Copper in PDB 8z77: The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours

Protein crystallography data

The structure of The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours, PDB code: 8z77 was solved by L.A.Varfolomeeva, A.Y.Solovieva, N.S.Shipkov, N.I.Dergousova, M.E.Minyaev, 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) 23.71 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 98.087, 101.987, 276.799, 90, 90, 90
R / Rfree (%) 17.5 / 22.2

Copper Binding Sites:

Pages:

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

Binding sites:

The binding sites of Copper atom in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours (pdb code 8z77). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 11 binding sites of Copper where determined in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours, PDB code: 8z77:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 11 in 8z77

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Copper binding site 1 out of 11 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours


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 Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:15.5
occ:1.00
 NE2 A:HIS346 2.0 18.7 1.0
NE2 A:HIS171 2.0 10.6 1.0
O A:HOH850 2.1 16.4 1.0
OD1 A:ASP279 2.3 11.6 1.0
OD2 A:ASP279 2.5 11.0 1.0
CG A:ASP279 2.7 10.6 1.0
O A:HOH712 2.7 13.2 1.0
CE1 A:HIS346 3.0 17.8 1.0
CD2 A:HIS346 3.0 17.9 1.0
CE1 A:HIS171 3.0 8.6 1.0
CD2 A:HIS171 3.0 8.9 1.0
ND1 A:HIS346 4.1 18.8 1.0
ND1 A:HIS171 4.1 8.5 1.0
CG A:HIS346 4.1 17.8 1.0
CG A:HIS171 4.1 8.6 1.0
CB A:ASP279 4.2 9.8 1.0
O A:HOH722 4.3 18.4 1.0
O A:HOH773 4.3 14.6 1.0
OG1 A:THR513 4.7 15.6 1.0
CG1 A:VAL170 4.7 8.5 1.0
O A:HOH726 4.8 9.6 1.0
CE1 A:HIS402 4.8 13.3 1.0
O A:HOH864 4.8 22.2 0.5
CB A:THR513 5.0 13.8 1.0
NE2 A:HIS101 5.0 7.6 1.0

Copper binding site 2 out of 11 in 8z77

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Copper binding site 2 out of 11 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours


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 Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:9.8
occ:0.50
 CU A:CU602 0.0 9.8 0.5
CU A:CU602 1.4 9.0 0.5
ND1 A:HIS493 1.8 10.4 1.0
NE2 A:HIS100 1.9 11.5 1.0
O A:HOH770 2.0 9.4 1.0
NZ A:LYS68 2.4 9.7 1.0
CE1 A:HIS493 2.6 10.5 1.0
CD2 A:HIS100 2.7 10.7 1.0
CG A:HIS493 2.8 9.4 1.0
CE1 A:HIS100 3.0 11.0 1.0
CE A:LYS68 3.3 9.8 1.0
O A:HOH773 3.3 14.6 1.0
CB A:HIS493 3.3 9.0 1.0
CD A:LYS68 3.7 9.1 1.0
NE2 A:HIS493 3.7 10.3 1.0
CD2 A:HIS493 3.8 10.2 1.0
CG A:HIS100 3.8 10.4 1.0
ND1 A:HIS100 4.0 10.5 1.0
OE1 A:GLU253 4.0 20.0 1.0
OH A:TYR129 4.1 25.1 1.0
OE1 A:GLN121 4.4 17.6 1.0
O A:HOH843 4.5 14.2 1.0
NE2 A:HIS101 4.5 7.6 1.0
O A:HOH864 4.6 22.2 0.5
CA A:HIS493 4.8 8.8 1.0
CD A:GLU253 5.0 18.1 1.0

Copper binding site 3 out of 11 in 8z77

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Copper binding site 3 out of 11 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours


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 Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:9.0
occ:0.50
 CU A:CU602 0.0 9.0 0.5
CU A:CU602 1.4 9.8 0.5
O A:HOH773 2.0 14.6 1.0
O A:HOH770 2.1 9.4 1.0
NE2 A:HIS100 2.1 11.5 1.0
ND1 A:HIS493 2.1 10.4 1.0
CG A:HIS493 3.0 9.4 1.0
CB A:HIS493 3.1 9.0 1.0
CE1 A:HIS100 3.1 11.0 1.0
CD2 A:HIS100 3.1 10.7 1.0
CE1 A:HIS493 3.2 10.5 1.0
O A:HOH864 3.4 22.2 0.5
NE2 A:HIS101 3.6 7.6 1.0
NZ A:LYS68 3.7 9.7 1.0
OE1 A:GLU253 4.0 20.0 1.0
CE1 A:HIS101 4.2 7.4 1.0
CD2 A:HIS493 4.2 10.2 1.0
ND1 A:HIS100 4.2 10.5 1.0
CG A:HIS100 4.2 10.4 1.0
NE2 A:HIS493 4.3 10.3 1.0
OE2 A:GLU253 4.4 18.5 1.0
O A:HOH850 4.5 16.4 1.0
CD2 A:HIS101 4.6 6.9 1.0
CE A:LYS68 4.6 9.8 1.0
CD A:GLU253 4.6 18.1 1.0
CA A:HIS493 4.6 8.8 1.0
CD A:LYS68 4.9 9.1 1.0
CU A:CU603 4.9 20.1 1.0

Copper binding site 4 out of 11 in 8z77

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Copper binding site 4 out of 11 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours


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 Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:20.1
occ:1.00
 ND1 A:HIS447 2.0 14.3 1.0
NE2 A:HIS402 2.0 16.0 1.0
O A:HOH864 2.0 22.2 0.5
CD2 A:HIS402 2.8 13.4 1.0
CE1 A:HIS447 2.9 12.7 1.0
CG A:HIS447 3.0 13.0 1.0
CE1 A:HIS402 3.1 13.3 1.0
CB A:HIS447 3.3 12.2 1.0
CZ A:PHE401 3.4 24.7 1.0
CE1 A:PHE401 3.7 24.9 1.0
CA A:HIS447 3.7 11.7 1.0
O A:HIS493 3.9 8.9 1.0
CG A:HIS402 4.0 13.8 1.0
CE2 A:PHE401 4.0 25.0 1.0
CB A:HIS493 4.0 9.0 1.0
NE2 A:HIS447 4.0 13.2 1.0
ND1 A:HIS402 4.1 14.0 1.0
CD2 A:HIS447 4.1 12.8 1.0
CA A:HIS493 4.2 8.8 1.0
CG A:HIS493 4.4 9.4 1.0
C A:HIS447 4.4 11.5 1.0
C A:HIS493 4.4 8.8 1.0
O A:HOH850 4.4 16.4 1.0
N A:THR448 4.6 10.9 1.0
CD1 A:PHE401 4.6 29.0 1.0
ND1 A:HIS493 4.7 10.4 1.0
CG2 A:THR448 4.8 10.7 1.0
CD2 A:HIS493 4.8 10.2 1.0
O A:MET446 4.9 12.4 1.0
CD2 A:PHE401 4.9 26.3 1.0
CU A:CU602 4.9 9.0 0.5
N A:HIS447 5.0 10.9 1.0

Copper binding site 5 out of 11 in 8z77

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Copper binding site 5 out of 11 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours


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 Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu602

b:14.4
occ:1.00
 NE2 B:HIS346 1.9 14.0 1.0
NE2 B:HIS171 2.1 12.8 1.0
O B:HOH848 2.1 13.1 1.0
OD2 B:ASP279 2.2 13.9 1.0
OD1 B:ASP279 2.4 12.0 1.0
CG B:ASP279 2.7 11.9 1.0
CD2 B:HIS346 2.9 13.7 1.0
OE1 B:GLN347 3.0 12.1 1.0
CE1 B:HIS346 3.0 14.0 1.0
CD2 B:HIS171 3.0 11.8 1.0
CE1 B:HIS171 3.1 11.2 1.0
NE2 B:GLN347 3.5 11.6 1.0
O B:HOH854 3.6 20.1 1.0
CD B:GLN347 3.6 11.7 1.0
ND1 B:HIS346 4.1 14.0 1.0
CG B:HIS346 4.1 13.6 1.0
O B:HOH770 4.2 19.1 1.0
CG B:HIS171 4.2 11.2 1.0
CB B:ASP279 4.2 10.9 1.0
ND1 B:HIS171 4.2 11.6 1.0
O B:HOH716 4.5 10.8 1.0
CG1 B:VAL170 4.6 11.0 1.0
O B:HOH898 4.7 17.8 1.0
CE1 B:HIS402 4.7 12.0 1.0
NE2 B:HIS101 4.9 8.4 1.0
CB B:THR513 5.0 9.8 1.0
OG1 B:THR513 5.0 11.0 1.0
CG2 B:THR513 5.0 9.9 1.0

Copper binding site 6 out of 11 in 8z77

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Copper binding site 6 out of 11 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours


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 Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu603

b:19.1
occ:1.00
 O B:HOH770 1.9 19.1 1.0
ND1 B:HIS493 2.0 13.8 1.0
O B:HOH726 2.1 15.9 0.5
NE2 B:HIS100 2.1 12.5 1.0
O B:HOH898 2.8 17.8 1.0
CG B:HIS493 2.9 11.8 1.0
CE1 B:HIS100 3.0 10.9 1.0
CE1 B:HIS493 3.1 12.3 1.0
CD2 B:HIS100 3.1 10.8 1.0
CB B:HIS493 3.2 11.0 1.0
NE2 B:HIS101 3.6 8.4 1.0
NZ B:LYS68 3.9 10.0 1.0
CD2 B:HIS493 4.1 11.6 1.0
NE2 B:HIS493 4.1 11.7 1.0
OE1 B:GLU253 4.1 22.9 1.0
ND1 B:HIS100 4.2 11.1 1.0
CE1 B:HIS101 4.2 8.1 1.0
CG B:HIS100 4.3 10.8 1.0
O B:HOH854 4.3 20.1 1.0
O B:HOH848 4.4 13.1 1.0
CD2 B:HIS101 4.6 8.2 1.0
CG B:PRO256 4.6 23.9 1.0
CE B:LYS68 4.7 9.9 1.0
CA B:HIS493 4.7 10.0 1.0
O B:HOH712 4.8 18.4 1.0
CU B:CU604 4.8 16.8 1.0
CD B:LYS68 4.9 9.7 1.0
CD B:PRO256 4.9 26.7 1.0
OH B:TYR129 5.0 19.9 1.0

Copper binding site 7 out of 11 in 8z77

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Copper binding site 7 out of 11 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours


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 Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu604

b:16.8
occ:1.00
 ND1 B:HIS447 2.0 12.7 1.0
NE2 B:HIS402 2.0 14.1 1.0
O B:HOH898 2.6 17.8 1.0
CD2 B:HIS402 2.9 12.4 1.0
CE1 B:HIS447 2.9 12.4 1.0
CG B:HIS447 3.0 11.8 1.0
CE1 B:HIS402 3.1 12.0 1.0
CE2 B:PHE401 3.3 17.2 1.0
CB B:HIS447 3.4 10.9 1.0
CZ B:PHE401 3.5 18.6 1.0
O B:HIS493 3.8 9.9 1.0
CA B:HIS447 3.9 10.3 1.0
CB B:HIS493 4.0 11.0 1.0
NE2 B:HIS447 4.0 12.1 1.0
CG B:HIS402 4.1 11.5 1.0
O B:HOH848 4.1 13.1 1.0
CD2 B:HIS447 4.1 11.7 1.0
ND1 B:HIS402 4.1 11.2 1.0
CA B:HIS493 4.1 10.0 1.0
CG B:HIS493 4.3 11.8 1.0
NE2 B:GLN347 4.3 11.6 1.0
CD2 B:PHE401 4.4 15.6 1.0
C B:HIS493 4.4 9.7 1.0
C B:HIS447 4.6 9.8 1.0
CE1 B:PHE401 4.6 17.5 1.0
CD2 B:HIS493 4.7 11.6 1.0
ND1 B:HIS493 4.7 13.8 1.0
O B:HOH770 4.8 19.1 1.0
CG2 B:THR448 4.8 10.1 1.0
CU B:CU603 4.8 19.1 1.0
N B:THR448 4.8 9.2 1.0

Copper binding site 8 out of 11 in 8z77

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Copper binding site 8 out of 11 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours


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 Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu602

b:15.4
occ:1.00
 NE2 C:HIS171 2.0 12.3 1.0
NE2 C:HIS346 2.1 18.2 1.0
O C:HOH832 2.1 16.6 1.0
OD1 C:ASP279 2.1 12.6 1.0
OD2 C:ASP279 2.4 12.4 1.0
CG C:ASP279 2.6 11.3 1.0
CD2 C:HIS171 2.9 11.2 1.0
CE1 C:HIS171 3.0 11.8 1.0
CD2 C:HIS346 3.0 17.2 1.0
OE1 C:GLN347 3.1 28.2 1.0
CE1 C:HIS346 3.1 18.9 1.0
CD C:GLN347 3.8 29.5 1.0
NE2 C:GLN347 3.9 35.3 1.0
CG C:HIS171 4.1 10.9 1.0
ND1 C:HIS171 4.1 11.2 1.0
CB C:ASP279 4.1 11.6 1.0
ND1 C:HIS346 4.2 18.3 1.0
CG C:HIS346 4.2 16.9 1.0
O C:HOH807 4.3 16.0 1.0
O C:HOH884 4.6 10.2 0.5
CG1 C:VAL170 4.6 9.0 1.0
O C:HOH711 4.8 11.4 1.0
OG1 C:THR513 4.9 14.2 1.0
CE1 C:HIS402 4.9 17.7 1.0

Copper binding site 9 out of 11 in 8z77

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Copper binding site 9 out of 11 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours


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 Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu603

b:12.6
occ:0.50
 CU C:CU603 0.0 12.6 0.5
CU C:CU603 1.5 9.4 0.5
ND1 C:HIS493 1.7 11.8 1.0
NE2 C:HIS100 1.9 11.5 1.0
O C:HOH736 1.9 14.9 1.0
NZ C:LYS68 2.4 9.5 1.0
CE1 C:HIS493 2.5 12.1 1.0
CD2 C:HIS100 2.6 10.3 1.0
CG C:HIS493 2.8 11.6 1.0
CE1 C:HIS100 3.0 11.7 1.0
CE C:LYS68 3.3 9.9 1.0
O C:HOH807 3.3 16.0 1.0
CB C:HIS493 3.3 10.8 1.0
NE2 C:HIS493 3.6 13.7 1.0
CD C:LYS68 3.7 9.4 1.0
CD2 C:HIS493 3.8 11.7 1.0
O C:HOH869 3.8 11.8 0.5
CG C:HIS100 3.8 10.9 1.0
ND1 C:HIS100 4.0 10.7 1.0
OE1 C:GLU253 4.0 25.0 1.0
OH C:TYR129 4.1 26.0 1.0
O C:HOH884 4.3 10.2 0.5
OE1 C:GLN121 4.4 13.6 1.0
NE2 C:HIS101 4.5 10.8 1.0
CA C:HIS493 4.9 11.1 1.0
O C:HOH839 4.9 17.0 1.0

Copper binding site 10 out of 11 in 8z77

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Copper binding site 10 out of 11 in the The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours


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 Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu603

b:9.4
occ:0.50
 CU C:CU603 0.0 9.4 0.5
CU C:CU603 1.5 12.6 0.5
O C:HOH807 2.0 16.0 1.0
NE2 C:HIS100 2.1 11.5 1.0
ND1 C:HIS493 2.1 11.8 1.0
O C:HOH736 2.2 14.9 1.0
O C:HOH869 2.6 11.8 0.5
CG C:HIS493 3.0 11.6 1.0
CE1 C:HIS100 3.1 11.7 1.0
CB C:HIS493 3.1 10.8 1.0
O C:HOH884 3.1 10.2 0.5
CE1 C:HIS493 3.1 12.1 1.0
CD2 C:HIS100 3.1 10.3 1.0
NE2 C:HIS101 3.6 10.8 1.0
NZ C:LYS68 3.8 9.5 1.0
OE1 C:GLU253 4.0 25.0 1.0
CD2 C:HIS493 4.1 11.7 1.0
CE1 C:HIS101 4.2 11.8 1.0
NE2 C:HIS493 4.2 13.7 1.0
ND1 C:HIS100 4.2 10.7 1.0
CG C:HIS100 4.3 10.9 1.0
O C:HOH832 4.5 16.6 1.0
OE2 C:GLU253 4.5 17.8 1.0
CD2 C:HIS101 4.6 9.7 1.0
CA C:HIS493 4.6 11.1 1.0
CE C:LYS68 4.7 9.9 1.0
CD C:GLU253 4.7 20.9 1.0
CU C:CU604 4.8 20.4 1.0
CD C:LYS68 5.0 9.4 1.0

Reference:

L.A.Varfolomeeva, A.Y.Solovieva, N.S.Shipkov, N.I.Dergousova, M.E.Minyaev, K.M.Boyko, T.V.Tikhonova, V.O.Popov. The Structure of Thiocyanate Dehydrogenase From Pelomicrobium Methylotrophicum (Pmtcdh), Activated By Crystals Soaking with 1 Mm CUCL2 and Na Ascorbate During 12 Hours To Be Published.
Page generated: Wed Jul 31 10:28:18 2024

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