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Copper in PDB 6i3q: The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Acetate Ions.

Protein crystallography data

The structure of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Acetate Ions., PDB code: 6i3q was solved by K.M.Polyakov, A.N.Popov, T.V.Tikhkonova, V.O.Popov, A.A.Trofimov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.48 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.960, 162.700, 90.938, 90.00, 119.93, 90.00
R / Rfree (%) 14.2 / 16.5

Copper Binding Sites:

The binding sites of Copper atom in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Acetate Ions. (pdb code 6i3q). 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 From Thioalkalivibrio Paradoxus Complex with Acetate Ions., PDB code: 6i3q:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 6i3q

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Copper binding site 1 out of 8 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Acetate Ions.


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 Complex with Acetate Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:17.2
occ:1.00
 OXT A:ACT603 2.0 16.0 0.5
NE2 A:HIS206 2.0 13.0 1.0
NE2 A:HIS381 2.0 17.0 1.0
OD2 A:ASP314 2.1 17.0 1.0
O A:HOH757 2.4 25.7 1.0
CG A:ASP314 2.8 17.7 1.0
C A:ACT603 2.8 16.5 0.5
OD1 A:ASP314 2.8 17.5 1.0
CD2 A:HIS381 2.9 16.0 1.0
CD2 A:HIS206 2.9 13.1 1.0
CH3 A:ACT604 2.9 14.6 0.5
CE1 A:HIS206 3.0 11.4 1.0
CE1 A:HIS381 3.0 17.2 1.0
CH3 A:ACT603 3.2 16.9 0.5
O A:ACT603 3.9 16.8 0.5
CG A:HIS381 4.0 16.9 1.0
CG A:HIS206 4.1 11.5 1.0
ND1 A:HIS206 4.1 12.3 1.0
ND1 A:HIS381 4.1 17.7 1.0
CB A:ASP314 4.2 17.1 1.0
O A:HOH745 4.3 15.5 1.0
C A:ACT604 4.4 14.7 0.5
OG1 A:THR548 4.5 16.1 1.0
O A:PHE436 4.7 17.4 1.0
O A:ACT604 5.0 17.2 0.5
CG1 A:VAL205 5.0 12.8 1.0
CE1 A:HIS437 5.0 16.3 1.0

Copper binding site 2 out of 8 in 6i3q

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Copper binding site 2 out of 8 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Acetate Ions.


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 Complex with Acetate Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:15.8
occ:0.80
 ND1 A:HIS528 2.0 13.9 1.0
OXT A:ACT604 2.0 15.1 0.5
NE2 A:HIS135 2.1 13.2 1.0
O A:HOH830 2.1 16.4 0.5
O A:HOH702 2.5 21.9 0.5
C A:ACT604 2.8 14.7 0.5
O A:ACT604 2.9 17.2 0.5
CE1 A:HIS528 2.9 13.6 1.0
CD2 A:HIS135 3.0 12.5 1.0
CG A:HIS528 3.0 13.0 1.0
CE1 A:HIS135 3.1 12.2 1.0
CB A:HIS528 3.4 12.2 1.0
NZ A:LYS103 3.4 19.1 1.0
NE2 A:HIS136 3.8 11.9 1.0
OE1 A:GLU288 4.0 24.9 1.0
NE2 A:HIS528 4.1 13.3 1.0
CD2 A:HIS528 4.1 14.0 1.0
O A:ACT603 4.1 16.8 0.5
CG A:HIS135 4.2 11.8 1.0
ND1 A:HIS135 4.2 12.4 1.0
CH3 A:ACT603 4.2 16.9 0.5
CH3 A:ACT604 4.2 14.6 0.5
CE1 A:HIS136 4.5 12.4 1.0
CE A:LYS103 4.5 15.7 1.0
CD A:LYS103 4.5 14.8 1.0
CD2 A:HIS136 4.5 12.8 1.0
O A:HOH775 4.6 14.0 1.0
C A:ACT603 4.7 16.5 0.5
OE2 A:GLU288 4.7 24.3 1.0
CD A:GLU288 4.8 24.1 1.0
CA A:HIS528 4.8 12.1 1.0
OE1 A:GLN156 4.8 19.7 1.0

Copper binding site 3 out of 8 in 6i3q

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Copper binding site 3 out of 8 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Acetate Ions.


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 Complex with Acetate Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:17.2
occ:1.00
 O B:ACT603 1.9 12.3 0.5
NE2 B:HIS206 2.0 13.7 1.0
NE2 B:HIS381 2.0 16.9 1.0
OD2 B:ASP314 2.1 16.6 1.0
O B:HOH705 2.6 20.8 1.0
CG B:ASP314 2.8 18.2 1.0
CD2 B:HIS381 2.9 17.7 1.0
C B:ACT603 2.9 12.6 0.5
OD1 B:ASP314 2.9 17.2 1.0
CD2 B:HIS206 2.9 13.7 1.0
CE1 B:HIS206 2.9 13.0 1.0
CH3 B:ACT604 3.0 16.9 0.5
CE1 B:HIS381 3.1 17.8 1.0
CH3 B:ACT603 3.4 13.3 0.5
OXT B:ACT603 3.9 11.6 0.5
ND1 B:HIS206 4.0 13.7 1.0
CG B:HIS206 4.1 12.8 1.0
CG B:HIS381 4.1 16.6 1.0
ND1 B:HIS381 4.1 21.4 1.0
CB B:ASP314 4.3 16.5 1.0
O B:HOH728 4.3 18.6 1.0
OG1 B:THR548 4.4 20.0 1.0
C B:ACT604 4.5 17.0 0.5
O B:PHE436 4.7 18.1 1.0
CE1 B:HIS437 5.0 16.2 1.0

Copper binding site 4 out of 8 in 6i3q

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Copper binding site 4 out of 8 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Acetate Ions.


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 Complex with Acetate Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:14.7
occ:0.80
 NE2 B:HIS135 2.0 11.3 1.0
OXT B:ACT604 2.0 16.7 0.5
ND1 B:HIS528 2.0 14.6 1.0
O B:HOH702 2.2 21.9 0.5
O B:HOH918 2.2 13.2 0.5
CE1 B:HIS135 2.9 11.2 1.0
CD2 B:HIS135 2.9 11.8 1.0
CE1 B:HIS528 3.0 13.4 1.0
CG B:HIS528 3.0 14.4 1.0
C B:ACT604 3.0 17.0 0.5
CB B:HIS528 3.3 14.3 1.0
O B:ACT604 3.4 16.9 0.5
NZ B:LYS103 3.6 20.4 1.0
NE2 B:HIS136 3.8 11.4 1.0
ND1 B:HIS135 4.0 11.1 1.0
CG B:HIS135 4.1 11.4 1.0
CH3 B:ACT603 4.1 13.3 0.5
NE2 B:HIS528 4.1 13.1 1.0
OXT B:ACT603 4.1 11.6 0.5
CD2 B:HIS528 4.1 14.5 1.0
O B:HOH879 4.2 23.4 0.5
CH3 B:ACT604 4.3 16.9 0.5
CE1 B:HIS136 4.3 12.0 1.0
O B:HOH723 4.4 15.4 1.0
CD2 B:HIS136 4.5 11.4 1.0
CE B:LYS103 4.6 19.1 1.0
CD B:LYS103 4.6 17.5 1.0
C B:ACT603 4.6 12.6 0.5
O B:HOH1061 4.6 21.3 0.5
CA B:HIS528 4.8 13.0 1.0
OE1 B:GLN156 4.8 20.2 1.0

Copper binding site 5 out of 8 in 6i3q

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Copper binding site 5 out of 8 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Acetate Ions.


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 Complex with Acetate Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu601

b:16.7
occ:1.00
 NE2 C:HIS381 2.0 15.1 1.0
NE2 C:HIS206 2.0 13.9 1.0
OXT C:ACT603 2.1 12.4 0.5
OD2 C:ASP314 2.2 15.3 1.0
O C:HOH744 2.4 18.1 1.0
OD1 C:ASP314 2.7 16.8 1.0
CG C:ASP314 2.8 15.2 1.0
CD2 C:HIS381 2.9 15.3 1.0
C C:ACT603 2.9 12.9 0.5
CD2 C:HIS206 3.0 15.7 1.0
CE1 C:HIS206 3.1 16.2 1.0
CE1 C:HIS381 3.1 14.9 1.0
CH3 C:ACT604 3.1 14.4 0.5
CH3 C:ACT603 3.4 14.1 0.5
O C:ACT603 3.9 13.2 0.5
CG C:HIS381 4.1 14.4 1.0
CG C:HIS206 4.1 13.5 1.0
ND1 C:HIS381 4.1 15.2 1.0
ND1 C:HIS206 4.1 14.4 1.0
CB C:ASP314 4.3 16.4 1.0
O C:HOH743 4.4 17.7 1.0
OG1 C:THR548 4.4 17.1 1.0
C C:ACT604 4.6 14.0 0.5
O C:PHE436 4.8 18.8 1.0
CG1 C:VAL205 4.9 14.0 1.0

Copper binding site 6 out of 8 in 6i3q

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Copper binding site 6 out of 8 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Acetate Ions.


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 Complex with Acetate Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu602

b:14.0
occ:0.80
 O C:ACT604 1.9 12.9 0.5
ND1 C:HIS528 2.0 13.3 1.0
NE2 C:HIS135 2.0 11.3 1.0
O C:HOH801 2.3 14.7 0.5
O C:HOH702 2.4 11.4 0.5
C C:ACT604 2.7 14.0 0.5
CE1 C:HIS528 2.9 13.9 1.0
OXT C:ACT604 3.0 15.9 0.5
CD2 C:HIS135 3.0 10.0 1.0
CE1 C:HIS135 3.0 10.6 1.0
CG C:HIS528 3.0 11.7 1.0
CB C:HIS528 3.4 10.8 1.0
NZ C:LYS103 3.6 18.5 1.0
NE2 C:HIS136 3.7 11.6 1.0
OE1 C:GLU288 3.9 18.3 0.5
CH3 C:ACT604 4.0 14.4 0.5
O C:ACT603 4.1 13.2 0.5
NE2 C:HIS528 4.1 12.2 1.0
O C:HOH701 4.1 16.7 0.5
ND1 C:HIS135 4.1 11.2 1.0
CG C:HIS135 4.1 10.4 1.0
CD2 C:HIS528 4.1 12.8 1.0
CH3 C:ACT603 4.2 14.1 0.5
CE1 C:HIS136 4.3 11.8 1.0
O C:HOH806 4.4 13.3 1.0
CE C:LYS103 4.5 17.2 1.0
CD2 C:HIS136 4.5 12.9 1.0
CD C:LYS103 4.6 14.8 1.0
C C:ACT603 4.6 12.9 0.5
OE2 C:GLU288 4.7 20.5 0.5
CA C:HIS528 4.8 11.1 1.0
CD C:GLU288 4.8 19.1 0.5
OE1 C:GLN156 4.9 18.2 1.0
O C:HOH710 5.0 28.3 1.0

Copper binding site 7 out of 8 in 6i3q

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Copper binding site 7 out of 8 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Acetate Ions.


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 Complex with Acetate Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu601

b:16.3
occ:1.00
 NE2 D:HIS206 2.0 12.9 1.0
O D:ACT603 2.0 15.5 0.5
NE2 D:HIS381 2.0 18.3 1.0
OD2 D:ASP314 2.1 16.7 1.0
O D:HOH767 2.4 21.8 1.0
C D:ACT603 2.7 14.7 0.5
CG D:ASP314 2.8 16.9 1.0
OD1 D:ASP314 2.8 17.9 1.0
CD2 D:HIS206 2.9 13.5 1.0
CE1 D:HIS206 2.9 13.3 1.0
CD2 D:HIS381 2.9 18.2 1.0
CH3 D:ACT603 3.0 14.1 0.5
CE1 D:HIS381 3.0 19.0 1.0
CH3 D:ACT604 3.2 18.4 0.5
OXT D:ACT603 3.9 14.1 0.5
ND1 D:HIS206 4.0 13.6 1.0
CG D:HIS206 4.1 12.6 1.0
ND1 D:HIS381 4.1 18.9 1.0
CG D:HIS381 4.1 16.7 1.0
CB D:ASP314 4.2 16.0 1.0
O D:HOH742 4.3 14.8 1.0
OG1 D:THR548 4.5 17.4 1.0
C D:ACT604 4.6 18.6 0.5
O D:PHE436 4.7 15.8 1.0
CG1 D:VAL205 4.9 14.0 1.0

Copper binding site 8 out of 8 in 6i3q

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Copper binding site 8 out of 8 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Acetate Ions.


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 Complex with Acetate Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu602

b:13.9
occ:0.80
 O D:ACT604 2.0 16.1 0.5
NE2 D:HIS135 2.0 12.5 1.0
ND1 D:HIS528 2.0 13.9 1.0
O D:HOH801 2.2 14.8 0.5
CE1 D:HIS528 2.9 13.6 1.0
C D:ACT604 2.9 18.6 0.5
CE1 D:HIS135 3.0 12.2 1.0
CD2 D:HIS135 3.0 13.1 1.0
CG D:HIS528 3.0 12.4 1.0
OXT D:ACT604 3.3 19.2 0.5
CB D:HIS528 3.4 11.5 1.0
NZ D:LYS103 3.6 17.4 1.0
NE2 D:HIS136 3.8 13.3 1.0
NE2 D:HIS528 4.1 12.7 1.0
ND1 D:HIS135 4.1 12.5 1.0
OXT D:ACT603 4.1 14.1 0.5
CG D:HIS135 4.1 12.1 1.0
CD2 D:HIS528 4.1 12.2 1.0
CH3 D:ACT604 4.2 18.4 0.5
CE1 D:HIS136 4.4 13.1 1.0
O D:HOH796 4.5 14.6 1.0
CE D:LYS103 4.5 14.5 1.0
CH3 D:ACT603 4.5 14.1 0.5
CD2 D:HIS136 4.5 13.1 1.0
CD D:LYS103 4.6 14.4 1.0
C D:ACT603 4.8 14.7 0.5
OE1 D:GLU288 4.8 27.1 0.5
CA D:HIS528 4.8 10.3 1.0
OE1 D:GLN156 4.9 18.5 1.0

Reference:

K.M.Polyakov, S.I.Tsallagov, T.V.Tikhkonova, V.O.Popov. The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus Complex with Cu(I) Ions. To Be Published.
Page generated: Wed Jul 31 06:12:52 2024

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