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

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

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

Iodine

(I)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Copper 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 Copper atom.
In total 15 binding sites of Copper where determined in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus, PDB code: 5oex:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 15 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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:Cu601 b:23.9 occ:1.00 NE2 A:HIS206 2.0 18.8 1.0 NE2 A:HIS381 2.0 23.9 1.0 OD2 A:ASP314 2.1 29.0 1.0 O A:HOH756 2.1 22.3 0.5 OD1 A:ASP314 2.7 26.8 1.0 CG A:ASP314 2.7 27.8 1.0 CD2 A:HIS381 2.9 23.4 1.0 CD2 A:HIS206 2.9 18.2 1.0 O A:HOH902 2.9 22.7 0.5 CE1 A:HIS206 3.1 18.6 1.0 CE1 A:HIS381 3.1 23.1 1.0 CG A:HIS206 4.1 17.9 1.0 CG A:HIS381 4.1 23.2 1.0 ND1 A:HIS206 4.2 17.6 1.0 ND1 A:HIS381 4.2 24.2 1.0 CB A:ASP314 4.3 25.4 1.0 O A:HOH771 4.3 29.6 1.0 OG1 A:THR548 4.4 24.0 1.0 O A:HOH714 4.4 26.4 1.0 O A:HOH706 4.7 24.3 1.0 O A:PHE436 4.8 24.0 1.0 I A:IOD608 4.8 29.6 0.2 CE1 A:HIS437 4.9 23.8 1.0 CG1 A:VAL205 4.9 16.5 1.0

Copper binding site 2 out of 15 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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:Cu602 b:14.9 occ:0.40 CU A:CU603 1.1 12.2 0.4 ND1 A:HIS528 2.0 15.3 1.0 NE2 A:HIS135 2.0 15.6 1.0 O A:HOH734 2.2 27.3 1.0 NZ A:LYS103 2.7 13.9 1.0 CD2 A:HIS135 2.7 12.4 1.0 CE1 A:HIS528 2.8 16.8 1.0 CG A:HIS528 3.0 15.0 1.0 CE1 A:HIS135 3.0 13.5 1.0 CB A:HIS528 3.4 14.7 1.0 O A:HOH771 3.4 29.6 1.0 CE A:LYS103 3.5 15.6 1.0 I A:IOD608 3.7 29.6 0.2 CD A:LYS103 3.7 14.5 1.0 CG A:HIS135 3.9 13.1 1.0 NE2 A:HIS528 3.9 15.0 1.0 ND1 A:HIS135 4.0 14.1 1.0 CD2 A:HIS528 4.0 14.8 1.0 OE1 A:GLU288 4.1 29.4 1.0 OH A:TYR164 4.3 35.8 1.0 NE2 A:HIS136 4.4 16.2 1.0 OE1 A:GLN156 4.5 23.5 1.0 O A:HOH842 4.7 33.9 1.0 CE1 A:HIS136 4.9 15.7 1.0 CA A:HIS528 4.9 16.3 1.0

Copper binding site 3 out of 15 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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:Cu603 b:12.2 occ:0.40 CU A:CU602 1.1 14.9 0.4 ND1 A:HIS528 2.1 15.3 1.0 NE2 A:HIS135 2.1 15.6 1.0 O A:HOH734 2.5 27.3 1.0 O A:HOH771 2.5 29.6 1.0 I A:IOD608 2.6 29.6 0.2 CG A:HIS528 3.0 15.0 1.0 CD2 A:HIS135 3.1 12.4 1.0 CE1 A:HIS135 3.1 13.5 1.0 CB A:HIS528 3.2 14.7 1.0 CE1 A:HIS528 3.2 16.8 1.0 NE2 A:HIS136 3.6 16.2 1.0 NZ A:LYS103 3.8 13.9 1.0 CE1 A:HIS136 4.0 15.7 1.0 OE1 A:GLU288 4.2 29.4 1.0 CD2 A:HIS528 4.2 14.8 1.0 O A:HOH902 4.3 22.7 0.5 ND1 A:HIS135 4.3 14.1 1.0 CG A:HIS135 4.3 13.1 1.0 NE2 A:HIS528 4.3 15.0 1.0 CU A:CU604 4.5 19.4 0.2 CD2 A:HIS136 4.6 15.3 1.0 CE A:LYS103 4.6 15.6 1.0 CA A:HIS528 4.7 16.3 1.0 O A:HOH901 4.7 38.2 1.0 CD A:LYS103 4.7 14.5 1.0 OE2 A:GLU288 4.8 27.8 1.0 O A:HIS528 4.9 18.2 1.0 CD A:GLU288 5.0 28.1 1.0

Copper binding site 4 out of 15 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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 A:Cu604 b:19.4 occ:0.20 ND1 A:HIS482 2.2 16.3 1.0 NE2 A:HIS437 2.2 24.6 1.0 I A:IOD608 2.7 29.6 0.2 CE1 A:HIS437 2.9 23.8 1.0 O A:HOH901 2.9 38.2 1.0 CE1 A:HIS482 3.2 16.6 1.0 CG A:HIS482 3.2 16.7 1.0 CD2 A:HIS437 3.3 23.5 1.0 O A:HIS528 3.4 18.2 1.0 CB A:HIS482 3.5 17.0 1.0 O A:HOH902 3.6 22.7 0.5 CB A:HIS528 3.9 14.7 1.0 CA A:HIS528 3.9 16.3 1.0 ND1 A:HIS437 4.0 22.1 1.0 C A:HIS528 4.0 17.5 1.0 CA A:HIS482 4.0 16.7 1.0 CG A:HIS528 4.1 15.0 1.0 CG A:HIS437 4.3 21.2 1.0 NE2 A:HIS482 4.3 16.4 1.0 CD2 A:HIS482 4.3 16.5 1.0 CG2 A:THR483 4.3 16.8 1.0 ND1 A:HIS528 4.4 15.3 1.0 O A:HOH867 4.4 25.9 1.0 C A:HIS482 4.5 17.8 1.0 N A:THR483 4.5 18.5 1.0 CU A:CU603 4.5 12.2 0.4 CE1 A:HIS136 4.7 15.7 1.0 CD2 A:HIS528 4.7 14.8 1.0

Copper binding site 5 out of 15 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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 B:Cu601 b:22.4 occ:1.00 NE2 B:HIS206 2.0 15.1 1.0 OD2 B:ASP314 2.1 31.1 1.0 NE2 B:HIS381 2.1 21.9 1.0 OD1 B:ASP314 2.6 26.4 1.0 CG B:ASP314 2.8 25.5 1.0 CD2 B:HIS206 2.8 14.4 1.0 CD2 B:HIS381 2.9 22.5 1.0 CE1 B:HIS206 3.1 15.8 1.0 CE1 B:HIS381 3.2 26.0 1.0 O B:HOH903 3.2 16.1 0.5 CG B:HIS206 4.0 14.7 1.0 CG B:HIS381 4.1 24.8 1.0 ND1 B:HIS206 4.2 16.0 1.0 ND1 B:HIS381 4.2 24.9 1.0 CB B:ASP314 4.3 22.7 1.0 O B:HOH831 4.4 28.3 1.0 OG1 B:THR548 4.4 27.2 1.0 O B:HOH735 4.6 26.9 1.0 O B:HOH707 4.7 25.1 1.0 O B:PHE436 4.8 18.7 1.0 CE1 B:HIS437 4.8 19.4 1.0 CG1 B:VAL205 4.9 13.8 1.0

Copper binding site 6 out of 15 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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 B:Cu602 b:15.7 occ:0.50 CU B:CU603 1.2 24.1 0.5 ND1 B:HIS528 1.9 19.5 1.0 NE2 B:HIS135 2.0 14.8 1.0 O B:HOH819 2.3 16.9 0.5 NZ B:LYS103 2.7 15.7 1.0 CD2 B:HIS135 2.7 13.1 1.0 CG B:HIS528 2.8 18.6 1.0 CE1 B:HIS528 2.9 17.2 1.0 CB B:HIS528 3.1 16.4 1.0 CE1 B:HIS135 3.1 14.7 1.0 O B:HOH831 3.5 28.3 1.0 CE B:LYS103 3.7 16.1 1.0 CD B:LYS103 3.8 15.7 1.0 CD2 B:HIS528 3.9 19.0 1.0 CG B:HIS135 3.9 14.2 1.0 NE2 B:HIS528 3.9 18.8 1.0 ND1 B:HIS135 4.1 14.6 1.0 NE2 B:HIS136 4.2 17.2 1.0 OE1 B:GLU288 4.3 24.8 1.0 OE1 B:GLN156 4.5 21.0 1.0 OH B:TYR164 4.5 30.8 1.0 CA B:HIS528 4.6 16.4 1.0 CE1 B:HIS136 4.8 17.4 1.0 O B:HOH782 4.9 19.3 1.0 CD2 B:HIS136 4.9 15.5 1.0

Copper binding site 7 out of 15 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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 B:Cu603 b:24.1 occ:0.50 CU B:CU602 1.2 15.7 0.5 O B:HOH819 2.1 16.9 0.5 NE2 B:HIS135 2.3 14.8 1.0 ND1 B:HIS528 2.3 19.5 1.0 O B:HOH831 2.4 28.3 1.0 CG B:HIS528 3.2 18.6 1.0 CE1 B:HIS135 3.3 14.7 1.0 CD2 B:HIS135 3.3 13.1 1.0 CB B:HIS528 3.3 16.4 1.0 CE1 B:HIS528 3.4 17.2 1.0 NE2 B:HIS136 3.6 17.2 1.0 NZ B:LYS103 3.8 15.7 1.0 O B:HOH903 4.0 16.1 0.5 CE1 B:HIS136 4.1 17.4 1.0 OE1 B:GLU288 4.1 24.8 1.0 O B:HOH782 4.2 19.3 1.0 CD2 B:HIS528 4.4 19.0 1.0 ND1 B:HIS135 4.4 14.6 1.0 CG B:HIS135 4.4 14.2 1.0 NE2 B:HIS528 4.5 18.8 1.0 OE2 B:GLU288 4.5 25.3 1.0 CD2 B:HIS136 4.5 15.5 1.0 CA B:HIS528 4.7 16.4 1.0 CD B:GLU288 4.8 24.2 1.0 O B:HOH906 4.8 28.2 1.0 CE B:LYS103 4.8 16.1 1.0 O B:HIS528 4.9 18.0 1.0 CD B:LYS103 5.0 15.7 1.0

Copper binding site 8 out of 15 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu 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 C:Cu601 b:20.5 occ:1.00 NE2 C:HIS206 2.0 19.6 1.0 NE2 C:HIS381 2.1 19.6 1.0 OD2 C:ASP314 2.1 27.6 1.0 O C:HOH800 2.5 21.0 0.5 O C:HOH919 2.6 22.0 0.5 OD1 C:ASP314 2.6 21.8 1.0 CG C:ASP314 2.7 23.5 1.0 CD2 C:HIS206 2.9 17.1 1.0 CE1 C:HIS381 3.0 18.0 1.0 CD2 C:HIS381 3.1 18.3 1.0 CE1 C:HIS206 3.1 16.7 1.0 CG C:HIS206 4.1 17.6 1.0 ND1 C:HIS381 4.1 16.3 1.0 ND1 C:HIS206 4.2 18.7 1.0 CG C:HIS381 4.2 17.2 1.0 O C:HOH785 4.2 26.4 1.0 CB C:ASP314 4.3 18.7 1.0 O C:HOH725 4.4 20.7 1.0 OG1 C:THR548 4.6 23.1 1.0 O C:HOH770 4.6 23.2 1.0 O C:PHE436 4.7 21.9 1.0 CE1 C:HIS437 4.8 22.7 1.0 CG1 C:VAL205 4.9 11.2 1.0 I C:IOD606 4.9 40.9 0.3

Copper binding site 9 out of 15 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu602 b:13.4 occ:0.40 CU C:CU603 1.1 11.7 0.4 ND1 C:HIS528 2.2 12.7 1.0 NE2 C:HIS135 2.2 14.6 1.0 O C:HOH839 2.4 28.0 1.0 O C:HOH785 2.8 26.4 1.0 I C:IOD606 2.8 40.9 0.3 CG C:HIS528 3.1 12.0 1.0 CD2 C:HIS135 3.1 13.4 1.0 CE1 C:HIS528 3.2 11.6 1.0 CE1 C:HIS135 3.2 14.4 1.0 CB C:HIS528 3.3 12.0 1.0 NZ C:LYS103 3.7 18.7 1.0 NE2 C:HIS136 3.7 16.2 1.0 CE1 C:HIS136 4.1 14.1 1.0 CD2 C:HIS528 4.2 11.3 1.0 OE1 C:GLU288 4.3 24.6 1.0 NE2 C:HIS528 4.3 12.2 1.0 ND1 C:HIS135 4.3 14.8 1.0 CG C:HIS135 4.3 12.7 1.0 OE2 C:GLU288 4.6 26.4 1.0 CD2 C:HIS136 4.6 13.8 1.0 CU C:CU604 4.7 18.3 0.3 CE C:LYS103 4.7 18.4 1.0 O C:HOH919 4.7 22.0 0.5 CA C:HIS528 4.7 12.3 1.0 CD C:LYS103 4.8 16.8 1.0 CD C:GLU288 4.9 23.1 1.0 O C:HIS528 5.0 18.7 1.0

Copper binding site 10 out of 15 in the Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Complex with Iodine Ion For Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu603 b:11.7 occ:0.40 CU C:CU602 1.1 13.4 0.4 NE2 C:HIS135 2.0 14.6 1.0 ND1 C:HIS528 2.0 12.7 1.0 O C:HOH839 2.3 28.0 1.0 NZ C:LYS103 2.6 18.7 1.0 CD2 C:HIS135 2.7 13.4 1.0 CE1 C:HIS528 2.9 11.6 1.0 CG C:HIS528 2.9 12.0 1.0 CE1 C:HIS135 3.1 14.4 1.0 CB C:HIS528 3.4 12.0 1.0 CE C:LYS103 3.6 18.4 1.0 O C:HOH785 3.6 26.4 1.0 CD C:LYS103 3.8 16.8 1.0 CG C:HIS135 3.9 12.7 1.0 I C:IOD606 3.9 40.9 0.3 NE2 C:HIS528 4.0 12.2 1.0 ND1 C:HIS135 4.0 14.8 1.0 CD2 C:HIS528 4.0 11.3 1.0 OE1 C:GLU288 4.3 24.6 1.0 OH C:TYR164 4.3 31.5 1.0 NE2 C:HIS136 4.4 16.2 1.0 OE1 C:GLN156 4.4 21.4 1.0 CE1 C:HIS136 4.9 14.1 1.0 CA C:HIS528 4.9 12.3 1.0

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.