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Zinc in PDB 2xqc: Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn

Protein crystallography data

The structure of Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn, PDB code: 2xqc 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 (°) 49.762, 92.716, 126.070, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn (pdb code 2xqc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn, PDB code: 2xqc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 2xqc

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Zinc binding site 1 out of 9 in the Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1138

b:16.8
occ:1.00
 NE2 A:HIS67 2.0 13.3 1.0
NE2 A:HIS69 2.0 13.3 1.0
OP1 C:DG6 2.0 17.2 1.0
NE2 D:HIS137 2.0 15.6 1.0
CD2 A:HIS69 2.9 12.6 1.0
CD2 A:HIS67 3.0 13.1 1.0
CD2 D:HIS137 3.0 15.9 1.0
CE1 A:HIS69 3.1 13.3 1.0
CE1 A:HIS67 3.1 13.0 1.0
CE1 D:HIS137 3.1 16.1 1.0
P C:DG6 3.2 16.8 1.0
O3' C:DT5 3.3 17.0 1.0
O5' C:DG6 3.8 15.9 1.0
O C:HOH2013 4.0 32.4 1.0
CG A:HIS69 4.1 12.5 1.0
CG A:HIS67 4.1 13.1 1.0
ND1 A:HIS69 4.1 12.7 1.0
ND1 A:HIS67 4.2 13.1 1.0
CG D:HIS137 4.2 16.9 1.0
ND1 D:HIS137 4.2 16.8 1.0
CG2 D:ILE133 4.2 12.9 1.0
CG A:MET64 4.2 23.2 1.0
OP2 C:DG6 4.4 18.8 1.0
C3' C:DT5 4.6 16.1 1.0
C4' C:DT5 4.6 16.0 1.0
O A:HOH2034 4.9 30.4 1.0

Zinc binding site 2 out of 9 in 2xqc

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Zinc binding site 2 out of 9 in the Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1139

b:31.2
occ:1.00
 O A:HOH2135 2.1 18.9 1.0
O A:HOH2133 2.1 19.6 1.0
O A:HOH2136 2.1 15.7 1.0
OP2 B:DC31 2.1 16.2 1.0
O A:PRO114 2.1 15.2 1.0
O A:HOH2134 2.1 14.4 1.0
C A:PRO114 3.2 14.8 1.0
P B:DC31 3.2 14.7 1.0
O5' B:DC31 3.5 14.2 1.0
CA A:PRO114 3.8 13.7 1.0
OP1 B:DC31 3.9 15.8 1.0
CB A:PRO114 3.9 12.7 1.0
OP2 B:DA32 4.0 13.8 1.0
O4 B:DT33 4.2 21.8 1.0
O B:HOH2051 4.2 42.6 1.0
O B:HOH2019 4.3 22.8 1.0
O B:HOH2049 4.3 13.4 1.0
N A:SER115 4.3 15.5 1.0
C5 B:DC31 4.4 17.7 1.0
C6 B:DC31 4.4 16.7 1.0
O D:GLY15 4.4 15.7 1.0
O3' B:DT30 4.6 14.3 1.0
CA D:GLY15 4.6 15.3 1.0
CA A:SER115 4.6 14.9 1.0
C5' B:DC31 4.8 13.5 1.0
C3' B:DT30 4.9 15.3 1.0
N7 B:DA32 5.0 18.5 1.0

Zinc binding site 3 out of 9 in 2xqc

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Zinc binding site 3 out of 9 in the Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1140

b:21.2
occ:1.00
 OD2 A:ASP45 1.9 19.1 1.0
OD1 A:ASP49 2.0 19.0 1.0
CG A:ASP45 2.7 23.6 1.0
CG A:ASP49 2.7 16.6 1.0
OD2 A:ASP49 2.8 20.1 1.0
OD1 A:ASP45 2.8 26.8 1.0
O A:ASP45 4.0 18.2 1.0
CB A:ASP45 4.1 19.7 1.0
CB A:ASP49 4.2 13.9 1.0
NH1 A:ARG94 4.3 18.9 1.0
NH2 A:ARG94 4.3 22.0 1.0
C A:ASP45 4.4 17.4 1.0
O A:HOH2053 4.4 36.7 1.0
O A:HOH2052 4.6 30.8 1.0
CZ A:ARG94 4.8 24.3 1.0
CA A:ASP45 4.8 18.2 1.0
N A:ILE46 4.9 16.1 1.0

Zinc binding site 4 out of 9 in 2xqc

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Zinc binding site 4 out of 9 in the Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1038

b:41.4
occ:1.00
 O B:HOH2057 2.1 33.0 1.0
O B:HOH2060 2.1 31.9 1.0
O B:HOH2059 2.1 34.1 1.0
O B:HOH2058 2.1 37.9 1.0
O B:HOH2061 2.1 33.2 1.0
O B:HOH2062 2.1 45.6 1.0
O4 B:DT37 4.0 32.1 1.0
O B:HOH2056 4.2 33.3 1.0
OP2 B:DA14 4.3 24.4 1.0
N7 B:DG36 4.3 31.1 1.0
O6 B:DG36 4.4 29.1 1.0
C2' B:DA14 4.6 21.6 1.0
O B:HOH2013 4.6 28.1 1.0
N7 B:DA35 4.6 32.9 1.0
O5' B:DA14 5.0 25.8 1.0

Zinc binding site 5 out of 9 in 2xqc

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Zinc binding site 5 out of 9 in the Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1007

b:54.4
occ:1.00
 O C:HOH2019 2.1 55.6 1.0
O C:HOH2023 2.1 43.7 1.0
O C:HOH2020 2.1 46.6 1.0
O C:HOH2022 2.1 47.5 1.0
O C:HOH2021 2.1 55.9 1.0
N7 C:DG3 2.3 18.9 1.0
C8 C:DG3 3.2 18.8 1.0
C5 C:DG3 3.3 19.6 1.0
O6 C:DG3 3.6 22.2 1.0
O C:HOH2004 3.6 38.2 1.0
C6 C:DG3 3.8 20.4 1.0
O B:HOH2008 4.2 27.1 1.0
N9 C:DG3 4.4 19.5 1.0
C4 C:DG3 4.4 19.9 1.0
OP2 C:DG3 4.5 22.8 1.0
O B:HOH2002 4.5 34.3 1.0
C5 C:DT2 4.9 25.8 1.0
C6 C:DT2 5.0 24.6 1.0

Zinc binding site 6 out of 9 in 2xqc

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Zinc binding site 6 out of 9 in the Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1141

b:23.4
occ:1.00
 NE2 D:HIS67 2.0 18.4 1.0
OP1 F:DG6 2.0 24.9 1.0
NE2 A:HIS137 2.0 27.0 1.0
NE2 D:HIS69 2.0 16.7 1.0
CD2 D:HIS69 3.0 15.9 1.0
CD2 D:HIS67 3.0 18.3 1.0
CD2 A:HIS137 3.0 27.3 1.0
CE1 D:HIS67 3.0 18.6 1.0
CE1 D:HIS69 3.1 16.4 1.0
CE1 A:HIS137 3.1 27.4 1.0
P F:DG6 3.1 25.1 1.0
O3' F:DT5 3.2 25.9 1.0
O5' F:DG6 3.7 23.8 1.0
ND1 D:HIS67 4.2 18.7 1.0
CG D:HIS67 4.2 18.4 1.0
CG D:HIS69 4.2 15.2 1.0
ND1 D:HIS69 4.2 15.4 1.0
CG A:HIS137 4.2 28.6 1.0
ND1 A:HIS137 4.2 27.7 1.0
OP2 F:DG6 4.4 25.9 1.0
C3' F:DT5 4.5 24.2 1.0
CG D:MET64 4.5 23.9 1.0
O F:HOH2020 4.6 31.8 1.0
C4' F:DT5 4.7 23.6 1.0
CG2 A:ILE133 4.8 30.7 1.0
O F:HOH2013 5.0 38.9 1.0

Zinc binding site 7 out of 9 in 2xqc

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Zinc binding site 7 out of 9 in the Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1142

b:43.7
occ:1.00
 O D:HOH2125 2.1 45.9 1.0
O D:HOH2126 2.1 44.8 1.0
O D:HOH2128 2.1 41.2 1.0
O D:HOH2129 2.1 45.1 1.0
O D:HOH2127 2.1 45.0 1.0
OD2 D:ASP45 2.2 22.0 1.0
CG D:ASP45 3.1 20.9 1.0
OD1 D:ASP45 3.3 26.1 1.0
O D:HOH2011 4.1 42.8 1.0
O D:HOH2042 4.3 45.0 1.0
O D:HOH2046 4.3 34.5 1.0
O D:ASP45 4.4 13.7 1.0
CB D:ASP45 4.4 16.6 1.0
O D:HOH2084 4.5 39.8 1.0
CA D:ASP45 4.8 14.4 1.0
C D:ASP45 4.9 13.8 1.0

Zinc binding site 8 out of 9 in 2xqc

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Zinc binding site 8 out of 9 in the Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1038

b:31.9
occ:1.00
 O E:HOH2095 2.1 20.3 1.0
O E:HOH2096 2.1 19.6 1.0
O E:HOH2098 2.1 14.1 1.0
O E:HOH2097 2.1 21.3 1.0
O D:PRO114 2.1 15.8 1.0
OP2 E:DC31 2.1 14.8 1.0
P E:DC31 3.2 14.2 1.0
C D:PRO114 3.2 15.2 1.0
O5' E:DC31 3.5 14.2 1.0
CA D:PRO114 3.8 15.1 1.0
OP1 E:DC31 3.8 13.8 1.0
CB D:PRO114 3.9 14.7 1.0
OP2 E:DA32 4.0 13.4 1.0
O4 E:DT33 4.2 17.7 1.0
O E:HOH2018 4.3 20.0 1.0
C5 E:DC31 4.3 12.7 1.0
N D:SER115 4.3 16.7 1.0
O E:HOH2079 4.4 32.1 1.0
O A:GLY15 4.4 13.4 1.0
C6 E:DC31 4.4 13.2 1.0
O E:HOH2076 4.4 16.0 1.0
O3' E:DT30 4.5 13.7 1.0
CA A:GLY15 4.6 14.9 1.0
CA D:SER115 4.6 16.8 1.0
C5' E:DC31 4.8 13.6 1.0
C3' E:DT30 4.9 12.7 1.0
N7 E:DA32 4.9 13.9 1.0
C3' E:DC31 5.0 12.8 1.0
C A:GLY15 5.0 13.7 1.0

Zinc binding site 9 out of 9 in 2xqc

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Zinc binding site 9 out of 9 in the Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Deinococcus Radiodurans ISDRA2 Transposase Complexed with Left End Recognition and Cleavage Site and Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1039

b:37.6
occ:1.00
 O E:HOH2100 2.1 25.3 1.0
O E:HOH2101 2.1 29.5 1.0
O E:HOH2102 2.1 37.7 1.0
O E:HOH2099 2.1 26.0 1.0
O E:HOH2104 2.1 31.6 1.0
O E:HOH2103 2.1 29.7 1.0
O E:HOH2093 4.0 38.4 1.0
N7 E:DA35 4.0 25.2 1.0
O4 E:DT37 4.0 28.7 1.0
O E:HOH2017 4.2 23.3 1.0
O E:HOH2094 4.2 31.2 1.0
O E:HOH2012 4.3 19.8 1.0
OP2 E:DA14 4.3 23.5 1.0
N7 E:DG36 4.4 26.7 1.0
O6 E:DG36 4.4 25.4 1.0
C8 E:DA35 4.5 25.8 1.0
C2' E:DA14 4.6 21.3 1.0
O E:HOH2092 4.8 28.8 1.0
C5 E:DA35 4.9 24.9 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: Thu Oct 17 05:28:28 2024

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