Copper in PDB 8p3l: The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus

Protein crystallography data

The structure of The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus, PDB code: 8p3l was solved by L.A.Varfolomeeva, K.M.Polyakov, A.S.Komolov, T.V.Rakitina, N.I.Dergousova, P.V.Dorovatovskii, 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) 81.12 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.81, 162.24, 90.76, 90, 119.74, 90
R / Rfree (%) 18.6 / 25.4

Copper Binding Sites:

The binding sites of Copper atom in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus (pdb code 8p3l). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 10 binding sites of Copper where determined in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus, PDB code: 8p3l:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 10 in 8p3l

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Copper binding site 1 out of 10 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:15.7
occ:1.00
 O A:HOH702 1.9 9.4 1.0
NE2 A:HIS206 2.0 13.3 1.0
NE2 A:HIS381 2.1 27.8 1.0
OD1 A:ASP314 2.4 18.0 1.0
OD2 A:ASP314 2.9 17.8 1.0
CG A:ASP314 2.9 19.4 1.0
CE1 A:HIS206 3.0 14.4 1.0
CE1 A:HIS381 3.1 27.2 1.0
CD2 A:HIS206 3.1 12.5 1.0
CD2 A:HIS381 3.1 29.7 1.0
O4 A:SO4603 4.1 8.5 0.5
ND1 A:HIS206 4.1 11.3 1.0
ND1 A:HIS381 4.2 25.8 1.0
O A:HOH770 4.2 5.7 1.0
CG A:HIS206 4.2 11.9 1.0
CG A:HIS381 4.2 29.5 1.0
OG1 A:THR548 4.4 25.2 1.0
CB A:ASP314 4.4 15.1 1.0
O A:HOH717 4.8 14.8 1.0
CE1 A:HIS437 4.9 11.4 1.0
CG1 A:VAL205 4.9 10.1 1.0
O A:PHE436 5.0 12.3 1.0

Copper binding site 2 out of 10 in 8p3l

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Copper binding site 2 out of 10 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:22.4
occ:1.00
 ND1 A:HIS528 1.8 11.8 1.0
NZ A:LYS103 1.9 22.6 1.0
NE2 A:HIS135 1.9 10.2 1.0
O A:HOH757 2.5 3.5 0.5
CE1 A:HIS528 2.8 13.4 1.0
CG A:HIS528 2.8 13.6 1.0
CD2 A:HIS135 2.9 12.1 1.0
CE1 A:HIS135 3.0 9.6 1.0
CB A:HIS528 3.2 11.8 1.0
CE A:LYS103 3.3 22.3 1.0
O A:HOH782 3.4 4.7 0.5
O A:HOH770 3.6 5.7 1.0
NE2 A:HIS528 3.9 12.4 1.0
CD2 A:HIS528 3.9 15.5 1.0
CD A:LYS103 4.0 22.1 1.0
O2 A:SO4603 4.0 8.4 0.5
ND1 A:HIS135 4.0 13.8 1.0
CG A:HIS135 4.0 15.2 1.0
OH A:TYR164 4.1 30.3 1.0
NE2 A:HIS136 4.1 12.1 1.0
OE1 A:GLU288 4.2 19.9 1.0
CE1 A:HIS136 4.5 10.5 1.0
CA A:HIS528 4.8 14.2 1.0
OE1 A:GLN156 4.8 19.2 1.0
O A:HOH800 4.9 17.7 1.0
O A:HOH775 5.0 10.3 1.0

Copper binding site 3 out of 10 in 8p3l

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Copper binding site 3 out of 10 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu601

b:18.9
occ:1.00
 NE2 D:HIS206 2.1 19.8 1.0
NE2 D:HIS381 2.1 10.0 1.0
OD1 D:ASP314 2.3 12.5 1.0
OD2 D:ASP314 2.3 9.1 1.0
CG D:ASP314 2.6 13.1 1.0
O D:HOH732 2.7 17.9 1.0
CD2 D:HIS381 2.9 11.7 1.0
CE1 D:HIS206 3.0 17.1 1.0
CD2 D:HIS206 3.2 15.5 1.0
CE1 D:HIS381 3.2 10.3 1.0
CB D:ASP314 4.1 13.6 1.0
CG D:HIS381 4.1 14.4 1.0
ND1 D:HIS206 4.1 21.8 1.0
ND1 D:HIS381 4.2 12.5 1.0
O3 D:SO4604 4.2 12.2 0.7
CG D:HIS206 4.3 17.6 1.0
OG1 D:THR548 4.5 15.9 1.0
O D:HOH753 4.5 11.4 1.0
O D:HOH767 4.6 1.5 0.2
CE1 D:HIS437 4.8 21.7 1.0
O D:PHE436 4.9 14.7 1.0
O D:HOH711 4.9 11.9 1.0
O D:ASP314 4.9 17.7 1.0

Copper binding site 4 out of 10 in 8p3l

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Copper binding site 4 out of 10 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu602

b:14.7
occ:0.80
 CU D:CU602 0.0 14.7 0.8
CU D:CU602 1.1 6.2 0.2
ND1 D:HIS528 1.7 5.1 1.0
O D:HOH747 1.9 5.6 0.8
NE2 D:HIS135 2.0 11.2 1.0
CE1 D:HIS528 2.4 5.0 1.0
NZ D:LYS103 2.8 15.0 1.0
CD2 D:HIS135 2.8 21.4 1.0
CG D:HIS528 2.9 7.1 1.0
CE1 D:HIS135 3.0 14.2 1.0
CE D:LYS103 3.1 10.1 1.0
O D:HOH767 3.4 1.5 0.2
CB D:HIS528 3.6 9.4 1.0
NE2 D:HIS528 3.7 8.3 1.0
CD D:LYS103 3.8 15.8 1.0
OH D:TYR164 3.9 20.8 1.0
CD2 D:HIS528 3.9 6.3 1.0
CG D:HIS135 4.0 18.3 1.0
OE1 D:GLN156 4.0 17.3 1.0
ND1 D:HIS135 4.0 18.7 1.0
OE1 D:GLU288 4.2 9.6 1.0
O4 D:SO4604 4.3 13.3 0.7
O D:HOH712 4.3 9.9 1.0
NE2 D:HIS136 4.3 10.4 1.0
CE1 D:HIS136 4.5 16.2 1.0
CD D:GLN156 4.9 16.0 1.0
OE2 D:GLU288 5.0 13.1 1.0

Copper binding site 5 out of 10 in 8p3l

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Copper binding site 5 out of 10 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu602

b:6.2
occ:0.20
 CU D:CU602 0.0 6.2 0.2
O D:HOH747 0.9 5.6 0.8
CU D:CU602 1.1 14.7 0.8
ND1 D:HIS528 1.8 5.1 1.0
NE2 D:HIS135 2.1 11.2 1.0
CE1 D:HIS528 2.6 5.0 1.0
O D:HOH767 2.7 1.5 0.2
CG D:HIS528 2.8 7.1 1.0
CE1 D:HIS135 3.1 14.2 1.0
CD2 D:HIS135 3.2 21.4 1.0
CB D:HIS528 3.3 9.4 1.0
O4 D:SO4604 3.5 13.3 0.7
NE2 D:HIS136 3.7 10.4 1.0
CE1 D:HIS136 3.8 16.2 1.0
NE2 D:HIS528 3.8 8.3 1.0
CD2 D:HIS528 3.8 6.3 1.0
NZ D:LYS103 3.9 15.0 1.0
CE D:LYS103 4.1 10.1 1.0
ND1 D:HIS135 4.3 18.7 1.0
O D:HOH814 4.3 13.4 1.0
CG D:HIS135 4.3 18.3 1.0
OE1 D:GLU288 4.4 9.6 1.0
CA D:HIS528 4.6 11.6 1.0
O D:HOH732 4.7 17.9 1.0
OE2 D:GLU288 4.7 13.1 1.0
CD D:LYS103 4.7 15.8 1.0
OH D:TYR164 4.7 20.8 1.0
S D:SO4604 4.8 14.1 0.7
OE1 D:GLN156 4.8 17.3 1.0
O D:HIS528 4.8 15.3 1.0
O3 D:SO4604 4.9 12.2 0.7
CD2 D:HIS136 4.9 14.5 1.0
ND1 D:HIS136 4.9 18.4 1.0
CD D:GLU288 5.0 12.3 1.0

Copper binding site 6 out of 10 in 8p3l

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Copper binding site 6 out of 10 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu601

b:12.7
occ:1.00
 O G:HOH748 1.9 8.8 1.0
O G:HOH741 1.9 4.8 0.5
NE2 G:HIS206 1.9 7.5 1.0
NE2 G:HIS381 2.0 9.4 1.0
OD1 G:ASP314 2.2 9.5 1.0
OD2 G:ASP314 2.8 18.8 1.0
CG G:ASP314 2.8 20.6 1.0
CE1 G:HIS206 2.8 8.1 1.0
CD2 G:HIS206 3.0 7.8 1.0
CE1 G:HIS381 3.0 11.0 1.0
CD2 G:HIS381 3.0 13.8 1.0
O G:HOH733 3.9 7.7 0.5
ND1 G:HIS206 3.9 8.2 1.0
CG G:HIS206 4.0 10.1 1.0
OG1 G:THR548 4.1 18.4 1.0
ND1 G:HIS381 4.1 12.4 1.0
CG G:HIS381 4.1 12.9 1.0
O4 G:SO4606 4.2 18.8 1.0
CB G:ASP314 4.3 17.6 1.0
O G:HOH723 4.6 10.3 1.0
CE1 G:HIS437 4.6 14.7 1.0
O G:PHE436 4.7 21.9 1.0
NE2 G:HIS136 4.9 13.1 1.0
CE1 G:HIS136 4.9 13.5 1.0
CG1 G:VAL205 5.0 17.5 1.0

Copper binding site 7 out of 10 in 8p3l

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Copper binding site 7 out of 10 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu602

b:17.1
occ:0.70
 CU G:CU602 0.0 17.1 0.7
CU G:CU602 0.7 15.1 0.3
NZ G:LYS103 1.6 17.8 1.0
ND1 G:HIS528 1.7 23.7 1.0
O G:HOH766 1.9 13.5 0.8
NE2 G:HIS135 1.9 14.5 1.0
CE1 G:HIS528 2.7 24.5 1.0
CG G:HIS528 2.8 27.4 1.0
CD2 G:HIS135 2.9 10.5 1.0
CE1 G:HIS135 3.0 10.2 1.0
CE G:LYS103 3.1 11.9 1.0
CB G:HIS528 3.2 22.7 1.0
CD G:LYS103 3.6 12.9 1.0
NE2 G:HIS528 3.9 23.9 1.0
CD2 G:HIS528 3.9 26.7 1.0
CG G:HIS135 4.0 9.0 1.0
ND1 G:HIS135 4.0 9.8 1.0
O G:HOH733 4.0 7.7 0.5
O1 G:SO4606 4.1 22.2 1.0
OH G:TYR164 4.2 43.3 1.0
OE1 G:GLN156 4.3 19.6 1.0
OE1 G:GLU288 4.3 11.4 1.0
NE2 G:HIS136 4.4 13.1 1.0
CA G:HIS528 4.7 22.7 1.0
O G:HOH732 4.9 18.1 1.0
CE1 G:HIS136 4.9 13.5 1.0

Copper binding site 8 out of 10 in 8p3l

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Copper binding site 8 out of 10 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala 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 The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu602

b:15.1
occ:0.30
 CU G:CU602 0.0 15.1 0.3
CU G:CU602 0.7 17.1 0.7
ND1 G:HIS528 1.8 23.7 1.0
O G:HOH766 1.9 13.5 0.8
NE2 G:HIS135 2.1 14.5 1.0
NZ G:LYS103 2.3 17.8 1.0
CG G:HIS528 2.8 27.4 1.0
CE1 G:HIS528 2.8 24.5 1.0
CE1 G:HIS135 3.1 10.2 1.0
CB G:HIS528 3.2 22.7 1.0
CD2 G:HIS135 3.2 10.5 1.0
O G:HOH733 3.4 7.7 0.5
O1 G:SO4606 3.6 22.2 1.0
CE G:LYS103 3.8 11.9 1.0
CD2 G:HIS528 3.9 26.7 1.0
NE2 G:HIS528 4.0 23.9 1.0
NE2 G:HIS136 4.0 13.1 1.0
ND1 G:HIS135 4.2 9.8 1.0
CD G:LYS103 4.2 12.9 1.0
O G:HOH732 4.2 18.1 1.0
CG G:HIS135 4.3 9.0 1.0
OE1 G:GLU288 4.3 11.4 1.0
CE1 G:HIS136 4.4 13.5 1.0
CA G:HIS528 4.6 22.7 1.0
OH G:TYR164 4.6 43.3 1.0
CD2 G:HIS136 4.8 12.2 1.0
OE1 G:GLN156 4.8 19.6 1.0
S G:SO4606 4.8 19.6 1.0

Copper binding site 9 out of 10 in 8p3l

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Copper binding site 9 out of 10 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus


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 Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cu601

b:23.3
occ:1.00
 O J:HOH711 1.9 21.9 1.0
NE2 J:HIS381 2.0 11.8 1.0
NE2 J:HIS206 2.1 13.3 1.0
OD2 J:ASP314 2.3 21.7 1.0
OD1 J:ASP314 2.8 23.4 1.0
CD2 J:HIS206 2.8 14.5 1.0
CD2 J:HIS381 2.9 13.6 1.0
CG J:ASP314 2.9 20.5 1.0
CE1 J:HIS381 3.0 13.9 1.0
CE1 J:HIS206 3.2 13.3 1.0
ND1 J:HIS381 4.0 16.1 1.0
CG J:HIS381 4.0 12.8 1.0
CG J:HIS206 4.0 18.5 1.0
O J:HOH708 4.1 28.9 1.0
ND1 J:HIS206 4.2 21.9 1.0
O J:HOH714 4.2 13.5 1.0
O1 J:SO4603 4.4 23.9 1.0
CB J:ASP314 4.4 23.1 1.0
O J:HOH773 4.4 17.1 1.0
OG1 J:THR548 4.6 14.9 1.0
O J:PHE436 4.7 21.8 1.0
CE1 J:HIS437 4.9 18.8 1.0
NE2 J:HIS136 5.0 24.9 1.0

Copper binding site 10 out of 10 in 8p3l

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Copper binding site 10 out of 10 in the The Structure of Thiocyanate Dehydrogenase Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus


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 Mutant Form with Thr 169 Replaced By Ala From Thioalkalivibrio Paradoxus within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cu602

b:19.9
occ:1.00
 O J:HOH734 1.8 11.2 1.0
ND1 J:HIS528 1.9 7.3 1.0
NZ J:LYS103 1.9 16.1 1.0
NE2 J:HIS135 2.2 20.1 1.0
CE1 J:HIS528 2.9 6.0 1.0
CD2 J:HIS135 2.9 19.3 1.0
CG J:HIS528 3.0 7.1 1.0
CE J:LYS103 3.2 24.1 1.0
CB J:HIS528 3.3 11.3 1.0
CE1 J:HIS135 3.4 17.1 1.0
O J:HOH708 3.7 28.9 1.0
CD J:LYS103 3.8 20.6 1.0
NE2 J:HIS528 4.0 5.6 1.0
CD2 J:HIS528 4.0 6.5 1.0
O2 J:SO4603 4.1 18.2 1.0
OE1 J:GLU288 4.1 21.3 1.0
CG J:HIS135 4.1 17.4 1.0
OH J:TYR164 4.3 42.1 1.0
NE2 J:HIS136 4.3 24.9 1.0
ND1 J:HIS135 4.4 16.5 1.0
OE1 J:GLN156 4.5 12.8 1.0
O J:HOH784 4.5 13.5 0.5
OE2 J:GLU288 4.7 18.5 1.0
CD J:GLU288 4.7 18.6 1.0
CE1 J:HIS136 4.8 18.9 1.0
CA J:HIS528 4.9 15.0 1.0

Reference:

L.A.Varfolomeeva, K.M.Polyakov, A.S.Komolov, T.V.Rakitina, N.I.Dergousova, P.V.Dorovatovskii, K.M.Boyko, T.V.Tikhonova, V.O.Popov. Improvement of Diffraction Properties of Thiocyanate Dehydrogenase Crystals To Be Published.
Page generated: Wed Jul 26 17:38:02 2023

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