Copper in PDB 6uwe: Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper

The structure of Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper, PDB code: 6uwe was solved by I.G.Shabalin, E.Osipov, T.V.Tikhonova, T.V.Rakitina, K.M.Boyko, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.80 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.422, 163.149, 90.631, 90.00, 119.29, 90.00
R / Rfree (%)	14.2 / 16

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper (pdb code 6uwe). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 24 binding sites of Copper where determined in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper, PDB code: 6uwe:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 24 in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:13.2 occ:1.00 NE2 A:HIS206 2.0 10.6 1.0 NE2 A:HIS381 2.0 16.0 1.0 OD2 A:ASP314 2.1 13.5 1.0 CG A:ASP314 2.8 13.1 1.0 CD2 A:HIS206 2.9 10.0 1.0 CD2 A:HIS381 2.9 14.4 1.0 OD1 A:ASP314 2.9 16.1 1.0 CE1 A:HIS206 3.1 9.2 1.0 CE1 A:HIS381 3.1 17.2 1.0 OE1 A:GLN382 3.1 19.3 1.0 O A:HOH882 3.5 18.2 1.0 NE2 A:GLN382 3.5 18.6 1.0 CD A:GLN382 3.7 19.8 1.0 CU A:CU604 3.9 25.3 0.5 UNK A:UNX607 3.9 27.3 1.0 CG A:HIS206 4.0 8.9 1.0 CG A:HIS381 4.1 15.4 1.0 ND1 A:HIS206 4.1 12.4 1.0 ND1 A:HIS381 4.1 14.9 1.0 CB A:ASP314 4.3 12.4 1.0 O A:HOH740 4.4 17.5 1.0 CG1 A:VAL205 4.7 8.0 1.0 CE1 A:HIS437 4.8 11.9 1.0 NE2 A:HIS136 4.9 9.8 1.0 CB A:THR548 5.0 14.8 1.0 CG2 A:THR548 5.0 13.8 1.0

Copper binding site 2 out of 24 in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu602 b:11.5 occ:0.90 ND1 A:HIS528 2.0 10.2 1.0 NE2 A:HIS135 2.0 7.2 1.0 O A:HOH903 2.1 12.5 1.0 CU A:CU604 2.6 25.3 0.5 UNK A:UNX607 3.0 27.3 1.0 CD2 A:HIS135 3.0 8.3 1.0 CE1 A:HIS528 3.0 9.9 1.0 CE1 A:HIS135 3.0 8.1 1.0 CG A:HIS528 3.1 9.1 1.0 CB A:HIS528 3.4 9.2 1.0 NZ A:LYS103 3.5 12.3 1.0 NE2 A:HIS136 3.8 9.8 1.0 ND1 A:HIS135 4.1 6.6 1.0 CG A:HIS135 4.2 6.9 1.0 NE2 A:HIS528 4.2 9.9 1.0 OE1 A:GLU288 4.2 12.9 1.0 CD2 A:HIS528 4.2 9.4 1.0 O A:HOH882 4.3 18.2 1.0 O A:HOH901 4.4 16.4 1.0 CE1 A:HIS136 4.5 9.1 1.0 CD2 A:HIS136 4.5 9.9 1.0 CE A:LYS103 4.5 11.2 1.0 CD A:LYS103 4.8 9.1 1.0 CA A:HIS528 4.9 8.6 1.0 O A:HOH936 4.9 14.0 1.0 OE2 A:GLU288 5.0 16.3 1.0 CD A:GLU288 5.0 12.8 1.0 OH A:TYR164 5.0 17.8 1.0 CG A:PRO291 5.0 25.7 1.0

Copper binding site 3 out of 24 in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:13.3 occ:0.90 ND1 A:HIS482 1.9 13.7 1.0 NE2 A:HIS437 2.0 15.0 1.0 CG A:HIS482 2.9 10.6 1.0 CD2 A:HIS437 2.9 13.3 1.0 CE1 A:HIS482 3.0 10.5 1.0 CE1 A:HIS437 3.1 11.9 1.0 CB A:HIS482 3.2 9.3 1.0 UNK A:UNX607 3.2 27.3 1.0 CE2 A:PHE436 3.3 16.4 1.0 CZ A:PHE436 3.5 17.1 1.0 CA A:HIS482 3.6 11.2 1.0 O A:HIS528 3.8 8.5 1.0 CD2 A:HIS482 4.0 10.8 1.0 NE2 A:HIS482 4.0 11.3 1.0 CG A:HIS437 4.1 11.1 1.0 ND1 A:HIS437 4.1 12.4 1.0 CA A:HIS528 4.2 8.6 1.0 CB A:HIS528 4.2 9.2 1.0 CD2 A:PHE436 4.2 14.9 1.0 C A:HIS482 4.3 11.5 1.0 C A:HIS528 4.4 6.9 1.0 CG A:HIS528 4.4 9.1 1.0 NE2 A:GLN382 4.4 18.6 1.0 CE1 A:PHE436 4.5 16.8 1.0 N A:THR483 4.6 10.7 1.0 ND1 A:HIS528 4.7 10.2 1.0 CD2 A:HIS528 4.9 9.4 1.0 CG2 A:THR483 4.9 12.1 1.0 O A:MET481 4.9 13.5 1.0 N A:HIS482 4.9 10.9 1.0 CU A:CU604 5.0 25.3 0.5 O A:HIS482 5.0 15.0 1.0

Copper binding site 4 out of 24 in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu604 b:25.3 occ:0.50 NE2 A:HIS136 2.0 9.8 1.0 UNK A:UNX607 2.1 27.3 1.0 CU A:CU602 2.6 11.5 0.9 CE1 A:HIS136 2.8 9.1 1.0 O A:HOH882 3.1 18.2 1.0 CD2 A:HIS136 3.1 9.9 1.0 NE2 A:HIS135 3.1 7.2 1.0 CE1 A:HIS135 3.5 8.1 1.0 NE2 A:HIS206 3.7 10.6 1.0 CE1 A:HIS206 3.9 9.2 1.0 CU A:CU601 3.9 13.2 1.0 O A:HOH903 3.9 12.5 1.0 ND1 A:HIS136 4.0 9.2 1.0 CG1 A:VAL205 4.1 8.0 1.0 CD2 A:HIS135 4.1 8.3 1.0 CG A:HIS136 4.1 8.6 1.0 ND1 A:HIS528 4.3 10.2 1.0 CD2 A:HIS206 4.3 10.0 1.0 CB A:HIS528 4.4 9.2 1.0 ND1 A:HIS135 4.5 6.6 1.0 ND1 A:HIS206 4.6 12.4 1.0 O A:HOH936 4.8 14.0 1.0 O A:HOH901 4.8 16.4 1.0 CG A:HIS135 4.8 6.9 1.0 O A:HIS528 4.8 8.5 1.0 CG A:HIS528 4.9 9.1 1.0 CG A:HIS206 4.9 8.9 1.0 OD1 A:ASP314 4.9 16.1 1.0 CU A:CU603 5.0 13.3 0.9 NE2 A:HIS381 5.0 16.0 1.0

Copper binding site 5 out of 24 in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu605 b:41.4 occ:0.40 ND1 A:HIS411 2.0 19.0 1.0 O A:HOH1149 2.1 24.7 0.4 O A:HOH755 2.1 24.1 0.4 CG A:HIS411 3.0 17.8 1.0 CE1 A:HIS411 3.1 23.1 1.0 CB A:HIS411 3.2 17.6 1.0 C A:HIS411 3.7 22.9 1.0 O A:HIS411 3.8 20.6 1.0 N A:ASP412 3.8 18.7 1.0 CA A:HIS411 4.0 17.9 1.0 CD2 A:HIS411 4.1 18.1 1.0 CA A:ASP412 4.2 23.1 1.0 NE2 A:HIS411 4.2 17.9 1.0 O A:HOH1091 4.5 41.7 1.0 O A:HOH1192 4.6 42.1 1.0 CB A:ASP412 4.7 38.2 1.0 O A:HOH1033 4.9 27.0 1.0 N A:HIS411 5.0 17.5 1.0

Copper binding site 6 out of 24 in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu606 b:37.7 occ:0.50 NE2 A:HIS309 2.1 33.1 1.0 O A:HOH1117 2.1 21.4 0.5 CD2 A:HIS309 3.0 24.8 1.0 CE1 A:HIS309 3.1 35.0 1.0 O A:HOH945 3.4 42.4 1.0 O A:HOH1067 4.1 9.1 0.5 CG A:HIS309 4.1 25.2 1.0 ND1 A:HIS309 4.1 29.4 1.0 CB A:LEU308 4.4 18.9 1.0 CD1 A:LEU308 4.4 23.0 1.0

Copper binding site 7 out of 24 in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu601 b:13.8 occ:1.00 NE2 B:HIS206 2.0 10.3 1.0 NE2 B:HIS381 2.0 15.9 1.0 OD2 B:ASP314 2.1 18.9 1.0 CD2 B:HIS206 2.9 12.8 1.0 CG B:ASP314 2.9 15.6 1.0 CD2 B:HIS381 2.9 17.3 1.0 OD1 B:ASP314 2.9 16.3 1.0 CE1 B:HIS206 3.0 9.5 1.0 OE1 B:GLN382 3.1 15.3 1.0 CE1 B:HIS381 3.1 19.1 1.0 O B:HOH874 3.5 15.4 1.0 NE2 B:GLN382 3.5 18.6 1.0 CD B:GLN382 3.6 16.6 1.0 CU B:CU604 3.7 21.7 0.5 CG B:HIS206 4.0 8.9 1.0 CG B:HIS381 4.1 18.2 1.0 ND1 B:HIS206 4.1 10.5 1.0 ND1 B:HIS381 4.1 19.0 1.0 UNK B:UNX607 4.2 26.8 1.0 UNK B:UNX608 4.2 33.2 1.0 CB B:ASP314 4.3 14.9 1.0 O B:HOH760 4.4 17.0 1.0 CE1 B:HIS437 4.7 13.5 1.0 CG1 B:VAL205 4.7 9.4 1.0 NE2 B:HIS136 4.8 9.3 1.0 CB B:THR548 5.0 13.2 1.0

Copper binding site 8 out of 24 in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu602 b:10.7 occ:0.90 ND1 B:HIS528 2.0 9.2 1.0 NE2 B:HIS135 2.1 8.2 1.0 O B:HOH934 2.1 15.2 1.0 UNK B:UNX607 2.4 26.8 1.0 CU B:CU604 2.7 21.7 0.5 CE1 B:HIS528 3.0 8.4 1.0 CD2 B:HIS135 3.0 7.1 1.0 CG B:HIS528 3.0 7.4 1.0 CE1 B:HIS135 3.1 7.2 1.0 CB B:HIS528 3.3 6.6 1.0 NZ B:LYS103 3.6 10.4 1.0 NE2 B:HIS136 3.8 9.3 1.0 UNK B:UNX608 3.8 33.2 1.0 NE2 B:HIS528 4.1 9.5 1.0 CD2 B:HIS528 4.2 8.7 1.0 ND1 B:HIS135 4.2 6.2 1.0 CG B:HIS135 4.2 5.8 1.0 O B:HOH1041 4.2 17.5 1.0 OE1 B:GLU288 4.2 12.6 1.0 O B:HOH874 4.3 15.4 1.0 CE1 B:HIS136 4.4 9.9 1.0 CE B:LYS103 4.5 9.3 1.0 CD2 B:HIS136 4.6 9.2 1.0 CD B:LYS103 4.8 9.7 1.0 CA B:HIS528 4.8 8.2 1.0 CG B:PRO291 4.9 17.3 1.0 O B:HOH899 4.9 14.1 1.0 OH B:TYR164 5.0 15.8 1.0

Copper binding site 9 out of 24 in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu603 b:12.6 occ:0.90 ND1 B:HIS482 2.0 9.2 1.0 NE2 B:HIS437 2.0 13.2 1.0 UNK B:UNX608 2.6 33.2 1.0 CD2 B:HIS437 2.9 10.7 1.0 CG B:HIS482 2.9 10.1 1.0 CE1 B:HIS482 3.0 9.8 1.0 CE1 B:HIS437 3.0 13.5 1.0 CB B:HIS482 3.2 9.9 1.0 CE2 B:PHE436 3.3 14.2 1.0 CZ B:PHE436 3.5 12.8 1.0 CA B:HIS482 3.6 11.3 1.0 UNK B:UNX607 3.7 26.8 1.0 O B:HIS528 3.8 11.3 1.0 CG B:HIS437 4.0 11.1 1.0 CD2 B:HIS482 4.0 9.2 1.0 ND1 B:HIS437 4.1 10.9 1.0 NE2 B:HIS482 4.1 9.3 1.0 CD2 B:PHE436 4.2 12.8 1.0 CA B:HIS528 4.2 8.2 1.0 CB B:HIS528 4.2 6.6 1.0 C B:HIS482 4.3 11.5 1.0 NE2 B:GLN382 4.4 18.6 1.0 C B:HIS528 4.4 8.5 1.0 CG B:HIS528 4.4 7.4 1.0 CE1 B:PHE436 4.4 13.1 1.0 N B:THR483 4.6 11.5 1.0 ND1 B:HIS528 4.7 9.2 1.0 CG2 B:THR483 4.9 12.1 1.0 N B:HIS482 4.9 9.6 1.0 O B:MET481 4.9 11.3 1.0 CD2 B:HIS528 4.9 8.7 1.0 O B:HIS482 4.9 10.3 1.0

Copper binding site 10 out of 24 in the Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of Recombinant Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Saturated with Copper within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu604 b:21.7 occ:0.50 NE2 B:HIS136 2.0 9.3 1.0 UNK B:UNX607 2.1 26.8 1.0 CU B:CU602 2.7 10.7 0.9 CE1 B:HIS136 2.9 9.9 1.0 O B:HOH874 3.0 15.4 1.0 CD2 B:HIS136 3.1 9.2 1.0 NE2 B:HIS135 3.1 8.2 1.0 UNK B:UNX608 3.4 33.2 1.0 CE1 B:HIS135 3.5 7.2 1.0 NE2 B:HIS206 3.5 10.3 1.0 CU B:CU601 3.7 13.8 1.0 CE1 B:HIS206 3.8 9.5 1.0 CG1 B:VAL205 3.9 9.4 1.0 O B:HOH934 4.0 15.2 1.0 ND1 B:HIS136 4.0 9.0 1.0 CD2 B:HIS135 4.2 7.1 1.0 CG B:HIS136 4.2 8.4 1.0 CD2 B:HIS206 4.2 12.8 1.0 ND1 B:HIS528 4.4 9.2 1.0 O B:HOH1041 4.5 17.5 1.0 ND1 B:HIS135 4.5 6.2 1.0 ND1 B:HIS206 4.5 10.5 1.0 CB B:HIS528 4.6 6.6 1.0 OD1 B:ASP314 4.7 16.3 1.0 O B:HOH899 4.7 14.1 1.0 CG B:HIS206 4.8 8.9 1.0 CG B:HIS135 4.9 5.8 1.0 NE2 B:HIS381 4.9 15.9 1.0 O B:HIS528 4.9 11.3 1.0

I.G.Shabalin, T.V.Tikhonova, V.O.Popov. A Novel Copper Biocatalytic Center Forms An Active Site of the Thiocyanate Dehydrogenase To Be Published.