Copper in PDB 8bpn: The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus

The structure of The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus, PDB code: 8bpn was solved by L.A.Varfolomeeva, A.Y.Solovieva, N.S.Shipkov, O.G.Kulikova, N.I.Dergousova, T.V.Rakitina, K.M.Boyko, 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)	81.06 / 1.99
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	90.559, 162.122, 90.861, 90, 119.8, 90
R / Rfree (%)	17.4 / 21.4

The binding sites of Copper atom in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus (pdb code 8bpn). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus, PDB code: 8bpn:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu602 b:24.6 occ:1.00 ND1 A:HIS528 2.0 21.2 1.0 NE2 A:HIS135 2.0 16.0 1.0 O A:HOH704 2.0 35.3 1.0 CD2 A:HIS135 2.9 13.9 1.0 CG A:HIS528 3.0 24.5 1.0 CE1 A:HIS528 3.0 17.2 1.0 CE1 A:HIS135 3.1 14.8 1.0 CB A:HIS528 3.3 24.3 1.0 NZ A:LYS103 3.5 23.5 1.0 O A:HOH796 3.6 28.4 1.0 NE2 A:HIS136 3.7 23.2 1.0 O A:HOH789 4.0 14.6 1.0 CG A:HIS135 4.1 15.3 1.0 NE2 A:HIS528 4.1 14.9 1.0 CD2 A:HIS528 4.1 20.3 1.0 ND1 A:HIS135 4.1 20.2 1.0 OE1 A:GLU288 4.2 29.2 1.0 CD2 A:HIS136 4.4 18.7 1.0 CE A:LYS103 4.5 19.4 1.0 CE1 A:HIS136 4.5 21.1 1.0 CD A:LYS103 4.5 17.2 1.0 OE2 A:GLU288 4.6 31.2 1.0 CA A:HIS528 4.8 25.5 1.0 CD A:GLU288 4.8 34.7 1.0 OE1 A:GLN156 4.9 19.0 1.0

Copper binding site 2 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:26.4 occ:1.00 NE2 A:HIS381 2.0 23.2 1.0 NE2 A:HIS206 2.0 21.0 1.0 OD2 A:ASP314 2.2 20.6 1.0 OD1 A:ASP314 2.5 21.4 1.0 CG A:ASP314 2.7 20.3 1.0 CD2 A:HIS381 2.8 22.4 1.0 CD2 A:HIS206 2.8 17.3 1.0 CE1 A:HIS206 3.1 16.5 1.0 CE1 A:HIS381 3.1 29.1 1.0 OE1 A:GLN382 3.5 40.7 1.0 O A:HOH789 3.9 14.6 1.0 CG A:HIS206 4.0 14.2 1.0 CG A:HIS381 4.0 22.6 1.0 ND1 A:HIS381 4.1 23.7 1.0 ND1 A:HIS206 4.1 19.8 1.0 CB A:ASP314 4.2 18.5 1.0 OG1 A:THR548 4.5 25.2 1.0 CD A:GLN382 4.5 40.3 1.0 CE1 A:HIS437 4.7 23.6 1.0 CG1 A:VAL205 4.9 12.6 1.0

Copper binding site 3 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu602 b:20.0 occ:0.80 NE2 B:HIS206 2.1 15.9 1.0 NE2 B:HIS381 2.1 28.4 1.0 OD2 B:ASP314 2.1 22.5 1.0 OD1 B:ASP314 2.5 28.0 1.0 O B:HOH748 2.6 25.9 1.0 CG B:ASP314 2.6 21.8 1.0 O B:HOH787 2.7 22.4 0.5 CD2 B:HIS206 2.9 12.0 1.0 CD2 B:HIS381 2.9 27.1 1.0 CE1 B:HIS206 3.2 15.4 1.0 CE1 B:HIS381 3.2 37.0 1.0 CG B:HIS206 4.1 13.6 1.0 CG B:HIS381 4.1 27.2 1.0 CB B:ASP314 4.1 17.8 1.0 ND1 B:HIS206 4.2 17.9 1.0 ND1 B:HIS381 4.2 31.3 1.0 O B:HOH739 4.5 7.4 1.0 OG1 B:THR548 4.5 20.4 1.0 O B:HOH702 4.7 13.0 1.0 CG1 B:VAL205 4.8 15.2 1.0

Copper binding site 4 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu603 b:20.8 occ:1.00 ND1 B:HIS528 2.0 18.9 1.0 O B:HOH766 2.0 17.3 1.0 NE2 B:HIS135 2.1 26.8 1.0 CD2 B:HIS135 2.9 21.6 1.0 CG B:HIS528 3.0 17.6 1.0 CE1 B:HIS528 3.0 18.5 1.0 CE1 B:HIS135 3.1 22.5 1.0 CB B:HIS528 3.3 12.3 1.0 NZ B:LYS103 3.6 13.9 1.0 NE2 B:HIS136 3.7 14.8 1.0 CD2 B:HIS528 4.1 17.5 1.0 NE2 B:HIS528 4.1 23.8 1.0 CG B:HIS135 4.1 19.8 1.0 ND1 B:HIS135 4.2 21.4 1.0 OE1 B:GLU288 4.3 20.1 1.0 CE1 B:HIS136 4.3 16.5 1.0 CD2 B:HIS136 4.4 13.8 1.0 CE B:LYS103 4.5 16.8 1.0 OE2 B:GLU288 4.6 23.3 1.0 CD B:LYS103 4.6 14.7 1.0 CA B:HIS528 4.7 12.0 1.0 CD B:GLU288 4.9 23.4 1.0 O B:HOH787 5.0 22.4 0.5

Copper binding site 5 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu601 b:25.4 occ:1.00 NE2 C:HIS381 1.9 25.9 1.0 NE2 C:HIS206 2.0 23.0 1.0 OD2 C:ASP314 2.1 21.3 1.0 CG C:ASP314 2.7 19.0 1.0 OD1 C:ASP314 2.7 24.5 1.0 CD2 C:HIS381 2.8 22.4 1.0 CD2 C:HIS206 2.8 22.3 1.0 CE1 C:HIS381 3.0 27.7 1.0 CE1 C:HIS206 3.2 24.6 1.0 OE1 C:GLN382 3.2 43.2 1.0 CG C:HIS381 4.0 23.7 1.0 ND1 C:HIS381 4.0 24.4 1.0 CG C:HIS206 4.0 21.6 1.0 CB C:ASP314 4.2 18.8 1.0 ND1 C:HIS206 4.2 19.5 1.0 CD C:GLN382 4.3 38.6 1.0 O C:HOH722 4.5 15.7 1.0 CG1 C:VAL205 4.7 9.8 1.0 OG1 C:THR548 4.7 26.6 1.0 O C:HOH717 4.7 22.6 1.0 CE1 C:HIS437 4.9 17.9 1.0

Copper binding site 6 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu602 b:22.2 occ:1.00 ND1 C:HIS528 2.0 14.8 1.0 O C:HOH717 2.0 22.6 1.0 O C:HOH755 2.1 16.9 1.0 NE2 C:HIS135 2.1 21.1 1.0 CE1 C:HIS528 3.0 17.4 1.0 CG C:HIS528 3.0 17.3 1.0 CD2 C:HIS135 3.1 18.6 1.0 CE1 C:HIS135 3.1 18.4 1.0 CB C:HIS528 3.4 15.6 1.0 NE2 C:HIS136 3.6 11.6 1.0 NZ C:LYS103 3.8 34.6 1.0 NE2 C:HIS528 4.2 15.2 1.0 CD2 C:HIS528 4.2 18.9 1.0 CG C:HIS135 4.2 14.3 1.0 CE1 C:HIS136 4.2 14.0 1.0 ND1 C:HIS135 4.3 14.4 1.0 OE1 C:GLU288 4.3 31.2 1.0 CD2 C:HIS136 4.4 14.2 1.0 O C:HOH747 4.4 14.9 1.0 OE2 C:GLU288 4.6 16.7 1.0 CA C:HIS528 4.8 16.3 1.0 CD C:LYS103 4.8 23.0 1.0 CD C:GLU288 4.8 21.4 1.0 CE C:LYS103 4.8 22.5 1.0

Copper binding site 7 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu601 b:21.9 occ:1.00 NE2 D:HIS206 2.0 10.0 1.0 NE2 D:HIS381 2.0 16.6 1.0 OD2 D:ASP314 2.1 24.6 1.0 CG D:ASP314 2.8 23.2 1.0 OD1 D:ASP314 2.8 20.4 1.0 CD2 D:HIS206 2.8 11.1 1.0 CD2 D:HIS381 2.9 22.7 1.0 CE1 D:HIS206 3.1 9.4 1.0 CE1 D:HIS381 3.1 24.6 1.0 O D:HOH810 3.4 28.5 1.0 CG D:HIS206 4.0 11.2 1.0 ND1 D:HIS206 4.1 11.1 1.0 CG D:HIS381 4.1 21.3 1.0 ND1 D:HIS381 4.2 25.9 1.0 CB D:ASP314 4.2 18.5 1.0 OG1 D:THR548 4.5 17.0 1.0 CE1 D:HIS437 4.8 24.7 1.0 CG1 D:VAL205 4.8 20.4 1.0

Copper binding site 8 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Phe 436 Replaced By Gln From Thioalkalivibrio Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu602 b:25.2 occ:1.00 ND1 D:HIS528 2.0 21.5 1.0 NE2 D:HIS135 2.1 15.0 1.0 CE1 D:HIS528 2.9 11.6 1.0 CG D:HIS528 3.0 21.7 1.0 CD2 D:HIS135 3.0 13.1 1.0 CE1 D:HIS135 3.2 13.0 1.0 CB D:HIS528 3.4 14.6 1.0 NE2 D:HIS136 3.6 12.3 1.0 NZ D:LYS103 3.7 18.9 1.0 NE2 D:HIS528 4.0 23.2 1.0 CD2 D:HIS528 4.1 17.7 1.0 CG D:HIS135 4.2 10.6 1.0 ND1 D:HIS135 4.2 10.5 1.0 CE1 D:HIS136 4.2 12.6 1.0 O D:HOH810 4.3 28.5 1.0 O D:HOH738 4.4 13.2 1.0 OE1 D:GLU288 4.4 20.2 1.0 CD2 D:HIS136 4.4 10.6 1.0 OE2 D:GLU288 4.6 25.1 1.0 CE D:LYS103 4.6 21.4 1.0 CD D:LYS103 4.7 22.9 1.0 CA D:HIS528 4.8 15.6 1.0 CD D:GLU288 4.9 22.9 1.0

L.A.Varfolomeeva, A.Y.Solovieva, N.S.Shipkov, O.G.Kulikova, N.I.Dergousova, T.V.Rakitina, K.M.Boyko, T.V.Tikhonova, V.O.Popov. Probing the Role of A Conserved Phenylalanine in the Active Site of Thiocyanate Dehydrogenase Crystals V. 12 2022.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST12121787