Copper in PDB 8z75: The Structure of Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh)

The structure of The Structure of Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), PDB code: 8z75 was solved by L.A.Varfolomeeva, A.Y.Solovieva, N.S.Shipkov, N.I.Dergousova, 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)	49.04 / 1.45
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	97.99, 101.95, 276.17, 90, 90, 90
R / Rfree (%)	16.7 / 19.6

The structure of The Structure of Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh) also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Copper atom in the The Structure of Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh) (pdb code 8z75). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the The Structure of Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), PDB code: 8z75:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the The Structure of Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh)


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 Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu604 b:16.5 occ:0.20 O A:HOH781 1.8 15.2 1.0 O A:HOH801 1.8 19.6 1.0 ND1 A:HIS493 2.2 15.0 1.0 NE2 A:HIS100 2.4 13.1 1.0 CE1 A:HIS493 3.0 13.7 1.0 CE1 A:HIS100 3.1 12.5 1.0 CG A:HIS493 3.2 12.0 1.0 CD2 A:HIS100 3.5 12.5 1.0 CB A:HIS493 3.5 12.1 1.0 O A:HOH809 3.5 17.4 1.0 NE2 A:HIS101 3.7 12.8 1.0 O A:HOH916 4.0 15.9 1.0 NZ A:LYS68 4.0 15.9 1.0 O A:HOH908 4.1 20.6 1.0 OE1 A:GLU253 4.1 17.2 1.0 NE2 A:HIS493 4.2 11.8 1.0 ND1 A:HIS100 4.3 12.2 1.0 CD2 A:HIS493 4.3 13.2 1.0 CE1 A:HIS101 4.5 13.6 1.0 CG A:PRO256 4.5 14.7 1.0 CG A:HIS100 4.6 13.2 1.0 CD2 A:HIS101 4.7 11.6 1.0 O A:HOH820 4.8 19.5 1.0 O A:HOH1105 4.9 18.8 1.0 CD A:PRO256 4.9 15.9 1.0 CE A:LYS68 5.0 13.0 1.0 CE1 A:HIS447 5.0 13.6 1.0 CA A:HIS493 5.0 12.1 1.0

Copper binding site 2 out of 3 in the The Structure of Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh)


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 Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu606 b:15.4 occ:0.20 O B:HOH795 1.8 19.9 1.0 O B:HOH762 1.8 15.4 1.0 ND1 B:HIS493 2.1 13.1 1.0 NE2 B:HIS100 2.3 13.5 1.0 CE1 B:HIS100 3.1 15.1 1.0 CE1 B:HIS493 3.1 13.2 1.0 CG B:HIS493 3.2 12.1 1.0 CD2 B:HIS100 3.5 12.5 1.0 CB B:HIS493 3.5 11.7 1.0 O B:HOH736 3.7 19.4 1.0 NE2 B:HIS101 3.8 13.4 1.0 O B:HOH842 3.9 17.1 1.0 NZ B:LYS68 4.0 14.8 1.0 O B:HOH801 4.1 18.4 1.0 OE1 B:GLU253 4.1 14.1 1.0 NE2 B:HIS493 4.2 13.6 1.0 CD2 B:HIS493 4.3 12.9 1.0 ND1 B:HIS100 4.3 13.5 1.0 CE1 B:HIS101 4.5 13.9 1.0 CG B:HIS100 4.5 11.7 1.0 CG B:PRO256 4.5 16.6 1.0 CD2 B:HIS101 4.7 12.4 1.0 O B:HOH767 4.8 16.7 1.0 O B:HOH1091 4.9 21.4 1.0 CD B:GLU253 4.9 13.7 1.0 CE B:LYS68 4.9 12.6 1.0 OE2 B:GLU253 5.0 15.8 1.0 CD B:PRO256 5.0 16.4 1.0 OH B:TYR129 5.0 15.1 1.0 CE1 B:HIS447 5.0 13.0 1.0

Copper binding site 3 out of 3 in the The Structure of Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh)


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 Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu607 b:21.6 occ:0.20 O C:HOH863 1.8 22.2 1.0 O C:HOH802 1.8 21.1 1.0 ND1 C:HIS493 2.1 16.2 1.0 NE2 C:HIS100 2.4 17.1 1.0 CE1 C:HIS493 3.1 16.9 1.0 CE1 C:HIS100 3.2 17.8 1.0 CG C:HIS493 3.2 15.9 1.0 O C:HOH843 3.4 24.1 1.0 CD2 C:HIS100 3.5 15.2 1.0 CB C:HIS493 3.6 15.2 1.0 NE2 C:HIS101 3.8 14.1 1.0 NZ C:LYS68 4.0 16.6 1.0 O C:HOH881 4.0 20.9 1.0 O C:HOH888 4.2 22.6 1.0 NE2 C:HIS493 4.2 16.6 1.0 OE1 C:GLU253 4.2 19.2 1.0 CD2 C:HIS493 4.3 16.4 1.0 ND1 C:HIS100 4.4 14.0 1.0 CE1 C:HIS101 4.4 13.2 1.0 CG C:HIS100 4.6 15.1 1.0 CG C:PRO256 4.6 19.7 1.0 CD2 C:HIS101 4.8 15.1 1.0 O C:HOH798 4.9 22.1 1.0 CE1 C:HIS447 4.9 19.4 1.0 ND1 C:HIS447 4.9 17.6 1.0 CD C:PRO256 4.9 17.8 1.0 CE C:LYS68 5.0 14.9 1.0 OE2 C:GLU253 5.0 18.6 1.0 CD C:GLU253 5.0 22.7 1.0

L.A.Varfolomeeva, A.Y.Solovieva, N.S.Shipkov, N.I.Dergousova, K.M.Boyko, T.V.Tikhonova, V.O.Popov. The Structure of Non-Activated Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh) To Be Published.