1038

b:26.0
occ:1.00
 O B:HOH2045 2.0 24.7 1.0
O I:HOH2031 2.0 26.9 1.0
O I:HOH2026 2.1 27.4 1.0
O I:HOH2029 2.1 25.7 1.0
OP2 I:DC31 2.2 26.2 1.0
O B:PRO114 2.2 22.3 1.0
P I:DC31 3.3 23.6 1.0
C B:PRO114 3.3 22.2 1.0
O5' I:DC31 3.5 22.1 1.0
OP2 I:DA32 3.9 21.9 1.0
OP1 I:DC31 3.9 22.7 1.0
CA B:PRO114 4.0 21.3 1.0
CB B:PRO114 4.1 20.5 1.0
O4 I:DT33 4.1 21.3 1.0
O B:HOH2046 4.1 29.7 1.0
O A:GLY15 4.3 28.0 1.0
O I:HOH2025 4.3 22.6 1.0
C5 I:DC31 4.4 22.9 1.0
C6 I:DC31 4.4 22.9 1.0
N B:SER115 4.4 22.1 1.0
O3' I:DT30 4.6 23.4 1.0
CA A:GLY15 4.6 22.4 1.0
CA B:SER115 4.7 20.3 1.0
N7 I:DA32 4.9 22.9 1.0
C5' I:DC31 4.9 20.6 1.0
C3' I:DT30 4.9 22.6 1.0
C A:GLY15 5.0 24.7 1.0
C3' I:DC31 5.0 20.6 1.0
C7 I:DT33 5.0 23.1 1.0

Magnesium binding site 6 out of 12 in 2xm3

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Magnesium binding site 6 out of 12 in the Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex


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 Left End Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1116

b:34.7
occ:1.00
 O I:HOH2040 2.1 35.8 1.0
O I:HOH2010 2.1 34.1 1.0
O I:HOH2035 2.1 35.7 1.0
O I:HOH2037 2.1 35.0 1.0
O I:HOH2013 2.1 35.1 1.0
O I:HOH2038 2.1 34.9 1.0
O4 I:DT37 3.9 38.4 1.0
O I:HOH2003 4.2 34.3 1.0
OP2 I:DA14 4.3 34.5 1.0
N7 I:DA35 4.3 34.1 1.0
N7 I:DG36 4.4 36.4 1.0
O I:HOH2014 4.5 52.4 1.0
O6 I:DG36 4.5 35.9 1.0
C2' I:DA14 4.5 27.7 1.0
O I:HOH2036 4.7 36.7 1.0
C8 I:DA35 4.8 34.4 1.0
O5' I:DA14 5.0 32.7 1.0
C8 I:DA14 5.0 28.5 1.0

Magnesium binding site 7 out of 12 in 2xm3

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Magnesium binding site 7 out of 12 in the Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex


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 Left End Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1038

b:21.3
occ:1.00
 O C:PRO114 2.0 25.4 1.0
O C:HOH2049 2.1 20.6 1.0
O K:HOH2030 2.1 20.6 1.0
O K:HOH2035 2.1 21.3 1.0
O K:HOH2033 2.1 22.7 1.0
OP2 K:DC31 2.2 21.7 1.0
C C:PRO114 3.2 25.1 1.0
P K:DC31 3.2 20.4 1.0
O5' K:DC31 3.5 20.4 1.0
OP1 K:DC31 3.9 18.6 1.0
CA C:PRO114 3.9 26.1 1.0
OP2 K:DA32 4.0 20.3 1.0
CB C:PRO114 4.0 26.0 1.0
O4 K:DT33 4.1 25.6 1.0
O C:HOH2050 4.1 27.0 1.0
N C:SER115 4.3 22.5 1.0
O D:GLY15 4.3 28.0 1.0
O K:HOH2029 4.4 27.2 1.0
C6 K:DC31 4.4 15.9 1.0
O K:HOH2036 4.4 26.7 1.0
C5 K:DC31 4.4 15.0 1.0
CA C:SER115 4.5 19.1 1.0
O3' K:DT30 4.6 19.2 1.0
CA D:GLY15 4.6 24.1 1.0
C5' K:DC31 4.8 18.9 1.0
N7 K:DA32 5.0 21.5 1.0
C D:GLY15 5.0 25.4 1.0

Magnesium binding site 8 out of 12 in 2xm3

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Magnesium binding site 8 out of 12 in the Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex


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 Left End Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1039

b:34.3
occ:1.00
 O K:HOH2040 2.1 32.7 1.0
O K:HOH2039 2.1 35.1 1.0
O K:HOH2004 2.1 35.8 1.0
O K:HOH2045 2.1 33.7 1.0
O K:HOH2003 2.1 34.9 1.0
O K:HOH2043 2.1 33.5 1.0
O K:HOH2005 4.0 37.7 1.0
O4 K:DT37 4.1 32.2 1.0
O K:HOH2006 4.1 21.9 1.0
N7 K:DA35 4.2 29.2 1.0
N7 K:DG36 4.4 32.8 1.0
O6 K:DG36 4.4 30.0 1.0
C2' K:DA14 4.6 27.5 1.0
OP2 K:DA14 4.6 35.2 1.0
O K:HOH2014 4.6 47.5 1.0
C8 K:DA35 4.6 29.5 1.0
C5 K:DA35 4.9 29.4 1.0

Magnesium binding site 9 out of 12 in 2xm3

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Magnesium binding site 9 out of 12 in the Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1038

b:24.7
occ:1.00
 O D:HOH2040 2.0 25.2 1.0
O M:HOH2023 2.1 25.2 1.0
O M:HOH2018 2.1 25.8 1.0
O M:HOH2019 2.1 24.0 1.0
O D:PRO114 2.1 26.6 1.0
OP2 M:DC31 2.3 24.9 1.0
C D:PRO114 3.2 26.5 1.0
P M:DC31 3.3 24.2 1.0
O5' M:DC31 3.6 23.5 1.0
CA D:PRO114 3.8 25.7 1.0
OP1 M:DC31 3.9 25.2 1.0
CB D:PRO114 3.9 25.1 1.0
OP2 M:DA32 4.0 23.6 1.0
O4 M:DT33 4.0 26.2 1.0
O D:HOH2041 4.1 22.8 1.0
O C:GLY15 4.2 30.8 1.0
N D:SER115 4.3 25.9 1.0
O M:HOH2022 4.5 44.5 1.0
C5 M:DC31 4.5 27.7 1.0
C6 M:DC31 4.6 27.0 1.0
CA C:GLY15 4.6 27.5 1.0
CA D:SER115 4.6 23.3 1.0
O3' M:DT30 4.7 25.0 1.0
C C:GLY15 4.9 27.9 1.0
C7 M:DT33 5.0 24.6 1.0
C5' M:DC31 5.0 23.3 1.0

Magnesium binding site 10 out of 12 in 2xm3

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Magnesium binding site 10 out of 12 in the Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Deinococcus Radiodurans ISDRA2 Transposase Left End Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1121

b:43.5
occ:1.00
 O M:HOH2029 2.1 42.8 1.0
O M:HOH2008 2.1 43.9 1.0
O M:HOH2027 2.1 42.8 1.0
O M:HOH2028 2.1 42.6 1.0
O M:HOH2010 2.1 44.4 1.0
O M:HOH2026 2.1 43.6 1.0
N7 M:DA35 4.1 43.4 1.0
O4 M:DT37 4.4 48.0 1.0
N7 M:DG36 4.4 45.7 1.0
OP2 M:DA14 4.5 36.8 1.0
C8 M:DA35 4.5 43.9 1.0
O6 M:DG36 4.6 45.5 1.0
C2' M:DA14 4.8 33.3 1.0
C5 M:DA35 5.0 43.8 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 07:12:23 2024

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