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Arsenic in PDB 5vg2: Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae

Protein crystallography data

The structure of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae, PDB code: 5vg2 was solved by C.Schlachter, V.Klapper, M.Chruszcz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.46
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 60.494, 43.067, 165.708, 90.00, 95.18, 90.00
R / Rfree (%) 19.1 / 23.1

Other elements in 5vg2:

The structure of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae (pdb code 5vg2). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 9 binding sites of Arsenic where determined in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae, PDB code: 5vg2:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Arsenic binding site 1 out of 9 in 5vg2

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Arsenic binding site 1 out of 9 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range:
probe atom residue distance (Å) B Occ
U:As302

b:0.5
occ:1.00
 AS U:CAC302 0.0 0.5 1.0
O1 U:CAC302 1.7 0.3 1.0
O2 U:CAC302 1.7 0.2 1.0
C1 U:CAC302 2.0 0.5 1.0
C2 U:CAC302 2.0 0.1 1.0
ND1 U:HIS175 3.5 46.3 1.0
CB U:HIS175 4.1 46.4 1.0
NZ U:LYS106 4.1 63.2 1.0
CD U:LYS106 4.2 58.0 1.0
CG U:HIS175 4.2 46.2 1.0
CE1 U:HIS175 4.5 46.0 1.0
CA U:GLY178 4.6 69.8 1.0
CE U:LYS106 4.7 59.6 1.0

Arsenic binding site 2 out of 9 in 5vg2

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Arsenic binding site 2 out of 9 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As302

b:0.1
occ:1.00
 AS A:CAC302 0.0 0.1 1.0
O1 A:CAC302 1.7 0.5 1.0
O2 A:CAC302 1.7 0.3 1.0
C1 A:CAC302 2.0 0.2 1.0
C2 A:CAC302 2.0 0.8 1.0
ND1 A:HIS175 3.6 43.4 1.0
NZ A:LYS106 4.0 56.8 1.0
CG A:HIS175 4.4 43.6 1.0
CA A:GLY178 4.4 59.5 1.0
CB A:HIS175 4.4 42.9 1.0
CE1 A:HIS175 4.4 44.6 1.0
CD A:LYS106 4.6 54.3 1.0
CE A:LYS106 4.6 56.1 1.0
C A:GLY178 4.9 59.0 1.0

Arsenic binding site 3 out of 9 in 5vg2

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Arsenic binding site 3 out of 9 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As302

b:0.6
occ:1.00
 AS B:CAC302 0.0 0.6 1.0
O2 B:CAC302 1.7 0.8 1.0
O1 B:CAC302 1.7 0.1 1.0
C1 B:CAC302 2.0 0.4 1.0
C2 B:CAC302 2.0 0.6 1.0
ND1 B:HIS175 3.9 47.4 1.0
NZ B:LYS106 4.1 64.7 1.0
CB B:HIS175 4.5 45.8 1.0
CA B:GLY178 4.5 62.4 1.0
CG B:HIS175 4.6 45.9 1.0
CD B:LYS106 4.7 60.0 1.0
CE B:LYS106 4.7 62.8 1.0
CE1 B:HIS175 4.9 47.1 1.0

Arsenic binding site 4 out of 9 in 5vg2

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Arsenic binding site 4 out of 9 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As303

b:0.6
occ:1.00
 AS B:CAC303 0.0 0.6 1.0
O1 B:CAC303 1.7 0.8 1.0
O2 B:CAC303 1.7 0.9 1.0
C1 B:CAC303 2.0 0.1 1.0
C2 B:CAC303 2.0 0.0 1.0
O B:HOH405 3.8 41.8 1.0
O A:HOH416 4.2 43.7 1.0
N B:ASP72 4.2 47.8 1.0
O B:ASP72 4.6 50.3 1.0
CB B:ASP72 4.6 53.0 1.0
CA B:GLU71 4.9 49.2 1.0
CA B:ASP72 4.9 49.0 1.0

Arsenic binding site 5 out of 9 in 5vg2

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Arsenic binding site 5 out of 9 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As302

b:0.6
occ:1.00
 AS C:CAC302 0.0 0.6 1.0
O1 C:CAC302 1.7 0.3 1.0
O2 C:CAC302 1.7 0.3 1.0
C2 C:CAC302 2.0 0.2 1.0
C1 C:CAC302 2.0 0.1 1.0
NZ C:LYS106 4.0 68.0 1.0
ND1 C:HIS175 4.0 47.5 1.0
CA C:GLY178 4.3 68.6 1.0
CD C:LYS106 4.7 62.8 1.0
CE C:LYS106 4.7 65.7 1.0
CB C:HIS175 4.8 47.0 1.0
CG C:HIS175 4.8 46.6 1.0
CE1 C:HIS175 4.9 48.2 1.0
C C:GLY178 4.9 67.0 1.0

Arsenic binding site 6 out of 9 in 5vg2

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Arsenic binding site 6 out of 9 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As303

b:0.2
occ:1.00
 AS C:CAC303 0.0 0.2 1.0
O1 C:CAC303 1.7 0.4 1.0
O2 C:CAC303 1.7 0.1 1.0
C1 C:CAC303 2.0 0.0 1.0
C2 C:CAC303 2.0 0.2 1.0
NH1 A:ARG208 3.6 82.4 1.0
N C:ARG126 3.7 70.8 1.0
CA C:PRO125 3.8 70.0 1.0
CB C:PRO125 4.2 70.1 1.0
C C:PRO125 4.3 69.5 1.0
CZ A:ARG208 4.4 79.0 1.0
CB C:ARG126 4.5 74.9 1.0
OD2 C:ASP123 4.7 75.5 1.0
NH2 A:ARG208 4.7 83.6 1.0
CA C:ARG126 4.7 71.7 1.0
N C:PRO125 4.9 68.4 1.0

Arsenic binding site 7 out of 9 in 5vg2

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Arsenic binding site 7 out of 9 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As304

b:0.9
occ:1.00
 AS C:CAC304 0.0 0.9 1.0
O1 C:CAC304 1.7 0.7 1.0
O2 C:CAC304 1.7 0.9 1.0
C2 C:CAC304 2.0 0.5 1.0
C1 C:CAC304 2.0 0.6 1.0
ND2 C:ASN148 3.7 53.6 1.0
OD1 C:ASN150 4.1 73.3 1.0
CB C:THR152 4.6 52.9 1.0
CG2 C:THR152 4.6 52.8 1.0
OG1 C:THR152 4.7 56.0 1.0
CG C:ASN148 4.8 54.5 1.0
CB C:ASN150 4.9 68.5 1.0
CG C:ASN150 5.0 71.9 1.0

Arsenic binding site 8 out of 9 in 5vg2

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Arsenic binding site 8 out of 9 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As305

b:0.8
occ:1.00
 AS C:CAC305 0.0 0.8 1.0
O2 C:CAC305 1.7 0.3 1.0
O1 C:CAC305 1.7 0.0 1.0
C2 C:CAC305 2.0 0.8 1.0
C1 C:CAC305 2.0 0.9 1.0
N C:ASP72 4.3 49.7 1.0
CA C:GLU71 4.6 51.9 1.0
CG C:GLU71 4.9 58.6 1.0
CB C:ASP72 4.9 54.6 1.0
CB C:GLU71 4.9 54.6 1.0

Arsenic binding site 9 out of 9 in 5vg2

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Arsenic binding site 9 out of 9 in the Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 9 of Intradiol Ring-Cleavage Dioxygenase From Tetranychus Urticae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As306

b:0.1
occ:1.00
 AS C:CAC306 0.0 0.1 1.0
O2 C:CAC306 1.7 0.7 1.0
O1 C:CAC306 1.7 0.3 1.0
C1 C:CAC306 2.0 0.8 1.0
C2 C:CAC306 2.0 0.8 1.0
CD2 C:LEU256 3.9 61.2 1.0
CZ C:PHE221 4.8 66.1 1.0

Reference:

C.R.Schlachter, L.Daneshian, J.Amaya, V.Klapper, N.Wybouw, T.Borowski, T.Van Leeuwen, V.Grbic, M.Grbic, T.M.Makris, M.Chruszcz. Structural and Functional Characterization of An Intradiol Ring-Cleavage Dioxygenase From the Polyphagous Spider Mite Herbivore Tetranychus Urticae Koch. Insect Biochem.Mol.Biol. V. 107 19 2019.
ISSN: ISSN 0965-1748
PubMed: 30529144
DOI: 10.1016/J.IBMB.2018.12.001
Page generated: Wed Jul 10 13:07:36 2024

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