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Copper in PDB 5f75: Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus

Protein crystallography data

The structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus, PDB code: 5f75 was solved by S.I.Tsallagov, K.M.Polyakov, T.V.Tikhonova, A.A.Trofimov, I.G.Shabalin, A.N.Popov, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 98.780, 95.420, 107.000, 90.00, 100.66, 90.00
R / Rfree (%) 18.6 / 24.4

Copper Binding Sites:

The binding sites of Copper atom in the Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus (pdb code 5f75). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus, PDB code: 5f75:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 5f75

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Copper binding site 1 out of 8 in the Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:33.0
occ:1.00
 O A:HOH729 1.9 31.5 1.0
NE2 A:HIS381 2.0 32.4 1.0
OD2 A:ASP314 2.0 34.4 1.0
NE2 A:HIS206 2.0 33.7 1.0
O A:HOH840 2.6 28.3 1.0
OD1 A:ASP314 2.6 30.9 1.0
CG A:ASP314 2.6 29.3 1.0
CD2 A:HIS381 2.8 29.1 1.0
CD2 A:HIS206 2.9 33.9 1.0
CE1 A:HIS206 3.1 32.2 1.0
CE1 A:HIS381 3.1 29.7 1.0
CG A:HIS381 4.1 33.2 1.0
CG A:HIS206 4.1 32.7 1.0
ND1 A:HIS206 4.1 30.3 1.0
ND1 A:HIS381 4.1 33.2 1.0
CB A:ASP314 4.2 31.0 1.0
O A:HOH770 4.3 31.9 1.0
OG1 A:THR548 4.3 27.0 1.0
O A:HOH708 4.4 33.2 1.0
O A:PHE436 4.5 39.7 1.0
O A:HOH755 4.6 12.1 0.5
CG1 A:VAL205 4.9 28.3 1.0

Copper binding site 2 out of 8 in 5f75

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Copper binding site 2 out of 8 in the Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:32.8
occ:0.80
 O A:HOH719 1.8 23.5 1.0
ND1 A:HIS528 2.0 33.9 1.0
NE2 A:HIS135 2.0 34.5 1.0
O A:HOH756 2.1 40.3 1.0
NZ A:LYS103 2.2 26.1 1.0
CD2 A:HIS135 2.8 27.0 1.0
CE1 A:HIS528 2.9 32.6 1.0
CG A:HIS528 3.0 30.6 1.0
CE1 A:HIS135 3.1 30.2 1.0
CE A:LYS103 3.4 25.9 1.0
CB A:HIS528 3.5 27.6 1.0
CD A:LYS103 3.7 24.5 1.0
O A:HOH770 3.8 31.9 1.0
CG A:HIS135 4.0 30.6 1.0
NE2 A:HIS528 4.0 33.9 1.0
CD2 A:HIS528 4.1 35.3 1.0
ND1 A:HIS135 4.1 31.2 1.0
OH A:TYR164 4.1 47.0 1.0
OE1 A:GLU288 4.2 34.0 1.0
OE1 A:GLN156 4.2 36.5 1.0
NE2 A:HIS136 4.5 30.9 1.0
O A:HOH800 4.8 31.8 1.0
OE2 A:GLU288 4.9 31.9 1.0
O A:HOH837 4.9 44.6 1.0
CA A:HIS528 5.0 26.0 1.0
CD A:GLU288 5.0 32.1 1.0

Copper binding site 3 out of 8 in 5f75

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Copper binding site 3 out of 8 in the Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:37.3
occ:1.00
 OD2 B:ASP314 2.0 35.7 1.0
NE2 B:HIS381 2.0 42.6 1.0
NE2 B:HIS206 2.1 41.6 1.0
O B:HOH828 2.3 31.4 1.0
O B:HOH751 2.5 40.1 1.0
OD1 B:ASP314 2.6 36.8 1.0
CG B:ASP314 2.6 35.5 1.0
CD2 B:HIS206 2.9 34.8 1.0
CD2 B:HIS381 3.0 37.1 1.0
CE1 B:HIS381 3.1 39.1 1.0
CE1 B:HIS206 3.1 35.0 1.0
CG B:HIS206 4.1 33.6 1.0
CG B:HIS381 4.1 38.5 1.0
CB B:ASP314 4.2 35.0 1.0
ND1 B:HIS381 4.2 35.6 1.0
ND1 B:HIS206 4.2 32.6 1.0
O B:HOH773 4.3 29.2 1.0
O B:HOH747 4.4 34.8 1.0
OG1 B:THR548 4.6 34.4 1.0
O B:PHE436 4.9 43.6 1.0
CE1 B:HIS437 4.9 37.0 1.0
CG1 B:VAL205 5.0 33.0 1.0

Copper binding site 4 out of 8 in 5f75

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Copper binding site 4 out of 8 in the Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:34.3
occ:0.80
 O B:HOH712 1.6 22.2 1.0
ND1 B:HIS528 2.0 34.5 1.0
NE2 B:HIS135 2.0 32.7 1.0
O B:HOH714 2.3 43.1 1.0
NZ B:LYS103 2.5 32.7 1.0
CD2 B:HIS135 2.8 29.2 1.0
CE1 B:HIS528 2.9 39.2 1.0
CG B:HIS528 3.0 32.8 1.0
CE1 B:HIS135 3.1 31.6 1.0
CB B:HIS528 3.3 28.2 1.0
CE B:LYS103 3.6 32.5 1.0
O B:HOH773 3.6 29.2 1.0
CD B:LYS103 3.7 31.3 1.0
CG B:HIS135 4.0 31.4 1.0
NE2 B:HIS528 4.1 37.3 1.0
CD2 B:HIS528 4.1 31.7 1.0
ND1 B:HIS135 4.1 29.2 1.0
OH B:TYR164 4.1 75.4 1.0
OE1 B:GLU288 4.2 42.2 1.0
OE1 B:GLN156 4.4 37.5 1.0
NE2 B:HIS136 4.5 33.4 1.0
CA B:HIS528 4.9 27.6 1.0
CE1 B:HIS136 5.0 28.4 1.0

Copper binding site 5 out of 8 in 5f75

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Copper binding site 5 out of 8 in the Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu601

b:32.2
occ:1.00
 NE2 C:HIS381 2.0 30.2 1.0
OD2 C:ASP314 2.0 32.6 1.0
NE2 C:HIS206 2.0 29.6 1.0
O C:HOH769 2.3 38.6 1.0
O C:HOH810 2.3 22.3 1.0
OD1 C:ASP314 2.6 34.2 1.0
CG C:ASP314 2.6 32.3 1.0
CD2 C:HIS206 2.9 31.1 1.0
CD2 C:HIS381 3.0 33.0 1.0
CE1 C:HIS381 3.0 28.7 1.0
CE1 C:HIS206 3.1 31.6 1.0
O C:HOH714 4.1 30.8 1.0
ND1 C:HIS381 4.1 30.4 1.0
CG C:HIS381 4.1 31.8 1.0
CG C:HIS206 4.1 28.1 1.0
ND1 C:HIS206 4.2 32.4 1.0
CB C:ASP314 4.2 30.4 1.0
O C:HOH709 4.3 31.5 1.0
OG1 C:THR548 4.4 31.2 1.0
O C:HOH712 4.6 31.2 1.0
O C:PHE436 4.8 35.8 1.0
CG1 C:VAL205 4.9 24.5 1.0
CE1 C:HIS437 4.9 38.6 1.0

Copper binding site 6 out of 8 in 5f75

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Copper binding site 6 out of 8 in the Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu602

b:35.8
occ:0.80
 O C:HOH713 1.6 18.1 1.0
ND1 C:HIS528 2.0 29.8 1.0
NE2 C:HIS135 2.0 29.1 1.0
O C:HOH706 2.3 29.5 1.0
NZ C:LYS103 2.4 34.6 1.0
CD2 C:HIS135 2.7 22.6 1.0
CE1 C:HIS528 2.9 30.1 1.0
CG C:HIS528 3.0 29.6 1.0
CE1 C:HIS135 3.1 24.7 1.0
CB C:HIS528 3.3 26.6 1.0
CE C:LYS103 3.6 27.2 1.0
O C:HOH714 3.8 30.8 1.0
CD C:LYS103 3.9 25.5 1.0
CG C:HIS135 3.9 24.4 1.0
NE2 C:HIS528 4.0 29.3 1.0
ND1 C:HIS135 4.1 26.0 1.0
OE1 C:GLU288 4.1 30.6 1.0
CD2 C:HIS528 4.1 32.9 1.0
OH C:TYR164 4.2 41.4 1.0
NE2 C:HIS136 4.3 25.8 1.0
OE1 C:GLN156 4.4 29.9 1.0
O C:HOH811 4.7 33.6 1.0
O C:HOH780 4.7 34.4 1.0
CA C:HIS528 4.8 25.1 1.0
OE2 C:GLU288 4.8 31.4 1.0
CE1 C:HIS136 4.8 26.8 1.0
CD C:GLU288 4.9 32.8 1.0
CD2 C:HIS136 5.0 26.5 1.0

Copper binding site 7 out of 8 in 5f75

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Copper binding site 7 out of 8 in the Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu601

b:42.1
occ:1.00
 OD2 D:ASP314 1.9 54.1 1.0
NE2 D:HIS381 2.0 43.8 1.0
NE2 D:HIS206 2.0 38.1 1.0
O D:HOH736 2.4 37.5 1.0
O D:HOH783 2.6 34.8 1.0
CG D:ASP314 2.7 54.1 1.0
CD2 D:HIS381 2.8 46.3 1.0
OD1 D:ASP314 2.9 50.4 1.0
CD2 D:HIS206 3.0 36.9 1.0
CE1 D:HIS206 3.0 38.8 1.0
CE1 D:HIS381 3.1 44.3 1.0
CG D:HIS381 4.0 49.2 1.0
O D:HOH726 4.1 37.3 1.0
ND1 D:HIS206 4.1 36.2 1.0
CG D:HIS206 4.1 38.4 1.0
ND1 D:HIS381 4.1 40.5 1.0
CB D:ASP314 4.2 45.0 1.0
OG1 D:THR548 4.5 39.5 1.0
O D:HOH729 4.6 41.8 1.0
O D:PHE436 4.8 51.0 1.0
CG1 D:VAL205 4.9 36.5 1.0
CD2 D:PHE436 5.0 76.3 1.0

Copper binding site 8 out of 8 in 5f75

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Copper binding site 8 out of 8 in the Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu602

b:44.8
occ:0.80
 O D:HOH709 1.8 30.0 1.0
ND1 D:HIS528 2.0 34.4 1.0
NE2 D:HIS135 2.0 33.5 1.0
O D:HOH749 2.3 31.8 1.0
NZ D:LYS103 2.6 32.5 1.0
CD2 D:HIS135 2.8 32.3 1.0
CE1 D:HIS528 2.9 33.8 1.0
CG D:HIS528 3.0 34.0 1.0
CE1 D:HIS135 3.1 33.4 1.0
CB D:HIS528 3.4 34.8 1.0
CE D:LYS103 3.6 27.5 1.0
O D:HOH726 3.8 37.3 1.0
CD D:LYS103 3.9 30.3 1.0
CG D:HIS135 4.0 34.6 1.0
NE2 D:HIS528 4.1 31.6 1.0
ND1 D:HIS135 4.1 32.0 1.0
CD2 D:HIS528 4.1 35.8 1.0
OE1 D:GLU288 4.2 41.4 1.0
NE2 D:HIS136 4.3 28.6 1.0
OE1 D:GLN156 4.4 31.7 1.0
OH D:TYR164 4.5 50.8 1.0
O D:HOH737 4.6 38.4 1.0
CE1 D:HIS136 4.9 30.7 1.0
CA D:HIS528 4.9 32.4 1.0
OE2 D:GLU288 4.9 38.2 1.0
CD D:GLU288 5.0 41.5 1.0

Reference:

S.I.Tsallagov, K.M.Polyakov, T.V.Tikhonova, A.A.Trofimov, I.G.Shabalin, A.N.Popov, V.O.Popov. Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus To Be Published.
Page generated: Wed Jul 31 04:02:53 2024

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