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Copper in PDB 6sji: The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln

Protein crystallography data

The structure of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln, PDB code: 6sji was solved by K.M.Polyakov, T.V.Tikhonova, T.V.Rakitina, E.Osipov, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 89.97 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.080, 160.410, 90.880, 90.00, 98.11, 90.00
R / Rfree (%) 15.9 / 19.8

Copper Binding Sites:

The binding sites of Copper atom in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln (pdb code 6sji). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln, PDB code: 6sji:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 6sji

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Copper binding site 1 out of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln


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 Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:20.5
occ:0.80
NE2 A:HIS206 1.9 21.2 1.0
NE2 A:HIS381 1.9 20.8 1.0
OD2 A:ASP314 2.4 23.5 1.0
OD1 A:ASP314 2.5 23.5 1.0
O A:HOH945 2.7 24.6 0.5
CG A:ASP314 2.8 23.6 1.0
CD2 A:HIS381 2.9 22.0 1.0
CD2 A:HIS206 2.9 19.3 1.0
CE1 A:HIS206 2.9 21.4 1.0
CE1 A:HIS381 3.0 23.0 1.0
ND1 A:HIS206 4.0 18.8 1.0
CG A:HIS206 4.0 18.8 1.0
CG A:HIS381 4.1 21.4 1.0
ND1 A:HIS381 4.1 21.5 1.0
O A:HOH789 4.1 25.3 1.0
CB A:ASP314 4.3 21.9 1.0
O A:HOH715 4.3 21.8 1.0
OG1 A:THR548 4.4 25.4 1.0
O A:HOH725 4.6 26.9 1.0
O A:PHE436 4.8 30.4 1.0
CG1 A:VAL205 4.9 18.5 1.0

Copper binding site 2 out of 9 in 6sji

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Copper binding site 2 out of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln


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 Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:22.9
occ:0.80
ND1 A:HIS528 1.9 19.4 1.0
NE2 A:HIS135 1.9 16.7 1.0
O A:HOH824 2.0 34.1 0.8
O A:HOH838 2.0 27.8 1.0
CD2 A:HIS135 2.8 16.4 1.0
NZ A:LYS103 2.8 22.9 1.0
CE1 A:HIS528 2.9 19.7 1.0
CG A:HIS528 2.9 19.3 1.0
CE1 A:HIS135 3.0 15.9 1.0
CB A:HIS528 3.3 17.4 1.0
O A:HOH789 3.6 25.3 1.0
CE A:LYS103 3.6 22.9 1.0
CD A:LYS103 3.9 20.2 1.0
CG A:HIS135 4.0 16.0 1.0
NE2 A:HIS528 4.0 20.5 1.0
ND1 A:HIS135 4.0 16.0 1.0
CD2 A:HIS528 4.0 19.3 1.0
OE1 A:GLU288 4.2 22.8 1.0
O A:HOH815 4.2 22.0 0.5
NE2 A:HIS136 4.2 17.2 1.0
OH A:TYR164 4.3 25.5 1.0
OE1 A:GLN156 4.5 21.1 1.0
CE1 A:HIS136 4.6 18.2 1.0
CA A:HIS528 4.8 17.0 1.0
OE2 A:GLU288 4.9 23.6 1.0
CD A:GLU288 5.0 22.2 1.0

Copper binding site 3 out of 9 in 6sji

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Copper binding site 3 out of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln


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 Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:17.4
occ:0.80
NE2 B:HIS206 1.9 20.3 1.0
NE2 B:HIS381 1.9 22.9 1.0
O B:HOH890 2.1 22.6 0.5
OD2 B:ASP314 2.4 20.9 1.0
OD1 B:ASP314 2.5 23.9 1.0
CG B:ASP314 2.8 23.8 1.0
CD2 B:HIS206 2.8 22.2 1.0
CE1 B:HIS381 2.9 23.1 1.0
CE1 B:HIS206 2.9 18.6 1.0
CD2 B:HIS381 3.0 24.0 1.0
CG B:HIS206 4.0 16.7 1.0
ND1 B:HIS206 4.0 19.1 1.0
ND1 B:HIS381 4.0 22.8 1.0
CG B:HIS381 4.1 21.6 1.0
O B:HOH776 4.2 28.3 1.0
CB B:ASP314 4.3 21.0 1.0
O B:HOH709 4.3 21.6 1.0
OG1 B:THR548 4.5 24.7 1.0
O B:HOH716 4.6 23.6 1.0
O B:PHE436 4.7 29.5 1.0
CG1 B:VAL205 4.9 15.6 1.0

Copper binding site 4 out of 9 in 6sji

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Copper binding site 4 out of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln


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 Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:22.6
occ:0.80
O B:HOH738 2.0 42.0 0.8
ND1 B:HIS528 2.0 16.8 1.0
NE2 B:HIS135 2.0 18.4 1.0
O B:HOH894 2.0 22.0 1.0
NZ B:LYS103 2.7 22.7 1.0
CD2 B:HIS135 2.9 16.9 1.0
CG B:HIS528 2.9 16.5 1.0
CE1 B:HIS528 3.0 17.1 1.0
CE1 B:HIS135 3.1 16.5 1.0
CB B:HIS528 3.2 16.8 1.0
O B:HOH776 3.5 28.3 1.0
CE B:LYS103 3.6 21.7 1.0
CD B:LYS103 4.0 20.3 1.0
NE2 B:HIS528 4.0 16.1 1.0
CG B:HIS135 4.1 17.6 1.0
CD2 B:HIS528 4.1 17.4 1.0
ND1 B:HIS135 4.2 15.5 1.0
NE2 B:HIS136 4.2 19.4 1.0
OE1 B:GLU288 4.2 21.5 1.0
O B:HOH729 4.4 19.4 0.5
OH B:TYR164 4.4 29.0 1.0
CE1 B:HIS136 4.6 18.5 1.0
OE1 B:GLN156 4.6 20.3 1.0
CA B:HIS528 4.8 15.7 1.0
CD2 B:HIS136 5.0 18.4 1.0
OE2 B:GLU288 5.0 20.8 1.0

Copper binding site 5 out of 9 in 6sji

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Copper binding site 5 out of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln


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 Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cu601

b:21.0
occ:0.80
NE2 J:HIS381 2.0 23.0 1.0
NE2 J:HIS206 2.0 21.7 1.0
OD2 J:ASP314 2.4 22.7 1.0
OD1 J:ASP314 2.5 21.4 1.0
CG J:ASP314 2.8 23.0 1.0
CD2 J:HIS381 2.9 21.1 1.0
CD2 J:HIS206 2.9 22.4 1.0
CE1 J:HIS206 3.0 19.8 1.0
CE1 J:HIS381 3.0 21.6 1.0
CG J:HIS206 4.1 19.6 1.0
CG J:HIS381 4.1 21.0 1.0
ND1 J:HIS206 4.1 19.3 1.0
ND1 J:HIS381 4.1 20.9 1.0
O J:HOH785 4.2 25.0 1.0
CB J:ASP314 4.3 22.1 1.0
O J:HOH743 4.4 21.7 1.0
OG1 J:THR548 4.5 26.1 1.0
O J:HOH726 4.6 26.8 1.0
O J:PHE436 4.6 29.4 1.0
CG1 J:VAL205 4.9 19.1 1.0

Copper binding site 6 out of 9 in 6sji

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Copper binding site 6 out of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln


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 Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cu602

b:23.6
occ:0.80
NE2 J:HIS135 1.9 17.7 1.0
ND1 J:HIS528 1.9 18.6 1.0
O J:HOH821 2.0 47.2 0.8
O J:HOH807 2.0 25.4 1.0
NZ J:LYS103 2.8 21.2 1.0
CD2 J:HIS135 2.8 15.0 1.0
CE1 J:HIS528 2.9 18.1 1.0
CG J:HIS528 3.0 17.9 1.0
CE1 J:HIS135 3.0 17.2 1.0
CB J:HIS528 3.3 17.5 1.0
O J:HOH785 3.6 25.0 1.0
CE J:LYS103 3.7 20.5 1.0
CD J:LYS103 3.8 19.5 1.0
CG J:HIS135 4.0 16.0 1.0
NE2 J:HIS528 4.0 19.9 1.0
ND1 J:HIS135 4.0 17.4 1.0
CD2 J:HIS528 4.1 18.6 1.0
O J:HOH780 4.2 24.1 0.5
NE2 J:HIS136 4.2 20.9 1.0
OE1 J:GLU288 4.2 22.1 1.0
OH J:TYR164 4.3 31.1 1.0
OE1 J:GLN156 4.6 22.4 1.0
CE1 J:HIS136 4.6 19.2 1.0
CA J:HIS528 4.8 17.3 1.0
CD2 J:HIS136 4.9 20.0 1.0

Copper binding site 7 out of 9 in 6sji

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Copper binding site 7 out of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln


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 Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu601

b:20.4
occ:0.80
NE2 K:HIS206 1.9 21.0 1.0
NE2 K:HIS381 1.9 27.2 1.0
OD2 K:ASP314 2.4 27.0 1.0
OD1 K:ASP314 2.5 22.5 1.0
CG K:ASP314 2.8 24.5 1.0
O K:HOH948 2.8 25.3 0.5
CD2 K:HIS206 2.9 19.7 1.0
CE1 K:HIS381 2.9 27.6 1.0
CD2 K:HIS381 3.0 25.3 1.0
CE1 K:HIS206 3.0 20.1 1.0
ND1 K:HIS381 4.0 28.1 1.0
CG K:HIS206 4.0 16.7 1.0
ND1 K:HIS206 4.0 19.4 1.0
CG K:HIS381 4.1 25.9 1.0
O K:HOH821 4.3 23.9 1.0
CB K:ASP314 4.3 20.9 1.0
O K:HOH710 4.4 26.4 1.0
OG1 K:THR548 4.6 25.5 1.0
O K:HOH739 4.6 26.6 1.0
O K:PHE436 4.8 25.3 1.0
CE1 K:HIS437 4.9 27.4 1.0
CG1 K:VAL205 4.9 17.7 1.0
O K:HOH971 4.9 35.7 0.5

Copper binding site 8 out of 9 in 6sji

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Copper binding site 8 out of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln


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 Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu602

b:21.6
occ:0.80
ND1 K:HIS528 1.9 19.7 1.0
O K:HOH734 2.0 25.5 0.8
NE2 K:HIS135 2.0 18.6 1.0
O K:HOH790 2.0 25.5 1.0
NZ K:LYS103 2.6 26.3 1.0
CD2 K:HIS135 2.8 18.1 1.0
CE1 K:HIS528 2.9 17.8 1.0
CG K:HIS528 3.0 19.0 1.0
CE1 K:HIS135 3.0 18.6 1.0
CB K:HIS528 3.4 16.6 1.0
CE K:LYS103 3.5 23.4 1.0
O K:HOH821 3.5 23.9 1.0
CD K:LYS103 3.8 20.9 1.0
CG K:HIS135 4.0 16.9 1.0
NE2 K:HIS528 4.0 18.1 1.0
ND1 K:HIS135 4.1 17.0 1.0
CD2 K:HIS528 4.1 17.7 1.0
OH K:TYR164 4.1 29.9 1.0
OE1 K:GLU288 4.1 20.8 1.0
NE2 K:HIS136 4.3 19.0 1.0
OE1 K:GLN156 4.4 17.8 1.0
O K:HOH769 4.6 21.8 0.5
CE1 K:HIS136 4.8 17.6 1.0
CA K:HIS528 4.9 17.4 1.0
O K:HOH845 4.9 23.1 1.0
CD2 K:HIS136 5.0 17.5 1.0

Copper binding site 9 out of 9 in 6sji

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Copper binding site 9 out of 9 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln


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 Thioalkalivibrio Paradoxus Mutant with His 482 Replaced By Gln within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu603

b:29.7
occ:0.50
ND1 K:HIS411 1.9 30.0 1.0
CE1 K:HIS411 2.8 32.2 1.0
CG K:HIS411 3.1 29.9 1.0
CB K:HIS411 3.6 26.8 1.0
NE2 K:HIS411 4.0 30.1 1.0
CD2 K:HIS411 4.1 30.0 1.0
O K:HIS411 4.6 27.7 1.0
C K:HIS411 4.6 27.1 1.0
CA K:HIS411 4.7 24.8 1.0
OD2 K:ASP412 4.8 36.2 0.5
OD1 K:ASP412 5.0 35.9 0.5

Reference:

T.V.Tikhonova, D.Y.Sorokin, W.R.Hagen, M.G.Khrenova, G.Mauser, T.V.Rakitina, K.M.Polyakov, I.G.Shabalin, A.A.Trofimov, S.I.Tsalallagov, V.O.Popov. A Novel Copper Biocatalytic Center Forms An Active Site of the Thiocyanate Dehydrogenase To Be Published.
Page generated: Sun Dec 13 11:25:52 2020

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