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Arsenic in PDB 3i3o: 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone

Protein crystallography data

The structure of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone, PDB code: 3i3o was solved by A.S.Halavaty, G.Minasov, T.Skarina, O.Onopriyenko, S.Peterson, A.Savchenko, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.95 / 2.06
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 131.757, 168.156, 107.194, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.5

Other elements in 3i3o:

The structure of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Chlorine (Cl) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic atom in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone (pdb code 3i3o). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 9 binding sites of Arsenic where determined in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone, PDB code: 3i3o:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Arsenic binding site 1 out of 9 in 3i3o

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Arsenic binding site 1 out of 9 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As327

b:56.3
occ:0.50
 AS A:CAC327 0.0 56.3 0.5
O1 A:CAC327 1.7 51.8 0.5
O2 A:CAC327 1.7 53.6 0.5
C1 A:CAC327 2.0 54.3 0.5
C2 A:CAC327 2.0 53.5 0.5
O A:HOH417 3.2 13.0 1.0
O A:HOH538 3.4 38.3 1.0
NZ A:LYS163 3.7 15.9 1.0
NZ A:LYS110 3.9 16.3 1.0
O A:HOH467 4.1 25.7 1.0
CE A:LYS163 4.2 12.4 1.0
O A:HOH554 4.3 43.9 1.0
OE2 A:GLU106 4.5 13.0 1.0
O D:HOH556 4.6 26.1 1.0
CE A:LYS110 4.7 17.4 1.0
O A:HOH443 4.9 12.2 1.0

Arsenic binding site 2 out of 9 in 3i3o

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Arsenic binding site 2 out of 9 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As321

b:61.7
occ:0.65
 AS B:CAC321 0.0 61.7 0.7
O1 B:CAC321 1.7 54.8 0.7
O2 B:CAC321 1.7 58.9 0.7
C2 B:CAC321 2.0 59.5 0.7
C1 B:CAC321 2.0 58.1 0.7
O B:HOH549 3.4 24.8 1.0
OG B:SER122 3.7 12.3 1.0
ND2 B:ASN124 3.8 9.1 1.0
O B:HOH492 3.9 35.7 1.0
CE B:LYS170 4.0 25.8 1.0
CB B:SER122 4.1 14.1 1.0
NZ B:LYS170 4.1 17.4 1.0
O B:HOH501 4.2 25.2 1.0
O B:HOH512 4.2 25.1 1.0
CD B:LYS170 4.7 25.7 1.0
CG B:ASN124 4.7 11.5 1.0
OD1 B:ASN124 4.8 10.7 1.0

Arsenic binding site 3 out of 9 in 3i3o

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Arsenic binding site 3 out of 9 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As328

b:62.9
occ:0.50
 AS B:CAC328 0.0 62.9 0.5
O1 B:CAC328 1.7 62.7 0.5
O2 B:CAC328 1.7 61.1 0.5
C2 B:CAC328 2.0 62.5 0.5
C1 B:CAC328 2.0 61.5 0.5
O B:HOH560 3.5 33.3 1.0
OH B:TYR256 3.6 22.7 1.0
NH2 B:ARG251 4.0 15.8 1.0
CZ B:ARG251 4.2 15.3 1.0
OE2 B:GLU257 4.2 13.4 1.0
NH1 B:ARG251 4.5 13.5 1.0
O B:HOH582 4.6 19.7 1.0
NE B:ARG251 4.7 18.0 1.0
CD B:GLU257 4.7 16.3 1.0
CZ B:TYR256 4.9 19.3 1.0

Arsenic binding site 4 out of 9 in 3i3o

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Arsenic binding site 4 out of 9 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As322

b:54.9
occ:0.65
 AS C:CAC322 0.0 54.9 0.7
O2 C:CAC322 1.7 37.0 0.7
O1 C:CAC322 1.8 41.9 0.7
C2 C:CAC322 2.0 46.2 0.7
C1 C:CAC322 2.0 43.8 0.7
O C:HOH429 3.6 11.8 1.0
NZ C:LYS163 3.6 14.9 1.0
O C:HOH547 3.8 24.1 1.0
O C:HOH520 4.1 25.3 1.0
CE C:LYS163 4.1 14.1 1.0
NZ C:LYS110 4.4 10.4 1.0
O B:HOH528 4.6 22.0 1.0
O C:HOH574 4.9 33.9 1.0
CG2 B:THR143 4.9 5.5 1.0

Arsenic binding site 5 out of 9 in 3i3o

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Arsenic binding site 5 out of 9 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As324

b:53.4
occ:0.55
 AS D:CAC324 0.0 53.4 0.6
O1 D:CAC324 1.7 46.1 0.6
O2 D:CAC324 1.7 44.4 0.6
C1 D:CAC324 2.0 48.8 0.6
C2 D:CAC324 2.0 48.6 0.6
O D:HOH470 3.2 19.5 1.0
NZ D:LYS163 3.5 16.0 1.0
CE D:LYS163 4.2 15.0 1.0
NZ D:LYS110 4.4 21.3 1.0
O A:HOH473 4.4 25.3 1.0
CG2 A:THR143 4.6 10.5 1.0
OE2 D:GLU106 4.8 15.4 1.0
CA A:THR143 4.9 11.3 1.0

Arsenic binding site 6 out of 9 in 3i3o

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Arsenic binding site 6 out of 9 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
E:As325

b:53.0
occ:0.50
 AS E:CAC325 0.0 53.0 0.5
O1 E:CAC325 1.7 46.9 0.5
O2 E:CAC325 1.7 52.2 0.5
C2 E:CAC325 2.0 51.5 0.5
C1 E:CAC325 2.0 50.3 0.5
O E:HOH510 3.4 16.3 0.5
OG E:SER122 3.6 15.1 1.0
ND2 E:ASN124 3.9 10.9 1.0
CB E:SER122 4.0 15.2 1.0
O E:HOH552 4.0 22.7 1.0
O E:HOH467 4.2 19.3 1.0
O E:HOH510 4.6 20.7 0.5
O E:HOH496 4.7 27.9 1.0
CG E:ASN124 4.8 13.8 1.0
OD1 E:ASN124 4.8 13.6 1.0
CD E:LYS170 4.9 24.7 1.0
NZ E:LYS170 4.9 29.8 1.0
O E:HOH544 4.9 42.4 1.0

Arsenic binding site 7 out of 9 in 3i3o

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Arsenic binding site 7 out of 9 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As329

b:56.4
occ:0.50
 AS F:CAC329 0.0 56.4 0.5
O1 F:CAC329 1.7 53.4 0.5
O2 F:CAC329 1.7 53.4 0.5
C1 F:CAC329 2.0 54.0 0.5
C2 F:CAC329 2.0 52.5 0.5
O F:HOH483 3.1 17.9 1.0
NZ F:LYS163 3.9 14.3 1.0
CE F:LYS163 4.4 16.8 1.0
NZ F:LYS110 4.5 19.9 1.0
CG2 G:THR143 4.7 13.7 1.0

Arsenic binding site 8 out of 9 in 3i3o

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Arsenic binding site 8 out of 9 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As326

b:50.0
occ:0.50
 AS G:CAC326 0.0 50.0 0.5
O2 G:CAC326 1.7 47.2 0.5
O1 G:CAC326 1.7 49.5 0.5
C1 G:CAC326 2.0 46.6 0.5
C2 G:CAC326 2.0 48.8 0.5
OH G:TYR193 3.7 21.2 1.0
O G:HOH464 3.7 19.8 1.0
OG G:SER180 4.1 15.5 1.0
O G:GLY224 4.1 23.3 1.0
CZ G:TYR193 4.6 18.1 1.0
OE1 G:GLN133 4.6 29.1 1.0
CE2 G:TYR193 4.6 17.9 1.0
O G:PRO223 4.7 15.3 1.0
C G:GLY224 4.9 22.7 1.0
CB G:SER180 4.9 16.5 1.0

Arsenic binding site 9 out of 9 in 3i3o

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Arsenic binding site 9 out of 9 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 9 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
H:As323

b:58.6
occ:0.60
 AS H:CAC323 0.0 58.6 0.6
O2 H:CAC323 1.7 51.1 0.6
O1 H:CAC323 1.7 48.8 0.6
C2 H:CAC323 2.0 51.3 0.6
C1 H:CAC323 2.0 51.6 0.6
O H:HOH411 3.5 12.3 1.0
NZ H:LYS163 3.6 18.8 1.0
CE H:LYS163 4.1 21.3 1.0
NZ H:LYS110 4.3 18.7 1.0
O E:HOH475 4.4 30.8 1.0
OE2 H:GLU106 4.8 20.9 1.0
CG2 E:THR143 4.9 12.3 1.0
CA E:THR143 5.0 12.1 1.0

Reference:

A.S.Halavaty, G.Minasov, T.Skarina, O.Onopriyenko, S.Peterson, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone To Be Published.
Page generated: Wed Jul 10 11:43:36 2024

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