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Copper in PDB 6g50: The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated.

Protein crystallography data

The structure of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated., PDB code: 6g50 was solved by K.M.Polyakov, S.I.Tsallagov, T.V.Tikhkonova, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.31 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.630, 162.280, 90.570, 90.00, 119.51, 90.00
R / Rfree (%) 14.3 / 20.7

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Copper atom in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated. (pdb code 6g50). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 13 binding sites of Copper where determined in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated., PDB code: 6g50:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 13 in 6g50

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Copper binding site 1 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated.


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 As Isolated. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:20.8
occ:0.40
 OD2 A:ASP314 1.9 29.2 0.5
OD2 A:ASP314 2.0 33.4 0.5
NE2 A:HIS381 2.0 22.7 0.5
NE2 A:HIS206 2.1 15.6 1.0
CD2 A:HIS381 2.6 23.3 0.5
CG A:ASP314 2.8 23.2 0.5
CD2 A:HIS206 3.0 13.9 1.0
OD1 A:ASP314 3.0 22.4 0.5
CE1 A:HIS206 3.1 13.5 1.0
CG A:ASP314 3.2 28.8 0.5
CE1 A:HIS381 3.2 23.5 0.5
CE1 A:HIS437 3.3 29.8 1.0
O2 A:SO4604 3.4 32.0 1.0
O4 A:SO4604 3.5 26.0 1.0
O A:HOH730 3.5 23.7 1.0
NE2 A:HIS437 3.7 32.9 1.0
S A:SO4604 3.8 32.2 1.0
CG A:HIS381 3.9 23.5 0.5
O3 A:SO4604 4.0 31.2 1.0
CB A:ASP314 4.0 24.3 0.5
OD1 A:ASP314 4.1 31.6 0.5
ND1 A:HIS381 4.1 24.5 0.5
ND1 A:HIS206 4.2 15.1 1.0
CG A:HIS206 4.2 13.5 1.0
CB A:ASP314 4.2 21.9 0.5
O A:HOH701 4.2 17.3 0.5
ND1 A:HIS437 4.5 26.2 1.0
CD2 A:HIS381 4.7 15.3 0.5
OG1 A:THR548 4.8 20.6 1.0
O A:HIS381 4.8 22.1 0.5
CG A:HIS381 4.8 16.6 0.5

Copper binding site 2 out of 13 in 6g50

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Copper binding site 2 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated.


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 As Isolated. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:27.4
occ:0.20
 NH1 A:ARG193 1.9 17.8 1.0
CZ A:ARG193 2.6 22.6 1.0
NH2 A:ARG193 2.7 23.1 1.0
NH2 A:ARG181 3.5 14.2 1.0
CZ A:ARG181 3.5 14.2 1.0
NH1 A:ARG181 3.6 15.7 1.0
O A:HOH855 3.9 17.4 1.0
NE2 A:GLN192 3.9 18.2 1.0
OD2 A:ASP234 3.9 17.7 1.0
NE A:ARG193 3.9 20.5 1.0
O A:ARG231 4.1 14.6 1.0
OE2 A:GLU150 4.2 18.7 1.0
CD A:GLN192 4.2 17.4 1.0
NE A:ARG181 4.2 13.9 1.0
O A:HOH889 4.3 27.5 1.0
OE1 A:GLN192 4.4 16.2 1.0
O A:HOH854 4.4 23.3 1.0
CG A:ARG181 4.5 12.7 1.0
CB A:ARG181 4.6 12.2 1.0
CD A:ARG193 4.7 21.5 1.0
CB A:GLN192 4.8 14.1 1.0
O A:GLU232 4.9 15.7 1.0
O A:HOH756 4.9 39.5 1.0
CG A:ASP234 4.9 16.4 1.0
CD A:ARG181 4.9 12.3 1.0
O A:HOH807 5.0 14.1 1.0

Copper binding site 3 out of 13 in 6g50

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Copper binding site 3 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated.


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 As Isolated. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:33.6
occ:0.35
 OD2 A:ASP88 2.1 37.7 1.0
CG A:ASP88 2.9 34.9 1.0
N A:LYS85 2.9 24.4 1.0
O A:HOH947 3.2 29.4 1.0
OD1 A:ASP88 3.5 37.0 1.0
O A:LYS85 3.6 24.8 1.0
CA A:VAL84 3.7 28.6 1.0
C A:VAL84 3.8 26.1 1.0
CA A:LYS85 3.9 22.1 1.0
CB A:LYS85 3.9 22.6 1.0
CB A:ASP88 4.0 30.0 1.0
CG1 A:VAL84 4.1 29.5 1.0
O A:TYR83 4.1 33.0 1.0
C A:LYS85 4.2 21.6 1.0
CB A:VAL84 4.5 30.5 1.0
CG A:LYS85 4.6 24.0 1.0
O A:HOH1013 4.6 39.6 1.0
O A:HOH915 4.6 29.1 1.0
N A:VAL84 4.8 30.2 1.0
C A:TYR83 4.9 33.6 1.0

Copper binding site 4 out of 13 in 6g50

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Copper binding site 4 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated.


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 As Isolated. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu601

b:21.9
occ:0.30
 NE2 B:HIS206 2.1 16.1 1.0
O B:HOH1001 2.4 31.4 0.5
CD2 B:HIS206 3.0 14.7 1.0
CE1 B:HIS206 3.1 15.6 1.0
O3 B:SO4605 3.2 27.5 1.0
CE1 B:HIS437 3.3 24.0 1.0
O1 B:SO4605 3.4 26.8 1.0
NE2 B:HIS437 3.5 24.1 1.0
S B:SO4605 3.6 29.0 1.0
O2 B:SO4605 3.7 26.9 1.0
CB B:ASP314 4.2 21.9 1.0
CG B:HIS206 4.2 15.1 1.0
ND1 B:HIS206 4.2 15.6 1.0
O B:HOH713 4.2 23.8 1.0
ND1 B:HIS437 4.6 21.6 1.0
CD2 B:HIS381 4.8 26.1 1.0
OG1 B:THR548 4.8 18.4 1.0
CD2 B:HIS437 4.9 23.3 1.0
CG B:HIS381 4.9 25.9 1.0
CB B:HIS381 4.9 24.4 1.0
CB B:THR548 5.0 17.9 1.0
CG1 B:VAL205 5.0 11.2 1.0

Copper binding site 5 out of 13 in 6g50

Go back to Copper Binding Sites List in 6g50
Copper binding site 5 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated.


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 As Isolated. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:15.2
occ:0.10
 O B:HOH769 2.0 15.7 1.0
O4 B:SO4605 2.0 26.0 1.0
ND1 B:HIS528 2.0 13.8 1.0
NE2 B:HIS135 2.3 12.7 1.0
S B:SO4605 2.9 29.0 1.0
O2 B:SO4605 2.9 26.9 1.0
CE1 B:HIS528 3.0 14.3 1.0
CG B:HIS528 3.0 13.9 1.0
CD2 B:HIS135 3.2 12.4 1.0
CE1 B:HIS135 3.3 13.0 1.0
CB B:HIS528 3.4 13.8 1.0
NZ B:LYS103 3.7 12.6 1.0
NE2 B:HIS136 3.8 16.0 1.0
O1 B:SO4605 3.8 26.8 1.0
O3 B:SO4605 4.0 27.5 1.0
NE2 B:HIS528 4.1 14.1 1.0
CD2 B:HIS528 4.1 14.5 1.0
CE1 B:HIS136 4.2 13.8 1.0
O B:HOH823 4.3 18.9 1.0
OE1 B:GLU288 4.3 17.7 1.0
CG B:HIS135 4.4 11.2 1.0
ND1 B:HIS135 4.4 12.0 1.0
O B:HOH713 4.5 23.8 1.0
O B:HOH1026 4.5 29.9 1.0
CE B:LYS103 4.6 12.0 1.0
CD2 B:HIS136 4.7 14.4 1.0
CA B:HIS528 4.8 13.0 1.0
ND1 B:HIS482 4.8 17.8 1.0
CE1 B:HIS482 4.8 16.7 1.0
CD B:LYS103 4.8 12.2 1.0
OH B:TYR164 4.9 20.9 1.0

Copper binding site 6 out of 13 in 6g50

Go back to Copper Binding Sites List in 6g50
Copper binding site 6 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated.


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 As Isolated. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu603

b:35.1
occ:0.20
 NH2 B:ARG193 2.1 27.3 1.0
CZ B:ARG193 2.9 30.8 1.0
NH1 B:ARG193 3.4 32.5 1.0
O B:ARG231 3.6 16.1 1.0
O B:HOH871 3.6 19.7 1.0
O B:GLU232 3.6 17.8 1.0
O B:HOH810 3.8 21.0 1.0
NE B:ARG193 4.0 32.8 1.0
NH1 B:ARG181 4.0 13.5 1.0
NH2 B:ARG181 4.2 12.7 1.0
OD2 B:ASP234 4.2 17.3 1.0
CZ B:ARG181 4.3 12.9 1.0
C B:GLU232 4.3 16.6 1.0
CA B:GLU232 4.4 17.4 1.0
OE2 B:GLU150 4.6 20.3 1.0
NE2 B:GLN192 4.7 17.9 1.0
C B:ARG231 4.7 16.0 1.0

Copper binding site 7 out of 13 in 6g50

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Copper binding site 7 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated.


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 As Isolated. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:25.9
occ:0.25
 OG B:SER397 2.2 21.2 1.0
O B:ASN396 2.8 18.9 1.0
O B:THR435 2.9 18.5 1.0
CB B:SER397 2.9 18.7 1.0
CA B:SER397 3.1 17.8 1.0
OG1 B:THR435 3.3 19.6 1.0
C B:ASN396 3.3 16.6 1.0
N B:THR435 3.5 21.1 1.0
N B:SER397 3.5 18.9 1.0
CB B:ASN434 3.5 18.4 1.0
C B:THR435 3.7 19.2 1.0
CA B:ASN434 3.7 19.9 1.0
OD1 B:ASN401 3.8 19.4 1.0
CE1 B:HIS381 3.9 26.6 1.0
C B:ASN434 3.9 21.4 1.0
CB B:MET395 4.0 19.1 1.0
O B:HOH1011 4.0 23.8 1.0
CA B:THR435 4.1 19.9 1.0
CG B:ASN434 4.3 18.6 1.0
CB B:THR435 4.3 19.1 1.0
ND2 B:ASN434 4.4 17.9 1.0
ND1 B:HIS381 4.5 25.5 1.0
C B:MET395 4.5 18.4 1.0
C B:SER397 4.5 18.1 1.0
CA B:ASN396 4.5 16.2 1.0
O B:MET395 4.6 18.0 1.0
N B:ASN396 4.6 16.3 1.0
NE2 B:HIS381 4.7 25.5 1.0
CG B:ASN401 4.8 17.8 1.0
N B:LEU398 4.8 16.9 1.0
O B:ASN434 4.9 23.8 1.0
CA B:MET395 4.9 18.0 1.0
N B:PHE436 4.9 18.3 1.0
CA B:ASN401 5.0 17.9 1.0

Copper binding site 8 out of 13 in 6g50

Go back to Copper Binding Sites List in 6g50
Copper binding site 8 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated.


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 As Isolated. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu601

b:19.2
occ:0.40
 OD2 C:ASP314 2.0 20.1 0.5
NE2 C:HIS381 2.0 20.0 0.5
NE2 C:HIS206 2.1 14.3 1.0
O C:HOH716 2.5 25.4 1.0
OD1 C:ASP314 2.6 17.5 0.5
CG C:ASP314 2.6 17.4 0.5
CD2 C:HIS381 2.8 19.9 0.5
CD2 C:HIS206 2.8 13.7 1.0
CE1 C:HIS381 3.1 20.9 0.5
O3 C:SO4606 3.1 20.7 0.3
CE1 C:HIS206 3.2 13.2 1.0
OD2 C:ASP314 3.4 17.4 0.5
O1 C:SO4606 3.5 20.6 0.3
S C:SO4606 3.7 20.9 0.3
O2 C:SO4606 3.8 19.5 0.3
O3 C:SO4606 3.9 23.9 0.7
CB C:ASP314 3.9 16.4 0.5
CG C:ASP314 4.0 16.0 0.5
CG C:HIS381 4.0 19.1 0.5
CG C:HIS206 4.0 13.6 1.0
O C:HOH701 4.1 17.4 0.5
ND1 C:HIS381 4.1 18.5 0.5
CB C:ASP314 4.1 16.9 0.5
ND1 C:HIS206 4.2 14.8 1.0
O C:HOH708 4.3 20.0 1.0
CD2 C:HIS381 4.5 28.6 0.5
OG1 C:THR548 4.6 23.8 1.0
O C:HOH734 4.7 21.3 1.0
CE1 C:HIS437 4.7 32.1 1.0
CB C:HIS381 4.8 24.7 0.5
CG1 C:VAL205 4.9 14.2 1.0
CG C:HIS381 5.0 26.2 0.5
OD1 C:ASP314 5.0 15.5 0.5

Copper binding site 9 out of 13 in 6g50

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Copper binding site 9 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated.


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 As Isolated. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu602

b:29.4
occ:0.30
 OG C:SER397 1.7 25.4 1.0
O C:HOH779 1.8 23.0 0.9
O C:THR435 2.8 20.8 1.0
CB C:SER397 2.8 20.2 1.0
O C:ASN396 2.8 16.1 1.0
O C:HOH727 3.1 8.5 0.5
CA C:SER397 3.1 16.9 1.0
N C:THR435 3.3 24.6 1.0
CE1 C:HIS381 3.3 29.6 0.5
C C:ASN396 3.4 16.1 1.0
N C:SER397 3.6 16.6 1.0
CB C:ASN434 3.6 21.5 1.0
C C:THR435 3.7 25.3 1.0
CA C:ASN434 3.7 20.5 1.0
C C:ASN434 3.7 24.4 1.0
OD1 C:ASN401 3.8 16.8 1.0
CA C:THR435 4.0 29.8 1.0
CB C:MET395 4.0 27.7 1.0
ND1 C:HIS381 4.0 27.8 0.5
O C:HOH1014 4.1 24.4 0.5
NE2 C:HIS381 4.3 29.8 0.5
CG C:MET395 4.3 33.9 1.0
CG C:ASN434 4.4 22.6 1.0
C C:SER397 4.4 17.9 1.0
CD1 C:PHE436 4.5 22.5 0.5
CB C:THR435 4.5 32.8 1.0
CE1 C:PHE436 4.6 20.6 0.5
ND2 C:ASN434 4.7 16.3 1.0
CA C:ASN396 4.7 17.9 1.0
C C:MET395 4.7 19.8 1.0
N C:ASN396 4.7 17.3 1.0
O C:ASN434 4.7 28.1 1.0
N C:LEU398 4.8 17.9 1.0
N C:PHE436 4.8 26.3 1.0
CG C:ASN401 4.8 18.3 1.0
O C:MET395 4.9 18.2 1.0
CA C:MET395 4.9 21.4 1.0
OG1 C:THR435 5.0 42.3 1.0
CA C:ASN401 5.0 18.5 1.0

Copper binding site 10 out of 13 in 6g50

Go back to Copper Binding Sites List in 6g50
Copper binding site 10 out of 13 in the The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu603

b:25.4
occ:0.20
 OD1 C:ASP88 2.2 27.7 1.0
OD2 C:ASP91 2.7 29.4 1.0
CG C:ASP88 3.3 27.8 1.0
N C:ASP88 3.3 21.8 1.0
C C:GLN87 3.4 20.6 1.0
CG C:GLN87 3.4 20.6 1.0
CB C:GLN87 3.5 19.7 1.0
CA C:ASP88 3.5 22.8 1.0
O C:HOH980 3.5 34.7 1.0
O C:GLN87 3.6 23.4 1.0
CG C:ASP91 3.8 23.7 1.0
CB C:ASP88 4.0 26.3 1.0
CA C:GLN87 4.1 19.6 1.0
OD2 C:ASP88 4.2 30.4 1.0
OD1 C:ASP91 4.5 25.8 1.0
O C:HOH740 4.5 27.0 1.0
CD C:GLN87 4.7 22.7 1.0
CB C:ASP91 4.8 22.6 1.0
CD C:LYS85 4.8 30.0 1.0
C C:ASP88 4.9 21.6 1.0
N C:GLN87 4.9 19.3 1.0
NE2 C:GLN87 5.0 20.5 1.0
CB C:LYS85 5.0 23.5 1.0

Reference:

K.M.Polyakov, S.I.Tsallagov, T.V.Tikhkonova, V.O.Popov. The Structure of Thiocyanate Dehydrogenase From Thioalkalivibrio Paradoxus As Isolated. To Be Published.
Page generated: Wed Jul 31 06:05:43 2024

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