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Copper in PDB 5i28: Azurin T30R1, Crystal Form II

Protein crystallography data

The structure of Azurin T30R1, Crystal Form II, PDB code: 5i28 was solved by G.Hagelueken, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.22 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 242.478, 105.560, 100.051, 90.00, 114.42, 90.00
R / Rfree (%) 21.2 / 27.1

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Copper atom in the Azurin T30R1, Crystal Form II (pdb code 5i28). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 16 binding sites of Copper where determined in the Azurin T30R1, Crystal Form II, PDB code: 5i28:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 16 in 5i28

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Copper binding site 1 out of 16 in the Azurin T30R1, Crystal Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Azurin T30R1, Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:34.6
occ:1.00
ND1 A:HIS46 2.0 37.9 1.0
ND1 A:HIS117 2.1 37.7 1.0
O A:GLY45 2.1 37.5 1.0
SG A:CYS112 2.2 31.0 1.0
CE1 A:HIS46 2.9 31.8 1.0
CE1 A:HIS117 3.0 31.4 1.0
CG A:HIS46 3.1 37.2 1.0
C A:GLY45 3.1 41.2 1.0
CG A:HIS117 3.1 36.2 1.0
CA A:HIS46 3.2 32.2 1.0
CB A:CYS112 3.4 26.6 1.0
SD A:MET121 3.4 36.8 1.0
CB A:HIS46 3.5 27.4 1.0
CB A:HIS117 3.5 29.1 1.0
N A:HIS46 3.5 34.3 1.0
CB A:PHE114 3.8 37.4 1.0
NE2 A:HIS46 4.1 39.6 1.0
NE2 A:HIS117 4.1 37.0 1.0
CD2 A:HIS46 4.2 33.9 1.0
CE A:MET121 4.2 31.0 1.0
CD2 A:HIS117 4.2 34.7 1.0
CA A:GLY45 4.4 37.3 1.0
C A:HIS46 4.5 42.2 1.0
N A:GLY45 4.6 43.5 1.0
CG A:PHE114 4.7 37.4 1.0
N A:ASN47 4.7 37.2 1.0
N A:PHE114 4.7 40.6 1.0
CA A:CYS112 4.8 31.4 1.0
CA A:PHE114 4.9 35.4 1.0
C A:MET44 4.9 37.4 1.0
O A:MET44 4.9 41.1 1.0
CG A:MET121 4.9 27.5 1.0

Copper binding site 2 out of 16 in 5i28

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Copper binding site 2 out of 16 in the Azurin T30R1, Crystal Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Azurin T30R1, Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:35.9
occ:1.00
ND1 B:HIS117 2.0 41.4 1.0
ND1 B:HIS46 2.0 41.1 1.0
SG B:CYS112 2.3 33.4 1.0
O B:GLY45 2.3 43.6 1.0
CE1 B:HIS46 2.8 34.2 1.0
CE1 B:HIS117 2.9 34.7 1.0
CG B:HIS117 3.1 41.0 1.0
CG B:HIS46 3.1 43.6 1.0
CA B:HIS46 3.3 37.3 1.0
C B:GLY45 3.3 42.6 1.0
SD B:MET121 3.3 33.8 1.0
CB B:CYS112 3.3 27.9 1.0
CB B:HIS117 3.5 32.6 1.0
CB B:HIS46 3.6 31.4 1.0
N B:HIS46 3.7 34.8 1.0
CB B:PHE114 3.8 38.2 1.0
NE2 B:HIS46 4.0 34.2 1.0
NE2 B:HIS117 4.0 40.5 1.0
CE B:MET121 4.1 32.9 1.0
CD2 B:HIS117 4.2 39.1 1.0
CD2 B:HIS46 4.2 36.9 1.0
C B:HIS46 4.5 42.0 1.0
CA B:GLY45 4.6 40.8 1.0
CG B:PHE114 4.6 41.3 1.0
N B:ASN47 4.7 32.5 1.0
CA B:CYS112 4.8 26.1 1.0
CG B:MET121 4.8 27.3 1.0
N B:GLY45 4.8 38.9 1.0
N B:PHE114 4.9 36.6 1.0
O B:MET44 4.9 39.1 1.0
CA B:PHE114 4.9 34.2 1.0
C B:MET44 4.9 36.0 1.0

Copper binding site 3 out of 16 in 5i28

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Copper binding site 3 out of 16 in the Azurin T30R1, Crystal Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Azurin T30R1, Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:37.7
occ:1.00
ND1 C:HIS117 2.0 41.4 1.0
ND1 C:HIS46 2.1 32.5 1.0
O C:GLY45 2.2 39.6 1.0
SG C:CYS112 2.3 31.7 1.0
CE1 C:HIS117 2.8 36.2 1.0
CE1 C:HIS46 2.9 29.4 1.0
CG C:HIS117 3.1 38.3 1.0
CG C:HIS46 3.2 39.1 1.0
CA C:HIS46 3.3 36.3 1.0
C C:GLY45 3.3 39.3 1.0
SD C:MET121 3.3 37.4 1.0
CB C:CYS112 3.4 20.8 1.0
CB C:HIS117 3.5 32.0 1.0
CB C:HIS46 3.6 31.4 1.0
N C:HIS46 3.7 28.8 1.0
CB C:PHE114 3.8 39.9 1.0
NE2 C:HIS117 4.0 37.5 1.0
CE C:MET121 4.1 25.2 1.0
NE2 C:HIS46 4.1 33.3 1.0
CD2 C:HIS117 4.1 32.8 1.0
CD2 C:HIS46 4.2 35.1 1.0
C C:HIS46 4.5 41.4 1.0
CA C:GLY45 4.6 39.7 1.0
N C:ASN47 4.6 30.1 1.0
CG C:PHE114 4.7 41.5 1.0
N C:GLY45 4.8 41.5 1.0
CA C:CYS112 4.8 26.6 1.0
CG C:MET121 4.9 29.9 1.0
N C:PHE114 4.9 38.0 1.0
O C:MET44 4.9 41.1 1.0
C C:MET44 4.9 34.5 1.0
CA C:PHE114 4.9 34.0 1.0

Copper binding site 4 out of 16 in 5i28

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Copper binding site 4 out of 16 in the Azurin T30R1, Crystal Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Azurin T30R1, Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu201

b:40.9
occ:1.00
ND1 D:HIS117 1.8 37.6 1.0
ND1 D:HIS46 1.9 47.5 1.0
O D:GLY45 2.2 41.9 1.0
SG D:CYS112 2.3 35.4 1.0
CE1 D:HIS117 2.7 41.0 1.0
CE1 D:HIS46 2.7 41.0 1.0
CG D:HIS117 3.0 47.2 1.0
CG D:HIS46 3.1 47.9 1.0
SD D:MET121 3.2 36.2 1.0
C D:GLY45 3.3 46.6 1.0
CB D:CYS112 3.3 31.6 1.0
CA D:HIS46 3.3 46.0 1.0
CB D:HIS117 3.5 41.1 1.0
CB D:HIS46 3.7 36.3 1.0
N D:HIS46 3.7 41.5 1.0
CB D:PHE114 3.8 47.7 1.0
NE2 D:HIS117 3.9 46.1 1.0
NE2 D:HIS46 3.9 44.0 1.0
CE D:MET121 3.9 28.6 1.0
CD2 D:HIS117 4.0 44.4 1.0
CD2 D:HIS46 4.1 47.5 1.0
CA D:GLY45 4.6 55.9 1.0
C D:HIS46 4.6 44.9 1.0
CG D:PHE114 4.7 49.7 1.0
N D:ASN47 4.7 40.0 1.0
CG D:MET121 4.7 37.4 1.0
CA D:CYS112 4.7 38.6 1.0
N D:GLY45 4.8 52.1 1.0
N D:PHE114 4.9 43.7 1.0
CA D:HIS117 4.9 38.9 1.0
CA D:PHE114 5.0 50.4 1.0

Copper binding site 5 out of 16 in 5i28

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Copper binding site 5 out of 16 in the Azurin T30R1, Crystal Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Azurin T30R1, Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu201

b:37.3
occ:1.00
ND1 E:HIS117 1.9 36.4 1.0
ND1 E:HIS46 2.0 42.5 1.0
SG E:CYS112 2.2 31.9 1.0
O E:GLY45 2.3 34.7 1.0
CE1 E:HIS117 2.7 34.0 1.0
CE1 E:HIS46 2.9 34.3 1.0
CG E:HIS117 3.0 35.6 1.0
CG E:HIS46 3.1 36.3 1.0
CA E:HIS46 3.3 38.6 1.0
SD E:MET121 3.3 37.0 1.0
CB E:CYS112 3.3 30.9 1.0
C E:GLY45 3.3 39.5 1.0
CB E:HIS117 3.5 37.9 1.0
CB E:HIS46 3.6 38.4 1.0
CB E:PHE114 3.7 39.8 1.0
N E:HIS46 3.7 34.6 1.0
NE2 E:HIS117 3.9 35.6 1.0
CE E:MET121 4.0 35.5 1.0
NE2 E:HIS46 4.1 33.3 1.0
CD2 E:HIS117 4.1 33.5 1.0
CD2 E:HIS46 4.2 36.9 1.0
CG E:PHE114 4.5 36.8 1.0
C E:HIS46 4.5 31.8 1.0
CA E:GLY45 4.6 36.4 1.0
N E:ASN47 4.6 35.3 1.0
O E:MET44 4.7 43.2 1.0
CA E:CYS112 4.7 27.2 1.0
CG E:MET121 4.8 37.6 1.0
N E:PHE114 4.8 42.8 1.0
CA E:PHE114 4.8 37.2 1.0
N E:GLY45 4.9 42.2 1.0
C E:MET44 4.9 43.8 1.0
CD1 E:PHE114 4.9 39.5 1.0

Copper binding site 6 out of 16 in 5i28

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Copper binding site 6 out of 16 in the Azurin T30R1, Crystal Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Azurin T30R1, Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu201

b:38.1
occ:1.00
ND1 F:HIS46 2.0 39.4 1.0
ND1 F:HIS117 2.0 45.0 1.0
O F:GLY45 2.1 32.5 1.0
SG F:CYS112 2.3 32.0 1.0
CE1 F:HIS46 2.9 35.8 1.0
CE1 F:HIS117 3.0 41.3 1.0
CG F:HIS117 3.1 45.5 1.0
CG F:HIS46 3.2 42.0 1.0
C F:GLY45 3.2 39.5 1.0
CB F:CYS112 3.3 30.4 1.0
SD F:MET121 3.3 33.7 1.0
CA F:HIS46 3.4 41.4 1.0
CB F:HIS117 3.5 40.4 1.0
CB F:HIS46 3.6 39.6 1.0
N F:HIS46 3.7 42.4 1.0
CB F:PHE114 3.9 39.7 1.0
NE2 F:HIS46 4.0 37.1 1.0
CE F:MET121 4.1 33.5 1.0
NE2 F:HIS117 4.1 42.1 1.0
CD2 F:HIS117 4.2 38.2 1.0
CD2 F:HIS46 4.2 36.3 1.0
CA F:GLY45 4.5 37.8 1.0
C F:HIS46 4.6 43.3 1.0
CA F:CYS112 4.7 26.3 1.0
CG F:PHE114 4.7 39.1 1.0
N F:ASN47 4.7 39.4 1.0
O F:MET44 4.8 38.3 1.0
CG F:MET121 4.8 31.0 1.0
N F:PHE114 4.8 37.9 1.0
N F:GLY45 4.8 38.1 1.0
C F:MET44 4.9 38.6 1.0
CA F:PHE114 4.9 37.6 1.0
CA F:HIS117 5.0 36.2 1.0

Copper binding site 7 out of 16 in 5i28

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Copper binding site 7 out of 16 in the Azurin T30R1, Crystal Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Azurin T30R1, Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu201

b:37.6
occ:1.00
ND1 G:HIS46 1.9 44.4 1.0
ND1 G:HIS117 1.9 28.5 1.0
O G:GLY45 2.2 32.8 1.0
SG G:CYS112 2.4 30.2 1.0
CE1 G:HIS117 2.7 35.9 1.0
CE1 G:HIS46 2.8 37.7 1.0
CG G:HIS46 3.1 40.3 1.0
CG G:HIS117 3.1 34.8 1.0
C G:GLY45 3.2 44.6 1.0
CA G:HIS46 3.2 45.0 1.0
SD G:MET121 3.3 33.7 1.0
CB G:CYS112 3.3 31.9 1.0
CB G:HIS46 3.5 41.9 1.0
CB G:HIS117 3.6 33.5 1.0
N G:HIS46 3.6 38.9 1.0
CB G:PHE114 3.8 37.1 1.0
CE G:MET121 3.9 27.1 1.0
NE2 G:HIS117 3.9 37.6 1.0
NE2 G:HIS46 3.9 37.6 1.0
CD2 G:HIS46 4.1 38.2 1.0
CD2 G:HIS117 4.1 30.1 1.0
C G:HIS46 4.5 38.6 1.0
CA G:GLY45 4.5 40.5 1.0
CG G:PHE114 4.6 40.9 1.0
N G:ASN47 4.7 43.0 1.0
CA G:CYS112 4.7 36.1 1.0
N G:GLY45 4.8 41.3 1.0
CG G:MET121 4.8 31.6 1.0
N G:PHE114 4.8 40.4 1.0
CA G:PHE114 4.9 34.4 1.0
O G:MET44 4.9 45.1 1.0
C G:MET44 4.9 41.5 1.0

Copper binding site 8 out of 16 in 5i28

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Copper binding site 8 out of 16 in the Azurin T30R1, Crystal Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Azurin T30R1, Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu201

b:45.8
occ:1.00
ND1 H:HIS117 1.9 43.4 1.0
ND1 H:HIS46 2.2 46.9 1.0
SG H:CYS112 2.3 35.5 1.0
O H:GLY45 2.4 45.4 1.0
CE1 H:HIS117 2.8 42.5 1.0
CG H:HIS117 3.1 43.5 1.0
CE1 H:HIS46 3.1 50.6 1.0
SD H:MET121 3.2 48.6 1.0
CG H:HIS46 3.3 50.7 1.0
CA H:HIS46 3.3 44.7 1.0
CB H:CYS112 3.4 29.2 1.0
C H:GLY45 3.4 41.8 1.0
CB H:HIS117 3.5 42.1 1.0
CB H:HIS46 3.6 40.1 1.0
N H:HIS46 3.8 40.6 1.0
CB H:PHE114 3.8 43.1 1.0
NE2 H:HIS117 4.0 44.3 1.0
CD2 H:HIS117 4.1 42.5 1.0
CE H:MET121 4.2 44.4 1.0
NE2 H:HIS46 4.3 51.8 1.0
CD2 H:HIS46 4.4 45.0 1.0
C H:HIS46 4.5 39.7 1.0
CG H:MET121 4.6 35.1 1.0
N H:ASN47 4.6 37.5 1.0
CG H:PHE114 4.7 46.1 1.0
CA H:GLY45 4.7 45.0 1.0
CA H:CYS112 4.8 38.1 1.0
N H:PHE114 4.9 41.9 1.0
N H:GLY45 4.9 48.3 1.0
CA H:PHE114 4.9 41.5 1.0
O H:MET44 5.0 46.7 1.0

Copper binding site 9 out of 16 in 5i28

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Copper binding site 9 out of 16 in the Azurin T30R1, Crystal Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Azurin T30R1, Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu201

b:44.9
occ:1.00
ND1 I:HIS117 1.9 36.9 1.0
ND1 I:HIS46 2.1 48.8 1.0
SG I:CYS112 2.3 39.1 1.0
O I:GLY45 2.3 40.5 1.0
CE1 I:HIS117 2.8 46.2 1.0
CE1 I:HIS46 3.0 49.9 1.0
CG I:HIS117 3.1 40.8 1.0
CG I:HIS46 3.2 52.9 1.0
SD I:MET121 3.3 45.2 1.0
CA I:HIS46 3.3 44.3 1.0
C I:GLY45 3.3 44.3 1.0
CB I:CYS112 3.4 34.8 1.0
CB I:HIS117 3.6 39.6 1.0
CB I:HIS46 3.6 42.8 1.0
N I:HIS46 3.8 37.5 1.0
CB I:PHE114 3.8 36.6 1.0
NE2 I:HIS117 4.0 43.0 1.0
CD2 I:HIS117 4.1 37.2 1.0
NE2 I:HIS46 4.1 50.8 1.0
CE I:MET121 4.1 45.3 1.0
CD2 I:HIS46 4.2 50.7 1.0
C I:HIS46 4.5 39.1 1.0
CG I:PHE114 4.6 46.8 1.0
N I:ASN47 4.6 42.5 1.0
CA I:GLY45 4.6 41.1 1.0
CG I:MET121 4.7 33.6 1.0
CA I:CYS112 4.8 40.1 1.0
N I:GLY45 4.8 43.3 1.0
N I:PHE114 4.9 40.9 1.0
O I:MET44 4.9 48.6 1.0
CA I:PHE114 5.0 40.7 1.0
C I:MET44 5.0 48.6 1.0

Copper binding site 10 out of 16 in 5i28

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Copper binding site 10 out of 16 in the Azurin T30R1, Crystal Form II


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Azurin T30R1, Crystal Form II within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cu201

b:36.2
occ:1.00
ND1 J:HIS117 1.9 27.5 1.0
ND1 J:HIS46 2.1 40.4 1.0
O J:GLY45 2.2 34.5 1.0
SG J:CYS112 2.3 28.8 1.0
CE1 J:HIS117 2.7 37.9 1.0
CE1 J:HIS46 3.0 33.0 1.0
CG J:HIS117 3.1 35.7 1.0
CG J:HIS46 3.2 37.4 1.0
C J:GLY45 3.2 37.9 1.0
CA J:HIS46 3.2 46.6 1.0
CB J:CYS112 3.3 31.4 1.0
SD J:MET121 3.3 34.9 1.0
CB J:HIS46 3.6 41.9 1.0
N J:HIS46 3.6 39.1 1.0
CB J:HIS117 3.6 35.3 1.0
CB J:PHE114 3.8 36.4 1.0
NE2 J:HIS117 3.9 31.5 1.0
CE J:MET121 4.0 24.4 1.0
CD2 J:HIS117 4.1 36.7 1.0
NE2 J:HIS46 4.1 37.5 1.0
CD2 J:HIS46 4.2 35.0 1.0
C J:HIS46 4.4 35.7 1.0
CA J:GLY45 4.5 42.2 1.0
N J:ASN47 4.6 41.6 1.0
CG J:PHE114 4.6 41.0 1.0
N J:GLY45 4.7 44.0 1.0
CA J:CYS112 4.7 31.5 1.0
CG J:MET121 4.8 31.2 1.0
N J:PHE114 4.8 36.3 1.0
CA J:PHE114 4.9 32.9 1.0
C J:MET44 4.9 44.7 1.0

Reference:

D.Abdullin, G.Hagelueken, O.Schiemann. Determination of Nitroxide Spin Label Conformations Via Peldor and X-Ray Crystallography. Phys Chem Chem Phys V. 18 10428 2016.
ISSN: ESSN 1463-9084
PubMed: 27029516
DOI: 10.1039/C6CP01307D
Page generated: Sun Dec 13 11:17:53 2020

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