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Iodine in PDB 5oex: Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus

Protein crystallography data

The structure of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus, PDB code: 5oex was solved by K.M.Polyakov, S.I.Tsallagov, T.V.Tikhonova, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.820, 159.450, 91.000, 90.00, 97.77, 90.00
R / Rfree (%) 15.6 / 19.8

Other elements in 5oex:

The structure of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus also contains other interesting chemical elements:

Copper (Cu) 15 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus (pdb code 5oex). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus, PDB code: 5oex:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 5oex

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Iodine binding site 1 out of 8 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I606

b:23.9
occ:0.65
O C:HOH741 3.4 38.3 1.0
OE1 A:GLN278 3.7 16.7 1.0
OE1 C:GLN278 3.7 20.8 1.0
NH2 A:ARG274 3.7 13.5 1.0
NH2 C:ARG274 3.8 14.7 1.0
CG A:GLU197 4.3 22.2 1.0
O C:HOH761 4.4 22.8 1.0
O A:HOH704 4.4 25.5 1.0
CB A:GLU197 4.4 17.7 1.0
CG C:GLU197 4.4 25.8 1.0
NE2 C:GLN278 4.4 15.9 1.0
CD C:GLN278 4.5 17.4 1.0
CD A:GLN278 4.5 15.3 1.0
NE2 A:GLN278 4.6 11.7 1.0
O A:GLU197 4.6 14.5 1.0
CB C:GLU197 4.6 19.5 1.0
CD A:GLU197 4.6 28.7 1.0
CZ A:ARG274 4.8 15.1 1.0
CA A:GLU197 4.8 16.2 1.0
O C:GLU197 4.8 16.7 1.0
OE2 A:GLU197 4.8 29.7 1.0
CZ C:ARG274 4.8 16.2 1.0
CD C:GLU197 4.8 32.3 1.0
CA C:GLU197 4.9 17.7 1.0
OE2 C:GLU197 5.0 36.2 1.0

Iodine binding site 2 out of 8 in 5oex

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Iodine binding site 2 out of 8 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I607

b:34.5
occ:0.50
CG2 A:VAL290 3.3 25.0 1.0
NE1 A:TRP287 3.4 20.9 1.0
N A:VAL290 3.6 20.3 1.0
CB A:ALA296 3.7 18.6 1.0
CA A:GLY293 4.0 22.2 1.0
CG2 A:VAL302 4.1 19.9 1.0
CD1 A:TRP287 4.1 22.6 1.0
CB A:VAL290 4.1 24.6 1.0
CG1 A:VAL290 4.2 28.0 1.0
CA A:LEU289 4.2 20.1 1.0
CD2 A:LEU289 4.4 21.6 1.0
C A:LEU289 4.4 20.2 1.0
CA A:VAL290 4.5 22.1 1.0
O A:GLY293 4.5 24.2 1.0
CE2 A:TRP287 4.6 23.8 1.0
C A:GLY293 4.8 23.6 1.0
CB A:LEU289 4.8 19.7 1.0
O A:GLU288 4.8 22.0 1.0

Iodine binding site 3 out of 8 in 5oex

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Iodine binding site 3 out of 8 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I608

b:29.6
occ:0.20
O A:HOH902 2.0 22.7 0.5
O A:HOH901 2.4 38.2 1.0
O A:HOH771 2.5 29.6 1.0
CU A:CU603 2.6 12.2 0.4
CU A:CU604 2.7 19.4 0.2
ND1 A:HIS528 3.6 15.3 1.0
CU A:CU602 3.7 14.9 0.4
NE2 A:HIS437 3.8 24.6 1.0
CE1 A:HIS136 3.8 15.7 1.0
NE2 A:HIS136 3.9 16.2 1.0
CE1 A:HIS437 3.9 23.8 1.0
ND1 A:HIS482 4.0 16.3 1.0
CB A:HIS528 4.1 14.7 1.0
CG A:HIS528 4.1 15.0 1.0
O A:HOH734 4.1 27.3 1.0
CE1 A:HIS482 4.2 16.6 1.0
O A:HIS528 4.4 18.2 1.0
NE2 A:HIS135 4.4 15.6 1.0
CE1 A:HIS528 4.5 16.8 1.0
CU A:CU601 4.8 23.9 1.0
CE1 A:HIS206 5.0 18.6 1.0
CA A:HIS528 5.0 16.3 1.0

Iodine binding site 4 out of 8 in 5oex

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Iodine binding site 4 out of 8 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I605

b:30.3
occ:0.50
NE1 C:TRP287 3.4 15.1 1.0
N C:VAL290 3.7 20.6 1.0
CG2 C:VAL290 3.7 25.9 1.0
CG1 C:VAL290 3.8 23.0 1.0
CB C:ALA296 3.8 19.3 1.0
CA C:GLY293 3.8 21.0 1.0
O C:HOH920 3.9 38.4 1.0
CG2 C:VAL302 4.1 17.0 1.0
CD1 C:TRP287 4.1 16.0 1.0
CB C:VAL290 4.2 23.5 1.0
CA C:LEU289 4.3 19.1 1.0
O C:GLY293 4.3 21.5 1.0
C C:LEU289 4.5 19.9 1.0
CE2 C:TRP287 4.5 15.9 1.0
CA C:VAL290 4.5 21.5 1.0
C C:GLY293 4.6 23.5 1.0
CD2 C:LEU289 4.6 18.5 1.0
CB C:LEU289 4.9 18.5 1.0
N C:GLY293 4.9 23.8 1.0
CZ2 C:TRP287 5.0 16.4 1.0
O C:GLU288 5.0 19.0 1.0

Iodine binding site 5 out of 8 in 5oex

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Iodine binding site 5 out of 8 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I606

b:40.9
occ:0.30
O C:HOH919 2.4 22.0 0.5
CU C:CU604 2.6 18.3 0.3
CU C:CU602 2.8 13.4 0.4
O C:HOH785 2.9 26.4 1.0
O C:HOH931 3.0 26.8 0.5
NE2 C:HIS437 3.6 22.4 1.0
ND1 C:HIS528 3.7 12.7 1.0
CE1 C:HIS437 3.9 22.7 1.0
ND1 C:HIS482 3.9 17.4 1.0
CU C:CU603 3.9 11.7 0.4
CE1 C:HIS136 3.9 14.1 1.0
NE2 C:HIS136 4.0 16.2 1.0
CE1 C:HIS482 4.1 15.8 1.0
CB C:HIS528 4.1 12.0 1.0
CG C:HIS528 4.2 12.0 1.0
O C:HOH839 4.3 28.0 1.0
O C:HIS528 4.4 18.7 1.0
CE1 C:HIS528 4.5 11.6 1.0
NE2 C:HIS135 4.6 14.6 1.0
CU C:CU601 4.9 20.5 1.0
CD2 C:HIS437 5.0 20.9 1.0
CA C:HIS528 5.0 12.3 1.0
CE1 C:HIS206 5.0 16.7 1.0

Iodine binding site 6 out of 8 in 5oex

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Iodine binding site 6 out of 8 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I605

b:42.9
occ:0.50
CG2 D:VAL290 3.3 24.4 1.0
NE1 D:TRP287 3.4 16.5 1.0
N D:VAL290 3.6 18.2 1.0
CA D:GLY293 3.7 23.6 1.0
CB D:ALA296 3.7 22.2 1.0
CG1 D:VAL290 3.9 23.0 1.0
CB D:VAL290 4.1 22.3 1.0
CD1 D:TRP287 4.2 15.9 1.0
CG2 D:VAL302 4.2 19.3 1.0
CA D:LEU289 4.2 19.2 1.0
O D:GLY293 4.2 24.8 1.0
CD2 D:LEU289 4.3 23.4 1.0
C D:GLY293 4.5 23.4 1.0
CA D:VAL290 4.5 20.3 1.0
C D:LEU289 4.5 18.7 1.0
CE2 D:TRP287 4.6 16.3 1.0
CB D:LEU289 4.9 18.7 1.0
N D:GLY293 4.9 25.4 1.0

Iodine binding site 7 out of 8 in 5oex

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Iodine binding site 7 out of 8 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I606

b:37.3
occ:0.30
O D:HOH906 2.2 12.6 0.5
O D:HOH738 3.8 17.9 1.0
CE1 D:TYR164 4.0 31.1 1.0
NE2 D:HIS482 4.0 14.9 1.0
OD1 D:ASP480 4.0 18.6 1.0
CE1 D:HIS482 4.0 15.4 1.0
CZ2 D:TRP452 4.1 18.7 1.0
NE1 D:TRP452 4.2 17.7 1.0
CE1 D:HIS528 4.2 16.3 1.0
NE2 D:HIS528 4.3 16.0 1.0
CE2 D:TRP452 4.3 18.4 1.0
CD D:PRO291 4.4 28.8 1.0
CG D:PRO291 4.4 31.3 1.0
OH D:TYR164 4.8 33.6 1.0
CD1 D:TYR164 4.8 30.9 1.0
CZ D:TYR164 4.8 36.7 1.0
CG D:ASP480 4.9 18.8 1.0
CH2 D:TRP452 5.0 18.8 1.0

Iodine binding site 8 out of 8 in 5oex

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Iodine binding site 8 out of 8 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I607

b:31.0
occ:0.20
O D:HOH904 1.9 20.9 0.5
O D:HOH889 2.5 41.2 1.0
CU D:CU602 2.5 18.6 0.2
CU D:CU604 2.6 26.9 0.5
O D:HOH742 2.7 29.7 1.0
ND1 D:HIS528 3.6 14.7 1.0
CU D:CU603 3.6 16.7 0.5
NE2 D:HIS437 3.7 26.0 1.0
CE1 D:HIS437 3.8 25.2 1.0
CE1 D:HIS136 3.9 17.1 1.0
ND1 D:HIS482 3.9 16.8 1.0
NE2 D:HIS136 4.0 18.1 1.0
CG D:HIS528 4.1 16.2 1.0
CE1 D:HIS482 4.2 15.4 1.0
CB D:HIS528 4.2 14.9 1.0
O D:HIS528 4.3 18.8 1.0
O D:HOH711 4.4 22.0 1.0
CE1 D:HIS528 4.4 16.3 1.0
NE2 D:HIS135 4.6 16.0 1.0
CU D:CU601 4.9 23.4 1.0
CE1 D:HIS206 4.9 15.0 1.0
CA D:HIS528 5.0 15.6 1.0

Reference:

T.V.Tikhonova, D.I.Sorokin, S.I.Tsallagov, K.M.Polyakov, A.A.Trofimov, I.G.Shabalin, M.G.Khrenova, G.Muyser, T.V.Rakitina, V.O.Popov. Discovery and Characterization of A Novel Copper Containing Enzyme - Thiocyanate Dehydrogenase. To Be Published.
Page generated: Sun Dec 13 19:40:50 2020

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