Copper in PDB 8z76: The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months

The structure of The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months, PDB code: 8z76 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)	47.79 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	97.8, 101.75, 276.35, 90, 90, 90
R / Rfree (%)	16.8 / 21.7

The structure of The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months also contains other interesting chemical elements:

Sodium

(Na)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Copper atom in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months (pdb code 8z76). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 13 binding sites of Copper where determined in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months, PDB code: 8z76:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months


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 From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:26.3 occ:1.00 NE2 A:HIS171 2.0 22.8 1.0 NE2 A:HIS346 2.0 27.7 1.0 O A:HOH903 2.3 22.6 0.5 OD1 A:ASP279 2.4 28.0 1.0 OD2 A:ASP279 2.5 23.1 1.0 CG A:ASP279 2.7 27.1 1.0 NE2 A:GLN347 2.9 17.4 0.5 CD2 A:HIS346 2.9 23.6 1.0 CD2 A:HIS171 3.0 20.4 1.0 CE1 A:HIS171 3.0 18.6 1.0 CE1 A:HIS346 3.1 27.4 1.0 CD A:GLN347 4.0 28.1 0.5 CG A:HIS346 4.1 25.4 1.0 ND1 A:HIS171 4.1 20.4 1.0 CG A:HIS171 4.1 20.7 1.0 ND1 A:HIS346 4.1 25.3 1.0 O A:HOH701 4.1 19.6 0.5 O A:HOH753 4.2 26.6 1.0 CB A:ASP279 4.3 21.9 1.0 O A:HOH723 4.5 23.3 1.0 CG A:GLN347 4.6 31.3 0.5 OG1 A:THR513 4.6 29.5 1.0 CG1 A:VAL170 4.7 20.2 1.0 CB A:THR513 4.8 23.9 1.0 CE1 A:HIS402 4.9 24.5 1.0 OE1 A:GLN347 4.9 25.7 0.5

Copper binding site 2 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months


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 From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu604 b:24.1 occ:0.50 CU A:CU604 0.0 24.1 0.5 CU A:CU604 1.3 27.4 0.5 ND1 A:HIS493 1.8 22.5 1.0 NE2 A:HIS100 2.0 23.3 1.0 O A:HOH712 2.2 24.2 1.0 CE1 A:HIS493 2.8 19.5 1.0 CD2 A:HIS100 2.8 22.4 1.0 CG A:HIS493 2.8 20.8 1.0 NZ A:LYS68 2.8 26.0 1.0 CE1 A:HIS100 3.2 23.2 1.0 CB A:HIS493 3.2 20.3 1.0 O A:HOH753 3.4 26.6 1.0 CE A:LYS68 3.6 24.9 1.0 O A:HOH951 3.6 29.0 1.0 CD A:LYS68 3.8 22.8 1.0 NE2 A:HIS493 3.9 23.3 1.0 CD2 A:HIS493 3.9 22.4 1.0 CG A:HIS100 4.0 21.8 1.0 OE1 A:GLU253 4.0 14.7 0.5 ND1 A:HIS100 4.2 18.7 1.0 OE1 A:GLU253 4.2 30.8 0.5 OH A:TYR129 4.4 26.0 1.0 NE2 A:HIS101 4.4 23.6 1.0 OE2 A:GLU253 4.6 12.4 0.5 OE1 A:GLN121 4.7 29.6 1.0 CD A:GLU253 4.7 17.9 0.5 CA A:HIS493 4.8 17.8 1.0 CG A:PRO256 4.8 38.0 1.0 O A:HOH925 4.9 36.2 1.0 CE1 A:HIS101 4.9 23.8 1.0

Copper binding site 3 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months


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 From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu604 b:27.4 occ:0.50 CU A:CU604 0.0 27.4 0.5 CU A:CU604 1.3 24.1 0.5 NE2 A:HIS100 2.1 23.3 1.0 O A:HOH753 2.2 26.6 1.0 O A:HOH712 2.3 24.2 1.0 ND1 A:HIS493 2.5 22.5 1.0 O A:HOH951 2.7 29.0 1.0 CE1 A:HIS100 3.1 23.2 1.0 CD2 A:HIS100 3.1 22.4 1.0 CG A:HIS493 3.3 20.8 1.0 CB A:HIS493 3.3 20.3 1.0 NE2 A:HIS101 3.5 23.6 1.0 CE1 A:HIS493 3.6 19.5 1.0 NZ A:LYS68 4.0 26.0 1.0 CE1 A:HIS101 4.1 23.8 1.0 OE1 A:GLU253 4.2 30.8 0.5 O A:HOH701 4.2 19.6 0.5 ND1 A:HIS100 4.2 18.7 1.0 O A:HOH903 4.2 22.6 0.5 OE1 A:GLU253 4.3 14.7 0.5 CG A:HIS100 4.3 21.8 1.0 O A:HOH925 4.3 36.2 1.0 CD2 A:HIS493 4.5 22.4 1.0 CD2 A:HIS101 4.5 20.8 1.0 NE2 A:HIS493 4.6 23.3 1.0 OE2 A:GLU253 4.7 26.6 0.5 CG A:PRO256 4.8 38.0 1.0 CA A:HIS493 4.8 17.8 1.0 CE A:LYS68 4.8 24.9 1.0 CD A:GLU253 4.8 26.8 0.5 CU A:CU605 4.8 30.0 1.0 CD A:LYS68 5.0 22.8 1.0

Copper binding site 4 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months


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 From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu605 b:30.0 occ:1.00 NE2 A:HIS402 1.9 21.2 1.0 ND1 A:HIS447 2.0 19.5 1.0 O A:HOH951 2.5 29.0 1.0 CD2 A:HIS402 2.9 21.5 1.0 CE1 A:HIS447 2.9 21.6 1.0 CE1 A:HIS402 3.0 24.5 1.0 CG A:HIS447 3.0 20.5 1.0 CE1 A:PHE401 3.3 36.6 1.0 CB A:HIS447 3.3 21.6 1.0 CZ A:PHE401 3.5 35.2 1.0 CA A:HIS447 3.8 22.1 1.0 O A:HIS493 3.8 21.8 1.0 CB A:HIS493 4.0 20.3 1.0 CG A:HIS402 4.1 20.6 1.0 NE2 A:HIS447 4.1 18.9 1.0 ND1 A:HIS402 4.1 23.2 1.0 CD2 A:HIS447 4.1 22.5 1.0 CD1 A:PHE401 4.1 32.1 1.0 CA A:HIS493 4.2 17.8 1.0 O A:HOH903 4.2 22.6 0.5 CG A:HIS493 4.3 20.8 1.0 C A:HIS493 4.4 17.3 1.0 C A:HIS447 4.5 21.7 1.0 CE2 A:PHE401 4.6 36.8 1.0 ND1 A:HIS493 4.7 22.5 1.0 CD2 A:HIS493 4.7 22.4 1.0 N A:THR448 4.7 18.5 1.0 CU A:CU604 4.8 27.4 0.5 CG2 A:THR448 4.9 22.2 1.0 O A:MET446 4.9 19.9 1.0

Copper binding site 5 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months


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 From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu606 b:35.4 occ:0.20 ND1 A:HIS376 2.2 34.8 1.0 CG A:HIS376 3.2 32.8 1.0 CE1 A:HIS376 3.2 34.6 1.0 CB A:HIS376 3.4 27.6 1.0 O A:HOH891 3.5 31.1 0.5 CD2 A:HIS376 4.4 29.2 1.0 NE2 A:HIS376 4.4 30.7 1.0 C A:HIS376 4.5 27.4 1.0 O A:HIS376 4.5 24.8 1.0 CA A:HIS376 4.5 26.6 1.0 O A:HOH950 4.7 37.3 0.5 O A:HOH909 4.7 26.4 0.5 N A:ALA377 4.9 27.9 1.0

Copper binding site 6 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months


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 From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu603 b:25.5 occ:1.00 NE2 B:HIS346 2.0 24.5 1.0 NE2 B:HIS171 2.0 21.3 1.0 O B:HOH892 2.2 18.9 0.5 OD1 B:ASP279 2.3 27.9 1.0 OD2 B:ASP279 2.8 26.4 1.0 CG B:ASP279 2.9 29.4 1.0 CD2 B:HIS171 2.9 23.6 1.0 CD2 B:HIS346 2.9 23.8 1.0 OE1 B:GLN347 3.0 26.6 1.0 CE1 B:HIS346 3.0 23.9 1.0 CE1 B:HIS171 3.1 19.1 1.0 CD B:GLN347 3.6 25.4 1.0 NE2 B:GLN347 3.7 27.3 1.0 O B:HOH873 3.8 26.6 1.0 O B:HOH714 3.9 28.0 1.0 CG B:HIS171 4.1 18.5 1.0 CG B:HIS346 4.1 24.8 1.0 ND1 B:HIS346 4.1 24.5 1.0 ND1 B:HIS171 4.1 21.4 1.0 CB B:ASP279 4.4 24.5 1.0 O B:HOH779 4.5 22.5 1.0 CG1 B:VAL170 4.6 20.1 1.0 CE1 B:HIS402 4.8 22.6 1.0 CB B:THR513 4.9 23.8 1.0 O B:HOH936 4.9 26.9 1.0 NE2 B:HIS101 4.9 22.6 1.0 OG1 B:THR513 5.0 25.0 1.0 CG B:GLN347 5.0 25.6 1.0 CG2 B:THR513 5.0 22.0 1.0

Copper binding site 7 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months


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 From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu604 b:27.7 occ:0.30 CU B:CU604 0.0 27.7 0.3 CU B:CU604 1.3 23.2 0.7 ND1 B:HIS493 1.7 20.7 1.0 NE2 B:HIS100 1.8 20.7 1.0 O B:HOH750 2.4 25.0 1.0 CD2 B:HIS100 2.6 20.0 1.0 CE1 B:HIS493 2.6 19.9 1.0 NZ B:LYS68 2.7 22.3 1.0 CG B:HIS493 2.8 18.8 1.0 CE1 B:HIS100 2.9 21.7 1.0 CB B:HIS493 3.3 18.4 1.0 O B:HOH714 3.4 28.0 1.0 CE B:LYS68 3.6 18.9 1.0 NE2 B:HIS493 3.7 22.3 1.0 CD B:LYS68 3.7 25.4 1.0 CG B:HIS100 3.8 20.9 1.0 CD2 B:HIS493 3.8 22.0 1.0 O B:HOH936 3.9 26.9 1.0 ND1 B:HIS100 3.9 20.3 1.0 OE1 B:GLU253 3.9 28.9 1.0 NE2 B:HIS101 4.3 22.6 1.0 OE2 B:GLU253 4.4 25.4 1.0 OH B:TYR129 4.4 25.2 1.0 CD B:GLU253 4.6 34.7 1.0 OE1 B:GLN121 4.6 25.9 1.0 CA B:HIS493 4.9 18.6 1.0 CE1 B:HIS101 5.0 24.6 1.0 O B:HOH904 5.0 31.1 1.0

Copper binding site 8 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months


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 From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu604 b:23.2 occ:0.70 CU B:CU604 0.0 23.2 0.7 CU B:CU604 1.3 27.7 0.3 ND1 B:HIS493 2.1 20.7 1.0 NE2 B:HIS100 2.1 20.7 1.0 O B:HOH714 2.2 28.0 1.0 O B:HOH750 2.3 25.0 1.0 O B:HOH936 2.8 26.9 1.0 CG B:HIS493 3.0 18.8 1.0 CE1 B:HIS100 3.1 21.7 1.0 CE1 B:HIS493 3.1 19.9 1.0 CD2 B:HIS100 3.1 20.0 1.0 CB B:HIS493 3.2 18.4 1.0 NE2 B:HIS101 3.6 22.6 1.0 NZ B:LYS68 3.9 22.3 1.0 CD2 B:HIS493 4.1 22.0 1.0 CE1 B:HIS101 4.2 24.6 1.0 NE2 B:HIS493 4.2 22.3 1.0 ND1 B:HIS100 4.2 20.3 1.0 O B:HOH892 4.2 18.9 0.5 CG B:HIS100 4.3 20.9 1.0 OE1 B:GLU253 4.3 28.9 1.0 O B:HOH904 4.3 31.1 1.0 O B:HOH873 4.4 26.6 1.0 CD2 B:HIS101 4.5 21.0 1.0 CA B:HIS493 4.7 18.6 1.0 CU B:CU605 4.7 25.1 1.0 CG B:PRO256 4.8 27.1 1.0 CE B:LYS68 4.9 18.9 1.0 CD B:LYS68 4.9 25.4 1.0

Copper binding site 9 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu605 b:25.1 occ:1.00 NE2 B:HIS402 1.9 22.1 1.0 ND1 B:HIS447 1.9 22.5 1.0 O B:HOH936 2.3 26.9 1.0 CE1 B:HIS447 2.9 24.2 1.0 CE1 B:HIS402 2.9 22.6 1.0 CD2 B:HIS402 3.0 23.0 1.0 CG B:HIS447 3.0 20.4 1.0 CE1 B:PHE401 3.3 27.9 1.0 CB B:HIS447 3.4 15.9 1.0 CZ B:PHE401 3.5 26.8 1.0 O B:HIS493 3.8 18.6 1.0 O B:HOH892 3.9 18.9 0.5 CA B:HIS447 4.0 17.3 1.0 NE2 B:HIS447 4.0 21.2 1.0 CB B:HIS493 4.0 18.4 1.0 ND1 B:HIS402 4.1 21.9 1.0 CG B:HIS402 4.1 19.4 1.0 CD2 B:HIS447 4.1 20.7 1.0 CA B:HIS493 4.2 18.6 1.0 NE2 B:GLN347 4.2 27.3 1.0 CG B:HIS493 4.3 18.8 1.0 C B:HIS493 4.4 19.1 1.0 CD1 B:PHE401 4.4 19.5 1.0 CE2 B:PHE401 4.6 23.0 1.0 ND1 B:HIS493 4.7 20.7 1.0 C B:HIS447 4.7 16.8 1.0 CD2 B:HIS493 4.7 22.0 1.0 CU B:CU604 4.7 23.2 0.7 N B:THR448 4.9 16.7 1.0 O B:HOH714 4.9 28.0 1.0

Copper binding site 10 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 During 6 Months within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu602 b:28.2 occ:1.00 NE2 C:HIS171 2.0 26.2 1.0 NE2 C:HIS346 2.0 31.8 1.0 OD1 C:ASP279 2.3 26.2 1.0 OD2 C:ASP279 2.6 22.3 1.0 CG C:ASP279 2.8 24.8 1.0 CD2 C:HIS171 2.8 24.4 1.0 CD2 C:HIS346 3.0 27.9 1.0 CE1 C:HIS346 3.0 35.2 1.0 CE1 C:HIS171 3.1 22.6 1.0 OE1 C:GLN347 3.2 53.9 1.0 CG C:HIS171 4.0 20.7 1.0 CD C:GLN347 4.1 44.3 1.0 ND1 C:HIS171 4.1 19.3 1.0 ND1 C:HIS346 4.1 29.8 1.0 CG C:HIS346 4.2 28.6 1.0 O C:HOH785 4.2 27.9 1.0 CB C:ASP279 4.3 23.3 1.0 O C:HOH719 4.5 27.6 1.0 NE2 C:GLN347 4.5 55.0 1.0 OG1 C:THR513 4.7 38.1 1.0 CG1 C:VAL170 4.8 25.4 1.0 CE1 C:HIS402 4.9 26.9 1.0 CB C:THR513 4.9 28.8 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 Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 To Be Published.