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Chlorine in PDB 5lo9: Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form

Protein crystallography data

The structure of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form, PDB code: 5lo9 was solved by J.A.Brito, J.M.Kurth, J.Reuter, A.Flegler, T.Koch, T.Franke, E.Klein, S.Rowe, J.N.Butt, K.Denkmann, I.A.C.Pereira, C.Dahl, M.Archer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 113.13 / 2.75
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 159.753, 159.753, 393.086, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 19.8

Other elements in 5lo9:

The structure of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form (pdb code 5lo9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form, PDB code: 5lo9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 5lo9

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Chlorine binding site 1 out of 11 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1005

b:63.5
occ:1.00
NE1 A:TRP113 3.2 38.2 1.0
NE A:ARG123 3.3 38.6 1.0
O A:HOH1150 3.3 40.9 1.0
N A:ALA120 3.4 39.1 1.0
NH2 A:ARG123 3.8 66.3 1.0
CB A:ALA120 3.8 35.7 1.0
CG A:ARG123 4.0 35.4 1.0
CZ A:ARG123 4.0 37.0 1.0
CA A:PRO119 4.1 42.3 1.0
CD A:ARG123 4.1 41.4 1.0
CB A:ARG123 4.1 26.6 1.0
CE2 A:TRP113 4.2 37.4 1.0
CD1 A:TRP113 4.2 37.3 1.0
CA A:ALA120 4.2 41.7 1.0
C A:PRO119 4.2 40.8 1.0
CB A:PRO119 4.3 42.9 1.0
CZ2 A:TRP113 4.4 32.7 1.0
O A:THR110 4.5 33.5 1.0
C A:THR110 4.8 40.1 1.0
O2D A:HEC1004 4.9 49.4 1.0

Chlorine binding site 2 out of 11 in 5lo9

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Chlorine binding site 2 out of 11 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1006

b:92.8
occ:0.50
O A:HOH1139 2.8 68.7 1.0
O A:TRP154 3.8 46.9 1.0
O A:GLY168 3.8 40.3 1.0
O1 A:PGE1026 4.3 67.6 1.0
C A:GLY168 4.3 37.3 1.0
CA A:GLY168 4.4 42.0 1.0
O A:GLY155 4.8 43.6 1.0
C A:TRP154 4.9 41.9 1.0
C A:GLY155 5.0 44.4 1.0

Chlorine binding site 3 out of 11 in 5lo9

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Chlorine binding site 3 out of 11 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1009

b:91.9
occ:1.00
NH1 A:ARG158 3.0 67.3 1.0
NH2 A:ARG158 3.5 51.8 1.0
CZ A:ARG158 3.7 67.3 1.0
CG2 A:THR156 4.7 32.3 1.0

Chlorine binding site 4 out of 11 in 5lo9

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Chlorine binding site 4 out of 11 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1010

b:83.4
occ:1.00
C1 A:EDO1021 3.4 32.3 1.0
C2 A:EDO1021 3.7 56.9 1.0
O A:ARG249 4.4 52.3 1.0
O2 A:EDO1021 4.4 51.5 1.0
CD2 A:LEU252 4.4 56.0 1.0
CB A:ALA265 4.4 39.7 1.0
CB A:ARG249 4.6 41.8 1.0
CG A:ARG249 4.6 43.7 1.0
O1 A:EDO1021 4.7 44.4 1.0
CG A:LEU252 4.9 52.8 1.0
CA A:ARG249 4.9 42.5 1.0
CH2 A:TRP362 5.0 48.8 1.0

Chlorine binding site 5 out of 11 in 5lo9

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Chlorine binding site 5 out of 11 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1011

b:85.4
occ:1.00
O A:PRO427 3.4 48.6 1.0
NH1 A:ARG428 3.8 61.1 1.0
CB A:PRO427 4.1 43.8 1.0
OD2 A:ASP339 4.1 60.8 1.0
C A:PRO427 4.3 36.9 1.0
CG A:ASP339 4.5 50.6 1.0
CB A:ASP339 4.5 40.4 1.0
O A:GLY282 4.6 48.8 1.0
CA A:PRO427 4.6 42.8 1.0
CG2 A:VAL515 4.8 50.2 1.0
CD A:ARG428 4.9 45.8 1.0
ND2 A:ASN336 4.9 47.2 1.0

Chlorine binding site 6 out of 11 in 5lo9

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Chlorine binding site 6 out of 11 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1012

b:93.8
occ:1.00
O A:GLY131 3.6 48.0 1.0
N A:GLY133 3.6 43.3 1.0
C A:GLY131 3.7 41.4 1.0
N A:ALA132 4.1 40.0 1.0
O A:VAL130 4.1 49.7 1.0
CA A:ALA132 4.3 36.7 1.0
CA A:GLY131 4.3 47.4 1.0
CA A:GLY133 4.4 45.2 1.0
C A:ALA132 4.5 37.0 1.0
OE2 A:GLU44 4.5 61.5 1.0
C A:VAL130 4.9 37.4 1.0
CG1 A:VAL415 4.9 42.1 1.0
O A:GLY133 5.0 54.2 1.0

Chlorine binding site 7 out of 11 in 5lo9

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Chlorine binding site 7 out of 11 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1013

b:99.7
occ:1.00
OD1 A:ASP339 3.4 61.9 1.0
O A:HOH1145 3.8 50.5 1.0
OD2 A:ASP339 4.0 60.8 1.0
CD A:GLN338 4.1 45.8 1.0
CG A:ASP339 4.1 50.6 1.0
OE1 A:GLN338 4.2 46.5 1.0
NE2 A:GLN338 4.3 46.5 1.0
CG A:GLN338 4.5 42.4 1.0
CB A:GLN477 4.9 32.4 1.0

Chlorine binding site 8 out of 11 in 5lo9

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Chlorine binding site 8 out of 11 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1005

b:74.7
occ:1.00
NE1 B:TRP113 3.1 48.7 1.0
NE B:ARG123 3.1 55.3 1.0
N B:ALA120 3.4 44.7 1.0
NH2 B:ARG123 3.7 61.9 1.0
CB B:ALA120 3.8 49.8 1.0
CZ B:ARG123 3.9 48.4 1.0
CG B:ARG123 4.0 50.9 1.0
CE2 B:TRP113 4.0 62.7 1.0
CD B:ARG123 4.0 59.6 1.0
CA B:PRO119 4.1 56.4 1.0
CB B:ARG123 4.1 51.2 1.0
CD1 B:TRP113 4.2 59.5 1.0
CA B:ALA120 4.2 55.9 1.0
CZ2 B:TRP113 4.2 63.3 1.0
CB B:PRO119 4.2 53.6 1.0
C B:PRO119 4.2 53.4 1.0
O B:THR110 4.4 58.1 1.0
O1D B:HEC1004 4.7 60.6 1.0
C B:THR110 4.7 57.3 1.0

Chlorine binding site 9 out of 11 in 5lo9

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Chlorine binding site 9 out of 11 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1007

b:93.0
occ:1.00
NE2 B:HIS62 3.3 60.3 1.0
O B:LEU35 3.9 57.5 1.0
CE1 B:HIS62 4.0 60.6 1.0
CD2 B:HIS62 4.4 57.5 1.0
CA B:GLY36 4.8 54.1 1.0
C B:LEU35 4.8 60.1 1.0

Chlorine binding site 10 out of 11 in 5lo9

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Chlorine binding site 10 out of 11 in the Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Thiosulfate Dehydrogenase (Tsdba) From Marichromatium Purpuratum - "As Isolated" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1008

b:96.5
occ:1.00
CL B:CL1009 3.8 93.0 1.0
O B:ARG249 3.9 66.0 1.0
CB B:ARG249 4.1 56.9 1.0
CG B:ARG249 4.2 62.5 1.0
CA B:ARG249 4.5 61.4 1.0
O B:HOH1101 4.6 46.5 1.0
C B:ARG249 4.7 67.1 1.0
CD B:ARG249 4.8 58.9 1.0
CB B:ALA265 4.8 36.9 1.0
CD1 B:LEU252 4.9 86.1 1.0
CD2 B:LEU252 5.0 68.6 1.0

Reference:

J.M.Kurth, J.A.Brito, J.Reuter, A.Flegler, T.Koch, T.Franke, E.M.Klein, S.F.Rowe, J.N.Butt, K.Denkmann, I.A.Pereira, M.Archer, C.Dahl. Electron Accepting Units of the Diheme Cytochrome C Tsda, A Bifunctional Thiosulfate Dehydrogenase/Tetrathionate Reductase. J.Biol.Chem. V. 291 24804 2016.
ISSN: ESSN 1083-351X
PubMed: 27694441
DOI: 10.1074/JBC.M116.753863
Page generated: Sat Dec 12 12:03:39 2020

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