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Copper in PDB 3abg: X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal

Enzymatic activity of X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal

All present enzymatic activity of X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal:
1.3.3.5;

Protein crystallography data

The structure of X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal, PDB code: 3abg was solved by K.Mizutani, M.Toyoda, K.Sagara, N.Takahashi, A.Sato, Y.Kamitaka, S.Tsujimura, Y.Nakanishi, T.Sugiura, S.Yamaguchi, K.Kano, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.56 / 2.30
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 139.742, 139.742, 135.561, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 26.3

Copper Binding Sites:

The binding sites of Copper atom in the X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal (pdb code 3abg). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal, PDB code: 3abg:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 3abg

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Copper binding site 1 out of 8 in the X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:35.1
occ:1.00
 NE2 A:HIS136 2.0 29.9 1.0
NE2 A:HIS403 2.1 25.7 1.0
NE2 A:HIS456 2.2 27.3 1.0
O A:HOH662 2.3 26.6 1.0
CE1 A:HIS403 2.4 32.0 1.0
CE1 A:HIS456 2.9 26.4 1.0
CE1 A:HIS136 2.9 31.1 1.0
CD2 A:HIS136 3.1 28.5 1.0
CD2 A:HIS456 3.3 32.7 1.0
CD2 A:HIS403 3.4 35.2 1.0
ND1 A:HIS403 3.7 29.6 1.0
CD2 A:HIS401 3.8 31.7 1.0
ND1 A:HIS136 4.0 35.0 1.0
ND1 A:HIS456 4.1 28.3 1.0
CE A:MET454 4.1 34.2 1.0
CG A:HIS136 4.1 32.2 1.0
CG A:HIS403 4.2 29.1 1.0
CU A:CU703 4.2 43.8 1.0
CG A:HIS456 4.3 30.9 1.0
NE2 A:HIS401 4.3 30.4 1.0
OE1 A:GLU463 4.7 30.4 1.0
CE1 A:HIS94 4.7 35.8 1.0
ND1 A:HIS94 4.7 33.3 1.0
CU A:CU702 4.8 43.0 1.0
NE2 A:HIS94 4.8 28.8 1.0
CG A:HIS94 4.8 31.1 1.0
CD2 A:HIS94 4.8 31.0 1.0
NE2 A:HIS458 4.9 28.7 1.0
CB A:MET454 4.9 28.4 1.0
OE2 A:GLU463 4.9 38.0 1.0
CG A:HIS401 5.0 34.2 1.0

Copper binding site 2 out of 8 in 3abg

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Copper binding site 2 out of 8 in the X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:43.0
occ:1.00
 ND1 A:HIS96 2.1 37.8 1.0
NE2 A:HIS134 2.2 29.1 1.0
NE2 A:HIS458 2.3 28.7 1.0
O A:HOH662 2.5 26.6 1.0
CE1 A:HIS134 2.5 37.6 1.0
CE1 A:HIS96 3.0 34.4 1.0
CE1 A:HIS458 3.1 29.3 1.0
CG A:HIS96 3.2 37.5 1.0
CD2 A:HIS134 3.4 34.3 1.0
CD2 A:HIS458 3.5 28.6 1.0
CB A:HIS96 3.6 34.7 1.0
ND1 A:HIS134 3.7 40.5 1.0
CZ2 A:TRP132 3.7 27.1 1.0
CD2 A:HIS94 3.9 31.0 1.0
CE2 A:TRP132 4.0 27.6 1.0
NE1 A:TRP132 4.1 28.4 1.0
CG A:HIS134 4.1 29.4 1.0
CU A:CU703 4.2 43.8 1.0
NE2 A:HIS96 4.2 33.1 1.0
ND1 A:HIS458 4.3 36.5 1.0
CD2 A:HIS96 4.3 39.4 1.0
CH2 A:TRP132 4.5 29.5 1.0
NE2 A:HIS94 4.5 28.8 1.0
CG A:HIS458 4.5 33.2 1.0
CA A:HIS96 4.6 31.7 1.0
NE2 A:HIS401 4.6 30.4 1.0
CD2 A:HIS401 4.7 31.7 1.0
CB A:ALA274 4.7 34.2 1.0
CG A:HIS94 4.7 31.1 1.0
CU A:CU701 4.8 35.1 1.0
CD2 A:TRP132 5.0 27.8 1.0

Copper binding site 3 out of 8 in 3abg

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Copper binding site 3 out of 8 in the X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu703

b:43.8
occ:1.00
 NE2 A:HIS94 2.1 28.8 1.0
NE2 A:HIS401 2.2 30.4 1.0
O A:HOH563 2.7 36.6 1.0
CE1 A:HIS94 2.8 35.8 1.0
CD2 A:HIS94 3.0 31.0 1.0
CE1 A:HIS401 3.1 34.0 1.0
CD2 A:HIS401 3.3 31.7 1.0
O A:HOH662 3.5 26.6 1.0
NE2 A:HIS403 3.5 25.7 1.0
ND1 A:HIS96 3.6 37.8 1.0
CE1 A:HIS403 3.6 32.0 1.0
CD2 A:HIS403 3.7 35.2 1.0
CG A:HIS96 3.7 37.5 1.0
CA A:HIS96 3.8 31.7 1.0
ND1 A:HIS403 3.8 29.6 1.0
ND1 A:HIS94 3.8 33.3 1.0
CG A:HIS403 3.8 29.1 1.0
CE1 A:HIS96 3.9 34.4 1.0
CG A:HIS94 4.0 31.1 1.0
CD2 A:HIS96 4.1 39.4 1.0
CB A:HIS96 4.1 34.7 1.0
CU A:CU702 4.2 43.0 1.0
ND1 A:HIS401 4.2 37.6 1.0
CU A:CU701 4.2 35.1 1.0
NE2 A:HIS96 4.2 33.1 1.0
N A:GLY97 4.3 34.3 1.0
CG A:HIS401 4.3 34.2 1.0
O A:HOH548 4.4 35.8 1.0
O A:HOH569 4.5 37.5 1.0
C A:HIS96 4.6 35.5 1.0
CA A:HIS403 4.6 35.6 1.0
CB A:HIS403 4.7 36.4 1.0
N A:HIS96 4.7 36.2 1.0
O A:ILE402 4.8 41.4 1.0
O A:LEU95 5.0 37.1 1.0

Copper binding site 4 out of 8 in 3abg

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Copper binding site 4 out of 8 in the X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu704

b:34.3
occ:1.00
 ND1 A:HIS462 2.2 19.5 1.0
SG A:CYS457 2.3 38.1 1.0
ND1 A:HIS398 2.6 35.4 1.0
CG A:HIS462 3.0 27.7 1.0
CB A:HIS462 3.2 26.7 1.0
CB A:CYS457 3.2 28.8 1.0
CE1 A:HIS462 3.3 27.5 1.0
CG A:HIS398 3.4 31.8 1.0
SD A:MET467 3.5 30.2 1.0
CE1 A:HIS398 3.5 34.9 1.0
CB A:HIS398 3.6 36.7 1.0
CA A:HIS398 3.6 27.8 1.0
O A:THR397 3.7 37.6 1.0
CB A:ASN459 3.8 30.1 1.0
CE A:MET467 3.9 24.5 1.0
CD2 A:HIS462 4.2 31.3 1.0
NE2 A:HIS462 4.3 32.3 1.0
C A:THR397 4.4 36.6 1.0
CG A:ASN459 4.5 26.7 1.0
N A:HIS398 4.5 26.4 1.0
CD2 A:HIS398 4.5 31.4 1.0
NE2 A:HIS398 4.6 33.0 1.0
C A:HIS398 4.6 32.2 1.0
ND2 A:ASN459 4.6 32.0 1.0
CA A:CYS457 4.7 34.9 1.0
CA A:HIS462 4.7 27.5 1.0
N A:ASN459 4.8 29.0 1.0
O A:ASN459 4.8 31.5 1.0
CA A:ASN459 4.8 31.1 1.0
O A:HOH598 4.9 38.0 1.0
CG A:MET467 4.9 27.7 1.0

Copper binding site 5 out of 8 in 3abg

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Copper binding site 5 out of 8 in the X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:37.6
occ:1.00
 NE2 B:HIS136 2.2 31.6 1.0
NE2 B:HIS403 2.2 31.4 1.0
NE2 B:HIS456 2.2 26.6 1.0
O B:HOH713 2.7 40.2 1.0
CE1 B:HIS456 2.9 28.2 1.0
CD2 B:HIS136 3.1 28.0 1.0
CD2 B:HIS403 3.2 35.6 1.0
CE1 B:HIS403 3.2 32.5 1.0
CE1 B:HIS136 3.2 30.4 1.0
CD2 B:HIS456 3.4 33.6 1.0
CU B:CU703 3.9 43.4 1.0
CD2 B:HIS401 4.0 33.5 1.0
ND1 B:HIS456 4.1 28.6 1.0
CE B:MET454 4.2 34.0 1.0
CG B:HIS136 4.3 32.0 1.0
ND1 B:HIS403 4.3 29.7 1.0
ND1 B:HIS136 4.3 30.2 1.0
CG B:HIS403 4.3 29.5 1.0
CG B:HIS456 4.4 34.1 1.0
CE1 B:HIS94 4.6 34.0 1.0
CB B:MET454 4.6 29.3 1.0
NE2 B:HIS401 4.6 32.2 1.0
ND1 B:HIS94 4.6 31.7 1.0
NE2 B:HIS94 4.8 24.8 1.0
CG B:HIS94 4.9 30.1 1.0
CD2 B:HIS94 5.0 30.5 1.0

Copper binding site 6 out of 8 in 3abg

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Copper binding site 6 out of 8 in the X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:36.3
occ:1.00
 NE2 B:HIS134 2.2 29.4 1.0
NE2 B:HIS458 2.3 30.6 1.0
ND1 B:HIS96 2.4 37.6 1.0
O B:HOH713 2.5 40.2 1.0
CE1 B:HIS134 2.9 36.0 1.0
CE1 B:HIS458 3.1 30.0 1.0
CG B:HIS96 3.3 36.8 1.0
CE1 B:HIS96 3.3 32.4 1.0
CD2 B:HIS134 3.3 33.7 1.0
CZ2 B:TRP132 3.4 29.1 1.0
CD2 B:HIS458 3.5 29.8 1.0
CB B:HIS96 3.5 32.8 1.0
CE2 B:TRP132 4.0 28.9 1.0
CU B:CU703 4.0 43.4 1.0
ND1 B:HIS134 4.0 38.5 1.0
CD2 B:HIS94 4.1 30.5 1.0
CH2 B:TRP132 4.1 28.3 1.0
NE1 B:TRP132 4.2 30.1 1.0
CG B:HIS134 4.3 30.5 1.0
ND1 B:HIS458 4.3 36.2 1.0
NE2 B:HIS96 4.3 31.9 1.0
CD2 B:HIS96 4.3 39.5 1.0
CB B:ALA274 4.4 32.1 1.0
CD2 B:HIS401 4.5 33.5 1.0
CG B:HIS458 4.5 32.9 1.0
NE2 B:HIS94 4.5 24.8 1.0
NE2 B:HIS401 4.6 32.2 1.0
CA B:HIS96 4.7 29.7 1.0

Copper binding site 7 out of 8 in 3abg

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Copper binding site 7 out of 8 in the X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu703

b:43.4
occ:1.00
 NE2 B:HIS94 2.1 24.8 1.0
NE2 B:HIS401 2.2 32.2 1.0
CE1 B:HIS94 2.7 34.0 1.0
CD2 B:HIS401 2.9 33.5 1.0
CD2 B:HIS94 3.0 30.5 1.0
ND1 B:HIS96 3.1 37.6 1.0
CE1 B:HIS401 3.3 32.6 1.0
O B:HOH713 3.4 40.2 1.0
NE2 B:HIS403 3.6 31.4 1.0
ND1 B:HIS94 3.7 31.7 1.0
CG B:HIS96 3.7 36.8 1.0
CD2 B:HIS403 3.8 35.6 1.0
CE1 B:HIS96 3.8 32.4 1.0
CA B:HIS96 3.8 29.7 1.0
CE1 B:HIS403 3.9 32.5 1.0
CG B:HIS94 3.9 30.1 1.0
CU B:CU701 3.9 37.6 1.0
CU B:CU702 4.0 36.3 1.0
CB B:HIS96 4.0 32.8 1.0
CG B:HIS401 4.2 34.4 1.0
CG B:HIS403 4.2 29.5 1.0
ND1 B:HIS403 4.2 29.7 1.0
ND1 B:HIS401 4.3 34.8 1.0
CD2 B:HIS96 4.5 39.5 1.0
NE2 B:HIS96 4.6 31.9 1.0
N B:HIS96 4.7 36.5 1.0
N B:GLY97 4.7 36.1 1.0
C B:HIS96 4.7 37.0 1.0
CA B:HIS403 5.0 34.7 1.0

Copper binding site 8 out of 8 in 3abg

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Copper binding site 8 out of 8 in the X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of X-Ray Crystal Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 Angstrom Resolution Using A Twin Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu704

b:32.1
occ:1.00
 ND1 B:HIS462 2.2 20.9 1.0
SG B:CYS457 2.3 35.7 1.0
ND1 B:HIS398 2.4 34.6 1.0
CG B:HIS462 3.0 25.5 1.0
CB B:CYS457 3.0 30.7 1.0
CB B:HIS462 3.1 30.4 1.0
SD B:MET467 3.2 29.9 1.0
CG B:HIS398 3.2 33.6 1.0
CE1 B:HIS462 3.3 27.6 1.0
CB B:HIS398 3.3 36.0 1.0
CE1 B:HIS398 3.5 35.3 1.0
CA B:HIS398 3.6 30.9 1.0
O B:THR397 3.8 37.9 1.0
CB B:ASN459 4.0 29.9 1.0
CD2 B:HIS462 4.2 32.8 1.0
NE2 B:HIS462 4.3 30.2 1.0
CE B:MET467 4.4 27.0 1.0
CD2 B:HIS398 4.4 29.2 1.0
C B:THR397 4.4 34.6 1.0
N B:HIS398 4.4 28.1 1.0
CA B:CYS457 4.5 35.4 1.0
NE2 B:HIS398 4.5 32.3 1.0
CA B:HIS462 4.6 28.2 1.0
CG B:MET467 4.6 26.6 1.0
C B:HIS398 4.7 31.3 1.0
CD B:PRO399 4.7 33.7 1.0
CG B:ASN459 4.8 24.2 1.0
N B:ASN459 4.9 32.9 1.0
O B:ASN459 4.9 28.0 1.0
CA B:ASN459 5.0 31.6 1.0

Reference:

K.Mizutani, M.Toyoda, K.Sagara, N.Takahashi, A.Sato, Y.Kamitaka, S.Tsujimura, Y.Nakanishi, T.Sugiura, S.Yamaguchi, K.Kano, B.Mikami. X-Ray Analysis of Bilirubin Oxidase From Myrothecium Verrucaria at 2.3 A Resolution Using A Twinned Crystal Acta Crystallogr.,Sect.F V. 66 765 2010.
ISSN: ESSN 1744-3091
PubMed: 20606269
DOI: 10.1107/S1744309110018828
Page generated: Wed Jul 31 00:33:34 2024

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