Copper in PDB 8yu5: The Structure of Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q)

Protein crystallography data

The structure of The Structure of Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), PDB code: 8yu5 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) 45.88 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.77, 96.44, 147.67, 90, 90, 90
R / Rfree (%) 15 / 17.3

Other elements in 8yu5:

The structure of The Structure of Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the The Structure of Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q) (pdb code 8yu5). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the The Structure of Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q), PDB code: 8yu5:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 8yu5

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Copper binding site 1 out of 5 in the The Structure of Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q)


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 Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu605

b:23.6
occ:0.70
 ND1 A:HIS44 2.0 32.3 1.0
N A:HIS44 2.0 30.5 1.0
N A:GLY43 2.1 37.1 1.0
O A:HOH1084 2.6 26.2 1.0
C A:GLY43 2.9 39.2 1.0
CE1 A:HIS44 2.9 34.1 1.0
CG A:HIS44 2.9 35.9 1.0
CA A:GLY43 3.0 37.5 1.0
CA A:HIS44 3.1 34.9 1.0
CB A:HIS44 3.3 33.7 1.0
N A:MET45 3.6 36.1 1.0
C A:HIS44 3.9 39.2 1.0
NE2 A:HIS44 4.0 35.3 1.0
CD2 A:HIS44 4.1 34.0 1.0
O A:GLY43 4.1 43.4 1.0
O A:HOH1099 4.5 27.1 1.0
CG A:MET45 4.8 40.9 1.0
CA A:MET45 4.9 38.2 1.0

Copper binding site 2 out of 5 in 8yu5

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Copper binding site 2 out of 5 in the The Structure of Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q)


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 Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu606

b:16.9
occ:0.20
 O A:HOH822 2.0 13.8 1.0
O A:HOH927 2.0 16.6 1.0
ND1 A:HIS493 2.0 11.6 1.0
NE2 A:HIS100 2.1 10.7 1.0
CE1 A:HIS493 3.0 11.7 1.0
CE1 A:HIS100 3.0 10.1 1.0
CG A:HIS493 3.0 9.5 1.0
CD2 A:HIS100 3.3 10.1 1.0
CB A:HIS493 3.3 9.9 1.0
O A:HOH825 3.4 21.9 1.0
NE2 A:HIS101 3.7 11.2 1.0
NZ A:LYS68 3.8 12.0 1.0
NE2 A:HIS493 4.1 11.1 1.0
ND1 A:HIS100 4.2 9.6 1.0
CD2 A:HIS493 4.2 10.1 1.0
OE1 A:GLU253 4.2 12.2 1.0
O A:HOH925 4.2 14.8 1.0
O A:HOH829 4.3 18.7 1.0
CE1 A:HIS101 4.3 9.5 1.0
CG A:HIS100 4.3 9.0 1.0
O A:HOH813 4.5 17.9 0.2
CG A:PRO256 4.6 12.9 1.0
CD2 A:HIS101 4.6 9.8 1.0
CE A:LYS68 4.7 11.6 1.0
CA A:HIS493 4.9 9.3 1.0
OE1 A:GLN447 4.9 13.7 1.0
CD A:LYS68 4.9 11.1 1.0
O A:HOH876 5.0 15.4 1.0
CD A:PRO256 5.0 12.4 1.0

Copper binding site 3 out of 5 in 8yu5

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Copper binding site 3 out of 5 in the The Structure of Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q)


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 Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu607

b:18.8
occ:0.20
 O A:HOH813 2.0 17.9 0.2
OD2 A:ASP279 2.0 15.1 1.0
O A:HOH756 2.1 19.9 0.8
NE2 A:HIS171 2.1 14.5 1.0
NE2 A:GLN347 2.7 15.6 1.0
CG A:ASP279 2.7 13.1 1.0
OD1 A:ASP279 2.7 14.8 1.0
CD2 A:HIS171 2.9 9.4 1.0
CE1 A:HIS171 3.1 10.0 1.0
OE1 A:GLN347 3.3 17.9 1.0
CD A:GLN347 3.4 18.6 1.0
O A:HOH829 3.6 18.7 1.0
CG A:HIS171 4.1 10.4 1.0
O A:HOH927 4.1 16.6 1.0
CB A:ASP279 4.1 11.3 1.0
ND1 A:HIS171 4.2 14.2 1.0
CE1 A:HIS402 4.3 14.8 1.0
O A:HOH770 4.3 15.6 1.0
O A:HOH1162 4.5 22.6 1.0
CG1 A:VAL170 4.6 9.9 1.0
O A:HOH825 4.7 21.9 1.0
O A:ASP279 4.8 11.3 1.0
NE2 A:HIS402 4.8 13.7 1.0
CG A:GLN347 4.8 14.7 1.0
OG1 A:THR513 4.9 17.1 1.0

Copper binding site 4 out of 5 in 8yu5

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Copper binding site 4 out of 5 in the The Structure of Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q)


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 Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:10.4
occ:0.80
 O B:HOH902 2.0 13.6 0.8
NE2 B:HIS346 2.1 13.5 1.0
O B:HOH989 2.1 14.0 0.8
NE2 B:HIS171 2.1 11.2 1.0
OD1 B:ASP279 2.3 13.8 1.0
OD2 B:ASP279 2.4 13.0 1.0
CG B:ASP279 2.6 12.2 1.0
CD2 B:HIS171 3.0 10.4 1.0
CE1 B:HIS346 3.1 13.1 1.0
CD2 B:HIS346 3.1 13.8 1.0
CE1 B:HIS171 3.2 9.7 1.0
CB B:ASP279 4.2 11.8 1.0
CG B:HIS171 4.2 9.9 1.0
ND1 B:HIS346 4.2 13.2 1.0
CG B:HIS346 4.2 12.3 1.0
ND1 B:HIS171 4.3 11.1 1.0
O B:HOH876 4.3 14.1 1.0
OG1 B:THR513 4.3 14.2 1.0
O B:HOH737 4.3 12.4 1.0
O B:PHE401 4.5 15.7 1.0
O B:HOH742 4.7 13.6 1.0

Copper binding site 5 out of 5 in 8yu5

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Copper binding site 5 out of 5 in the The Structure of Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q)


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 Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu605

b:11.1
occ:0.50
 ND1 B:HIS493 1.9 13.9 1.0
O B:HOH760 2.0 9.1 0.5
NE2 B:HIS100 2.0 10.3 1.0
O B:HOH713 2.0 10.7 0.5
NZ B:LYS68 2.2 14.9 1.0
CE1 B:HIS493 2.7 11.7 1.0
CD2 B:HIS100 2.9 9.9 1.0
CE1 B:HIS100 3.0 10.0 1.0
CG B:HIS493 3.0 10.5 1.0
CE B:LYS68 3.3 13.1 1.0
CB B:HIS493 3.5 11.2 1.0
CD B:LYS68 3.7 13.4 1.0
NE2 B:HIS493 3.9 11.9 1.0
O B:HOH876 3.9 14.1 1.0
OH B:TYR129 4.0 19.9 1.0
CG B:HIS100 4.0 8.9 1.0
CD2 B:HIS493 4.1 11.7 1.0
OE1 B:GLU253 4.1 16.6 1.0
ND1 B:HIS100 4.1 9.6 1.0
O B:HOH1006 4.3 26.2 0.5
OE1 B:GLN121 4.3 15.1 1.0
O B:HOH971 4.5 17.2 1.0
NE2 B:HIS101 4.7 11.1 1.0

Reference:

L.A.Varfolomeeva, N.S.Shipkov, N.I.Dergousova, K.M.Boyko, T.V.Tikhonova, V.O.Popov. The Structure of Non-Activated Thiocyanate Dehydrogenase Mutant with the H447Q Substitution From Pelomicrobium Methylotrophicum (Pmtcdh H447Q) To Be Published.
Page generated: Wed Jul 31 10:25:12 2024

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