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Copper in PDB 3n2j: Azurin H117G, Oxidized Form

Protein crystallography data

The structure of Azurin H117G, Oxidized Form, PDB code: 3n2j was solved by M.Hoffmann, S.Alagaratnam, G.W.Canters, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.28 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.545, 170.008, 85.737, 90.00, 89.98, 90.00
R / Rfree (%) 17.2 / 20.2

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Copper atom in the Azurin H117G, Oxidized Form (pdb code 3n2j). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 24 binding sites of Copper where determined in the Azurin H117G, Oxidized Form, PDB code: 3n2j:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 24 in 3n2j

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Copper binding site 1 out of 24 in the Azurin H117G, Oxidized Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Azurin H117G, Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu130

b:22.2
occ:1.00
ND1 A:HIS46 2.0 18.7 1.0
SG A:CYS112 2.2 17.8 1.0
SD A:MET121 2.5 20.6 1.0
CE1 A:HIS46 3.0 15.5 1.0
CG A:HIS46 3.0 17.5 1.0
CB A:CYS112 3.1 14.2 1.0
CE A:MET121 3.3 20.5 1.0
CB A:HIS46 3.4 15.6 1.0
CA A:HIS46 3.4 16.1 1.0
O A:HOH218 3.5 19.6 1.0
O A:HOH815 3.5 26.9 1.0
O A:GLY45 3.5 20.1 1.0
CG A:MET121 4.0 17.9 1.0
O A:HOH562 4.0 28.1 1.0
NE2 A:HIS46 4.2 16.6 1.0
CD2 A:HIS46 4.2 16.9 1.0
CB A:MET121 4.2 19.1 1.0
N A:HIS46 4.3 16.4 1.0
C A:GLY45 4.3 18.5 1.0
N A:ASN47 4.5 16.2 1.0
CA A:CYS112 4.5 15.5 1.0
C A:HIS46 4.5 16.4 1.0
CB A:PHE114 4.5 18.8 1.0
O A:ASN47 4.9 16.3 1.0
CZ A:PHE15 4.9 22.6 1.0

Copper binding site 2 out of 24 in 3n2j

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Copper binding site 2 out of 24 in the Azurin H117G, Oxidized Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Azurin H117G, Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu131

b:21.3
occ:0.40
NE2 A:HIS83 1.8 18.8 1.0
O D:HOH1273 2.3 0.4 1.0
CE1 A:HIS83 2.7 19.4 1.0
CD2 A:HIS83 2.9 19.1 1.0
O D:HOH1381 2.9 91.6 1.0
OE1 D:GLU2 3.6 23.9 1.0
CD D:GLU2 3.8 32.9 1.0
OE2 D:GLU2 3.8 26.2 1.0
ND1 A:HIS83 3.9 19.3 1.0
SG D:CYS3 3.9 23.6 1.0
CG A:HIS83 3.9 17.1 1.0
O D:HOH838 4.2 24.3 1.0
CD1 A:LEU73 4.7 25.8 1.0
CG D:GLU2 4.7 34.6 1.0

Copper binding site 3 out of 24 in 3n2j

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Copper binding site 3 out of 24 in the Azurin H117G, Oxidized Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Azurin H117G, Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu130

b:18.3
occ:1.00
ND1 B:HIS46 1.8 11.9 1.0
SG B:CYS112 2.0 14.5 1.0
SD B:MET121 2.7 18.0 1.0
CG B:HIS46 2.9 14.6 1.0
CE1 B:HIS46 2.9 18.9 1.0
CB B:CYS112 3.0 8.9 1.0
CB B:HIS46 3.3 13.3 1.0
CE B:MET121 3.3 18.8 1.0
CA B:HIS46 3.4 12.2 1.0
O B:GLY45 3.5 15.0 1.0
O B:HOH1295 3.7 23.8 1.0
O B:HOH368 3.8 29.1 1.0
NE2 B:HIS46 4.0 18.3 1.0
CD2 B:HIS46 4.0 14.9 1.0
CG B:MET121 4.2 17.1 1.0
C B:GLY45 4.3 12.3 1.0
N B:HIS46 4.3 12.4 1.0
CB B:PHE114 4.3 13.5 1.0
CA B:CYS112 4.4 10.6 1.0
N B:ASN47 4.4 11.9 1.0
C B:HIS46 4.5 12.7 1.0
CB B:MET121 4.6 16.8 1.0
O B:ASN47 4.8 13.1 1.0

Copper binding site 4 out of 24 in 3n2j

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Copper binding site 4 out of 24 in the Azurin H117G, Oxidized Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Azurin H117G, Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu131

b:20.6
occ:0.50
NE2 B:HIS83 1.9 17.4 1.0
O B:HOH1085 2.4 34.8 1.0
CD2 B:HIS83 2.8 17.5 1.0
CE1 B:HIS83 3.0 17.6 1.0
O B:HOH136 3.8 37.2 1.0
CG B:HIS83 3.9 15.6 1.0
ND1 B:HIS83 4.0 18.2 1.0
CD1 B:LEU73 4.8 20.0 1.0
CG1 B:VAL80 5.0 15.1 1.0

Copper binding site 5 out of 24 in 3n2j

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Copper binding site 5 out of 24 in the Azurin H117G, Oxidized Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Azurin H117G, Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu130

b:41.3
occ:1.00
SG C:CYS112 1.8 19.3 1.0
ND1 C:HIS46 2.0 24.4 1.0
SD C:MET121 3.0 22.2 1.0
CB C:CYS112 3.0 17.1 1.0
CE1 C:HIS46 3.0 24.5 1.0
O C:GLY45 3.1 20.6 1.0
CG C:HIS46 3.1 22.8 1.0
CA C:HIS46 3.3 18.8 1.0
CB C:HIS46 3.4 20.3 1.0
O C:HOH738 3.5 22.6 1.0
CE C:MET121 3.8 17.6 1.0
C C:GLY45 3.9 19.2 1.0
N C:HIS46 4.1 18.2 1.0
O C:HOH1282 4.2 31.5 1.0
NE2 C:HIS46 4.2 24.6 1.0
CD2 C:HIS46 4.2 23.7 1.0
CB C:PHE114 4.2 21.0 1.0
N C:ASN47 4.3 17.7 1.0
C C:HIS46 4.3 19.5 1.0
CG C:MET121 4.3 23.2 1.0
CA C:CYS112 4.4 15.8 1.0
CB C:MET121 4.7 22.6 1.0
O C:ASN47 4.9 18.9 1.0
N C:PHE114 4.9 17.8 1.0
C C:CYS112 5.0 15.7 1.0

Copper binding site 6 out of 24 in 3n2j

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Copper binding site 6 out of 24 in the Azurin H117G, Oxidized Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Azurin H117G, Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu131

b:29.7
occ:0.80
NE2 C:HIS83 1.9 22.0 1.0
CD2 C:HIS83 2.8 22.2 1.0
CE1 C:HIS83 3.0 22.5 1.0
CG C:HIS83 4.0 21.1 1.0
ND1 C:HIS83 4.1 23.5 1.0
CG1 C:VAL80 4.8 18.3 1.0
O C:HOH139 4.9 19.9 1.0

Copper binding site 7 out of 24 in 3n2j

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Copper binding site 7 out of 24 in the Azurin H117G, Oxidized Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Azurin H117G, Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu130

b:20.4
occ:1.00
ND1 D:HIS46 1.9 16.5 1.0
SG D:CYS112 2.1 17.8 1.0
SD D:MET121 2.6 22.1 1.0
CE1 D:HIS46 2.9 19.3 1.0
CG D:HIS46 3.0 17.5 1.0
CB D:CYS112 3.0 15.8 1.0
O D:GLY45 3.4 17.8 1.0
CB D:HIS46 3.4 18.0 1.0
CA D:HIS46 3.4 17.2 1.0
CE D:MET121 3.5 21.6 1.0
O D:HOH1177 3.7 26.5 1.0
O D:HOH1394 3.8 41.7 1.0
CG D:MET121 3.8 21.8 1.0
NE2 D:HIS46 4.0 19.7 1.0
CD2 D:HIS46 4.1 18.2 1.0
C D:GLY45 4.2 18.4 1.0
N D:HIS46 4.3 16.3 1.0
CB D:MET121 4.4 20.9 1.0
N D:ASN47 4.4 16.2 1.0
CA D:CYS112 4.4 15.3 1.0
C D:HIS46 4.5 18.2 1.0
CB D:PHE114 4.5 16.4 1.0
O D:ASN47 4.9 15.9 1.0
CZ D:PHE15 4.9 19.5 1.0

Copper binding site 8 out of 24 in 3n2j

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Copper binding site 8 out of 24 in the Azurin H117G, Oxidized Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Azurin H117G, Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu131

b:24.9
occ:0.70
NE2 D:HIS83 2.0 19.9 1.0
O D:HOH1387 2.3 27.4 1.0
CD2 D:HIS83 2.9 19.8 1.0
CE1 D:HIS83 3.1 17.8 1.0
O D:HOH1469 3.4 35.2 1.0
CG D:HIS83 4.1 18.4 1.0
O D:HOH820 4.1 31.8 1.0
ND1 D:HIS83 4.2 17.3 1.0
O D:HOH1440 5.0 30.5 1.0
CD1 D:LEU73 5.0 17.9 1.0

Copper binding site 9 out of 24 in 3n2j

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Copper binding site 9 out of 24 in the Azurin H117G, Oxidized Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Azurin H117G, Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu130

b:22.9
occ:1.00
ND1 E:HIS46 1.9 22.9 1.0
SG E:CYS112 2.0 18.4 1.0
SD E:MET121 2.5 30.6 1.0
CE1 E:HIS46 2.9 24.2 1.0
CG E:HIS46 3.0 21.4 1.0
CB E:CYS112 3.0 17.0 1.0
CA E:HIS46 3.3 17.0 1.0
CB E:HIS46 3.4 18.3 1.0
CE E:MET121 3.4 25.8 1.0
O E:GLY45 3.4 18.0 1.0
CG E:MET121 4.0 30.1 1.0
NE2 E:HIS46 4.1 24.9 1.0
CD2 E:HIS46 4.1 24.5 1.0
N E:HIS46 4.2 17.2 1.0
C E:GLY45 4.2 17.6 1.0
N E:ASN47 4.2 15.7 1.0
CB E:MET121 4.3 28.0 1.0
C E:HIS46 4.3 19.2 1.0
CA E:CYS112 4.4 18.6 1.0
CB E:PHE114 4.6 20.5 1.0
O E:ASN47 4.7 16.9 1.0

Copper binding site 10 out of 24 in 3n2j

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Copper binding site 10 out of 24 in the Azurin H117G, Oxidized Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Azurin H117G, Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu131

b:30.7
occ:0.50
NE2 E:HIS83 2.1 21.5 1.0
O E:HOH1395 2.5 34.0 1.0
OE1 G:GLU2 2.8 32.6 1.0
CE1 E:HIS83 3.0 20.3 1.0
CD2 E:HIS83 3.1 21.2 1.0
CD G:GLU2 3.4 26.9 1.0
O E:HOH245 3.5 36.3 1.0
OE2 G:GLU2 3.9 41.4 1.0
SG G:CYS3 4.0 30.7 1.0
CG E:HIS83 4.2 20.3 1.0
ND1 E:HIS83 4.2 21.5 1.0
CG G:GLU2 4.2 30.5 1.0
O G:HOH1371 4.5 25.6 1.0
CB G:GLU2 4.6 31.4 1.0
O G:HOH1209 4.8 33.9 1.0

Reference:

S.Alagaratnam, N.J.Meeuwenoord, J.A.Navarro, M.Hervas, M.A.De La Rosa, M.Hoffmann, O.Einsle, M.Ubbink, G.W.Canters. Probing the Reactivity of Different Forms of Azurin By Flavin Photoreduction. Febs J. V. 278 1506 2011.
ISSN: ISSN 1742-464X
PubMed: 21352498
DOI: 10.1111/J.1742-4658.2011.08067.X
Page generated: Sun Dec 13 11:10:50 2020

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