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Copper in PDB 8yu6: The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate

Protein crystallography data

The structure of The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate, PDB code: 8yu6 was solved by L.A.Varfolomeeva, 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) 45.85 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.76, 96.3, 148.76, 90, 90, 90
R / Rfree (%) 16.4 / 19.5

Other elements in 8yu6:

The structure of The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate (pdb code 8yu6). 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 with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate, PDB code: 8yu6:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 8yu6

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Copper binding site 1 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate


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 with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:19.8
occ:0.80
 O A:HOH930 2.1 18.7 0.5
NE2 A:HIS171 2.1 16.1 1.0
NE2 A:HIS346 2.1 22.5 1.0
OD1 A:ASP279 2.1 20.3 1.0
CG A:ASP279 2.8 19.2 1.0
OD2 A:ASP279 2.8 20.1 1.0
CD2 A:HIS171 2.9 12.1 1.0
OE1 A:GLN347 3.0 24.7 1.0
CD2 A:HIS346 3.0 21.8 1.0
CE1 A:HIS346 3.0 20.3 1.0
CE1 A:HIS171 3.1 14.2 1.0
NE2 A:GLN347 3.5 27.9 1.0
CD A:GLN347 3.6 28.9 1.0
O A:HOH1074 3.6 24.2 0.5
O A:HOH876 3.6 24.0 1.0
O A:HOH767 4.1 16.3 0.5
CG A:HIS171 4.1 14.9 1.0
CG A:HIS346 4.2 20.8 1.0
ND1 A:HIS171 4.2 15.5 1.0
ND1 A:HIS346 4.2 20.3 1.0
CB A:ASP279 4.2 14.5 1.0
O A:HOH720 4.5 18.9 1.0
CE1 A:HIS402 4.6 23.6 1.0
CG1 A:VAL170 4.7 14.7 1.0
NE2 A:HIS101 4.9 16.6 1.0
CG A:GLN347 5.0 21.9 1.0
CG2 A:THR513 5.0 23.4 1.0
CB A:THR513 5.0 17.7 1.0

Copper binding site 2 out of 8 in 8yu6

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Copper binding site 2 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate


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 with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:16.9
occ:0.60
 CU A:CU603 0.0 16.9 0.6
CU A:CU603 1.2 23.1 0.3
O A:HOH755 2.1 19.4 1.0
ND1 A:HIS493 2.1 16.2 1.0
NE2 A:HIS100 2.1 15.9 1.0
O A:HOH767 2.1 16.3 0.5
CE1 A:HIS493 3.1 15.3 1.0
O A:HOH1074 3.1 24.2 0.5
CG A:HIS493 3.1 14.1 1.0
CD2 A:HIS100 3.1 13.8 1.0
CE1 A:HIS100 3.1 15.1 1.0
CB A:HIS493 3.3 14.0 1.0
NZ A:LYS68 3.7 17.9 1.0
NE2 A:HIS101 3.7 16.6 1.0
NE2 A:HIS493 4.2 16.6 1.0
ND1 A:HIS100 4.2 14.2 1.0
CD2 A:HIS493 4.2 14.8 1.0
OE1 A:GLU253 4.2 20.8 1.0
CG A:HIS100 4.3 13.8 1.0
CE1 A:HIS101 4.3 15.4 1.0
O A:HOH877 4.4 25.4 1.0
O A:HOH876 4.4 24.0 1.0
CU A:CU605 4.5 20.4 0.2
CE A:LYS68 4.6 16.8 1.0
O A:HOH930 4.6 18.7 0.5
CD2 A:HIS101 4.6 15.2 1.0
CG A:PRO256 4.7 24.4 1.0
CD A:LYS68 4.8 16.1 1.0
CA A:HIS493 4.9 12.8 1.0
O A:HOH763 4.9 24.3 1.0

Copper binding site 3 out of 8 in 8yu6

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Copper binding site 3 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate


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 with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:23.1
occ:0.30
 CU A:CU603 0.0 23.1 0.3
CU A:CU603 1.2 16.9 0.6
ND1 A:HIS493 1.9 16.2 1.0
NE2 A:HIS100 2.0 15.9 1.0
O A:HOH755 2.1 19.4 1.0
CE1 A:HIS493 2.5 15.3 1.0
NZ A:LYS68 2.5 17.9 1.0
CD2 A:HIS100 2.7 13.8 1.0
CG A:HIS493 2.9 14.1 1.0
CE1 A:HIS100 3.1 15.1 1.0
O A:HOH767 3.3 16.3 0.5
CE A:LYS68 3.4 16.8 1.0
CB A:HIS493 3.5 14.0 1.0
CD A:LYS68 3.6 16.1 1.0
NE2 A:HIS493 3.7 16.6 1.0
CD2 A:HIS493 3.9 14.8 1.0
OE1 A:GLU253 3.9 20.8 1.0
CG A:HIS100 3.9 13.8 1.0
ND1 A:HIS100 4.1 14.2 1.0
O A:HOH1074 4.2 24.2 0.5
OH A:TYR129 4.3 20.2 1.0
OE2 A:GLU253 4.3 20.8 1.0
NE2 A:HIS101 4.5 16.6 1.0
CD A:GLU253 4.6 19.4 1.0
OE1 A:GLN121 4.6 18.1 1.0
CG A:PRO256 5.0 24.4 1.0
O A:HOH877 5.0 25.4 1.0

Copper binding site 4 out of 8 in 8yu6

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Copper binding site 4 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate


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 with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:25.4
occ:0.70
 N A:HIS44 2.0 29.9 1.0
ND1 A:HIS44 2.1 28.2 1.0
N A:GLY43 2.1 43.5 1.0
O A:HOH1023 2.5 25.2 1.0
C A:GLY43 2.9 37.8 1.0
CG A:HIS44 3.0 30.4 1.0
CA A:GLY43 3.0 38.0 1.0
CE1 A:HIS44 3.1 31.3 1.0
CA A:HIS44 3.1 29.9 1.0
CB A:HIS44 3.3 28.1 1.0
N A:MET45 3.6 33.9 1.0
C A:HIS44 3.9 35.1 1.0
O A:GLY43 4.1 38.7 1.0
CD2 A:HIS44 4.2 29.6 1.0
NE2 A:HIS44 4.2 31.0 1.0
O A:HOH1056 4.5 29.0 1.0
CG A:MET45 4.8 44.0 1.0
CA A:MET45 5.0 37.3 1.0

Copper binding site 5 out of 8 in 8yu6

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Copper binding site 5 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate


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 with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu605

b:20.4
occ:0.20
 NE2 A:GLN447 2.1 19.1 1.0
NE2 A:HIS402 2.1 21.3 1.0
O A:HOH1074 2.7 24.2 0.5
CE1 A:HIS402 3.1 23.6 1.0
CD2 A:HIS402 3.1 21.8 1.0
CZ A:PHE401 3.2 23.7 1.0
CD A:GLN447 3.3 19.1 1.0
CE1 A:PHE401 3.4 22.1 1.0
O A:HOH930 3.5 18.7 0.5
OE1 A:GLN447 3.9 20.1 1.0
O A:HOH767 4.0 16.3 0.5
NE2 A:GLN347 4.0 27.9 1.0
CB A:HIS493 4.1 14.0 1.0
ND1 A:HIS402 4.2 19.5 1.0
CG A:HIS402 4.2 17.8 1.0
O A:HIS493 4.2 14.7 1.0
CE2 A:PHE401 4.2 22.3 1.0
CG A:HIS493 4.4 14.1 1.0
ND1 A:HIS493 4.4 16.2 1.0
CD1 A:PHE401 4.4 21.1 1.0
CB A:GLN447 4.4 16.6 1.0
CG A:GLN447 4.4 18.3 1.0
CU A:CU603 4.5 16.9 0.6
CA A:HIS493 4.6 12.8 1.0
CA A:GLN447 4.6 15.0 1.0
CG A:PRO256 4.8 24.4 1.0
C A:HIS493 4.8 14.7 1.0
CD2 A:HIS493 5.0 14.8 1.0

Copper binding site 6 out of 8 in 8yu6

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Copper binding site 6 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate


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 with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:15.6
occ:1.00
 NE2 B:HIS346 2.0 15.6 1.0
O B:HOH902 2.1 17.6 0.7
O B:HOH995 2.1 16.9 0.7
NE2 B:HIS171 2.1 13.1 1.0
OD1 B:ASP279 2.2 17.9 1.0
OD2 B:ASP279 2.4 15.2 1.0
CG B:ASP279 2.7 15.9 1.0
CD2 B:HIS171 3.0 12.3 1.0
CE1 B:HIS346 3.0 12.8 1.0
CD2 B:HIS346 3.1 15.4 1.0
CE1 B:HIS171 3.2 13.9 1.0
CG B:HIS171 4.2 12.7 1.0
ND1 B:HIS346 4.2 13.6 1.0
CB B:ASP279 4.2 14.2 1.0
CG B:HIS346 4.2 15.4 1.0
ND1 B:HIS171 4.2 13.0 1.0
OG1 B:THR513 4.2 15.9 1.0
O B:HOH844 4.3 19.0 1.0
O B:HOH788 4.3 16.0 1.0
O B:PHE401 4.6 17.0 1.0
O B:HOH787 4.7 16.2 1.0
CG1 B:VAL170 5.0 15.1 1.0

Copper binding site 7 out of 8 in 8yu6

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Copper binding site 7 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate


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 with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu605

b:20.6
occ:1.00
 O B:HOH803 1.9 25.9 1.0
ND1 B:HIS493 1.9 14.8 1.0
NE2 B:HIS100 2.0 14.1 1.0
O B:HOH786 2.1 21.5 1.0
NZ B:LYS68 2.4 19.3 1.0
CE1 B:HIS493 2.8 15.2 1.0
CD2 B:HIS100 2.9 13.0 1.0
CG B:HIS493 3.0 14.5 1.0
CE1 B:HIS100 3.1 13.9 1.0
CB B:HIS493 3.4 15.3 1.0
CE B:LYS68 3.5 21.1 1.0
CD B:LYS68 3.8 16.0 1.0
O B:HOH844 3.8 19.0 1.0
NE2 B:HIS493 4.0 14.9 1.0
CG B:HIS100 4.0 12.8 1.0
CD2 B:HIS493 4.0 15.4 1.0
ND1 B:HIS100 4.1 12.9 1.0
OH B:TYR129 4.2 21.3 1.0
OE1 B:GLU253 4.2 19.4 1.0
OE1 B:GLN121 4.4 19.3 1.0
O B:HOH1026 4.4 25.9 0.5
NE2 B:HIS101 4.5 15.2 1.0
O B:HOH872 4.9 19.8 1.0
CA B:HIS493 4.9 11.9 1.0
CE1 B:HIS101 4.9 14.2 1.0

Copper binding site 8 out of 8 in 8yu6

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Copper binding site 8 out of 8 in the The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate


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 with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu606

b:21.3
occ:0.20
 O B:HOH1026 2.1 25.9 0.5
NE2 B:GLN447 2.1 14.4 1.0
NE2 B:HIS402 2.1 22.2 1.0
CE1 B:HIS402 2.9 24.6 1.0
CD B:GLN447 3.2 16.6 1.0
CD2 B:HIS402 3.2 20.6 1.0
CE2 B:PHE401 3.2 21.8 1.0
CZ B:PHE401 3.4 25.7 1.0
CD2 B:PHE401 3.6 20.5 1.0
OE1 B:GLN447 3.6 18.1 1.0
CE1 B:PHE401 4.0 26.0 1.0
ND1 B:HIS402 4.1 20.9 1.0
CG B:PHE401 4.2 17.4 1.0
O B:HOH803 4.2 25.9 1.0
CG B:HIS402 4.3 19.0 1.0
CD1 B:PHE401 4.3 22.8 1.0
O B:HOH995 4.4 16.9 0.7
O B:HOH1065 4.4 22.1 0.5
CG B:GLN447 4.5 14.6 1.0
CB B:HIS493 4.5 15.3 1.0
CG B:HIS493 4.6 14.5 1.0
O B:HIS493 4.6 14.5 1.0
CB B:GLN447 4.6 15.1 1.0
ND1 B:HIS493 4.7 14.8 1.0
CA B:GLN447 4.7 14.1 1.0
CA B:HIS493 4.9 11.9 1.0
CD2 B:HIS493 4.9 15.4 1.0

Reference:

L.A.Varfolomeeva, N.S.Shipkov, N.I.Dergousova, K.M.Boyko, T.V.Tikhonova, V.O.Popov. The Structure of Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), Activated By Crystal Soaking with 1MM CUCL2 and 1 Mm Sodium Ascorbate To Be Published.
Page generated: Mon Jul 14 09:39:51 2025

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