Atomistry » Copper » PDB 1hc1-1jvo » 1jvo
Atomistry »
  Copper »
    PDB 1hc1-1jvo »
      1jvo »

Copper in PDB 1jvo: Azurin Dimer, Crosslinked Via Disulfide Bridge

Protein crystallography data

The structure of Azurin Dimer, Crosslinked Via Disulfide Bridge, PDB code: 1jvo was solved by I.M.C.Van Amsterdam, M.Ubbink, O.Einsle, A.Messerschmidt, A.Merli, D.Cavazzini, G.L.Rossi, G.W.Canters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.323, 94.425, 193.362, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 28.9

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Azurin Dimer, Crosslinked Via Disulfide Bridge (pdb code 1jvo). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Azurin Dimer, Crosslinked Via Disulfide Bridge, PDB code: 1jvo:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 1jvo

Go back to Copper Binding Sites List in 1jvo
Copper binding site 1 out of 12 in the Azurin Dimer, Crosslinked Via Disulfide Bridge


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Azurin Dimer, Crosslinked Via Disulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu129

b:47.6
occ:1.00
ND1 A:HIS46 2.0 39.3 1.0
ND1 A:HIS117 2.2 49.3 1.0
SG A:CYS112 2.3 44.6 1.0
CE1 A:HIS46 2.9 32.2 1.0
O A:GLY45 3.0 37.3 1.0
CG A:HIS46 3.0 37.5 1.0
CE1 A:HIS117 3.1 45.2 1.0
SD A:MET121 3.1 44.8 1.0
CG A:HIS117 3.1 47.1 1.0
CB A:CYS112 3.3 43.8 1.0
CA A:HIS46 3.4 42.8 1.0
CB A:HIS46 3.5 32.2 1.0
CB A:HIS117 3.5 45.2 1.0
C A:GLY45 3.9 32.1 1.0
CE A:MET121 3.9 40.2 1.0
CB A:PHE114 3.9 21.6 1.0
NE2 A:HIS46 4.0 32.2 1.0
N A:HIS46 4.1 44.1 1.0
CD2 A:HIS46 4.1 36.1 1.0
NE2 A:HIS117 4.2 51.1 1.0
CD2 A:HIS117 4.2 52.3 1.0
C A:HIS46 4.6 45.8 1.0
CG A:MET121 4.7 43.1 1.0
CA A:CYS112 4.7 37.6 1.0
N A:ASN47 4.7 37.2 1.0
CG A:PHE114 4.7 20.7 1.0
N A:PHE114 4.9 35.6 1.0
CA A:HIS117 5.0 41.5 1.0
CB A:MET121 5.0 40.2 1.0

Copper binding site 2 out of 12 in 1jvo

Go back to Copper Binding Sites List in 1jvo
Copper binding site 2 out of 12 in the Azurin Dimer, Crosslinked Via Disulfide Bridge


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Azurin Dimer, Crosslinked Via Disulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu129

b:47.6
occ:1.00
ND1 B:HIS117 2.0 40.3 1.0
ND1 B:HIS46 2.1 37.9 1.0
SG B:CYS112 2.2 27.8 1.0
O B:GLY45 2.8 29.8 1.0
CE1 B:HIS46 3.0 30.8 1.0
CE1 B:HIS117 3.0 36.2 1.0
CG B:HIS117 3.1 38.1 1.0
CG B:HIS46 3.1 36.1 1.0
SD B:MET121 3.2 38.3 1.0
CB B:CYS112 3.3 27.0 1.0
CB B:HIS117 3.4 36.2 1.0
CA B:HIS46 3.5 23.5 1.0
CB B:HIS46 3.5 30.8 1.0
CB B:PHE114 3.8 20.6 1.0
C B:GLY45 3.8 24.6 1.0
CE B:MET121 3.8 33.8 1.0
N B:HIS46 4.1 24.7 1.0
NE2 B:HIS46 4.1 30.8 1.0
NE2 B:HIS117 4.1 42.1 1.0
CD2 B:HIS117 4.2 43.3 1.0
CD2 B:HIS46 4.2 34.7 1.0
CG B:PHE114 4.6 19.7 1.0
C B:HIS46 4.7 26.4 1.0
CA B:CYS112 4.7 42.6 1.0
N B:PHE114 4.8 27.9 1.0
CG B:MET121 4.8 36.6 1.0
N B:ASN47 4.8 18.8 1.0
CA B:PHE114 4.9 28.1 1.0
CA B:HIS117 4.9 37.1 1.0

Copper binding site 3 out of 12 in 1jvo

Go back to Copper Binding Sites List in 1jvo
Copper binding site 3 out of 12 in the Azurin Dimer, Crosslinked Via Disulfide Bridge


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Azurin Dimer, Crosslinked Via Disulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu129

b:47.6
occ:1.00
ND1 C:HIS117 2.0 35.1 1.0
ND1 C:HIS46 2.0 48.1 1.0
SG C:CYS112 2.3 43.6 1.0
CE1 C:HIS117 2.9 31.0 1.0
CE1 C:HIS46 2.9 41.0 1.0
O C:GLY45 3.0 37.6 1.0
CG C:HIS46 3.0 46.4 1.0
CG C:HIS117 3.0 33.0 1.0
SD C:MET121 3.2 38.2 1.0
CB C:CYS112 3.4 42.8 1.0
CA C:HIS46 3.4 33.9 1.0
CB C:HIS46 3.4 41.0 1.0
CB C:HIS117 3.4 31.0 1.0
CB C:PHE114 3.8 44.6 1.0
C C:GLY45 3.8 32.4 1.0
CE C:MET121 3.9 33.7 1.0
N C:HIS46 4.0 35.1 1.0
NE2 C:HIS117 4.0 36.9 1.0
NE2 C:HIS46 4.0 41.0 1.0
CD2 C:HIS117 4.1 38.1 1.0
CD2 C:HIS46 4.1 44.9 1.0
CG C:PHE114 4.6 43.8 1.0
C C:HIS46 4.6 36.9 1.0
N C:ASN47 4.7 57.8 1.0
CA C:CYS112 4.8 38.5 1.0
CG C:MET121 4.8 36.6 1.0
N C:PHE114 4.9 31.9 1.0
CA C:PHE114 4.9 32.1 1.0
O C:MET44 4.9 38.1 1.0
CA C:HIS117 4.9 31.4 1.0

Copper binding site 4 out of 12 in 1jvo

Go back to Copper Binding Sites List in 1jvo
Copper binding site 4 out of 12 in the Azurin Dimer, Crosslinked Via Disulfide Bridge


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Azurin Dimer, Crosslinked Via Disulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu129

b:47.6
occ:1.00
ND1 D:HIS117 2.1 29.1 1.0
ND1 D:HIS46 2.1 36.8 1.0
SG D:CYS112 2.3 34.4 1.0
O D:GLY45 3.0 29.7 1.0
CE1 D:HIS46 3.0 29.7 1.0
CE1 D:HIS117 3.0 25.1 1.0
CG D:HIS117 3.1 27.0 1.0
CG D:HIS46 3.1 35.1 1.0
SD D:MET121 3.2 28.2 1.0
CB D:CYS112 3.3 33.6 1.0
CA D:HIS46 3.4 32.6 1.0
CB D:HIS117 3.4 25.1 1.0
CB D:HIS46 3.5 29.7 1.0
CB D:PHE114 3.8 21.6 1.0
C D:GLY45 3.8 24.5 1.0
N D:HIS46 4.0 33.8 1.0
CE D:MET121 4.1 23.7 1.0
NE2 D:HIS46 4.1 29.7 1.0
NE2 D:HIS117 4.1 31.0 1.0
CD2 D:HIS117 4.2 32.2 1.0
CD2 D:HIS46 4.2 33.6 1.0
C D:HIS46 4.5 35.5 1.0
N D:ASN47 4.6 38.4 1.0
CG D:PHE114 4.6 20.7 1.0
CG D:MET121 4.7 26.6 1.0
CA D:CYS112 4.7 38.0 1.0
N D:PHE114 4.8 29.2 1.0
CA D:PHE114 4.9 29.4 1.0
CA D:HIS117 4.9 26.6 1.0

Copper binding site 5 out of 12 in 1jvo

Go back to Copper Binding Sites List in 1jvo
Copper binding site 5 out of 12 in the Azurin Dimer, Crosslinked Via Disulfide Bridge


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Azurin Dimer, Crosslinked Via Disulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu129

b:47.6
occ:1.00
ND1 E:HIS117 2.0 59.0 1.0
ND1 E:HIS46 2.1 49.7 1.0
SG E:CYS112 2.2 39.0 1.0
O E:GLY45 2.7 44.0 1.0
CE1 E:HIS117 2.9 55.0 1.0
CE1 E:HIS46 3.0 42.6 1.0
CG E:HIS117 3.1 56.9 1.0
CG E:HIS46 3.1 47.9 1.0
SD E:MET121 3.1 48.5 1.0
CB E:CYS112 3.3 38.1 1.0
CA E:HIS46 3.3 37.7 1.0
CB E:HIS46 3.5 42.6 1.0
CB E:HIS117 3.5 55.0 1.0
C E:GLY45 3.6 38.8 1.0
CB E:PHE114 3.8 36.8 1.0
CE E:MET121 3.9 44.0 1.0
N E:HIS46 3.9 39.0 1.0
NE2 E:HIS117 4.1 60.9 1.0
NE2 E:HIS46 4.1 42.6 1.0
CD2 E:HIS117 4.2 62.1 1.0
CD2 E:HIS46 4.2 46.5 1.0
C E:HIS46 4.6 40.7 1.0
CG E:PHE114 4.6 36.0 1.0
N E:ASN47 4.7 48.9 1.0
CA E:CYS112 4.7 36.3 1.0
CG E:MET121 4.8 46.9 1.0
N E:PHE114 4.9 44.3 1.0
CA E:PHE114 4.9 44.5 1.0
CA E:HIS117 5.0 42.1 1.0
CA E:GLY45 5.0 48.1 1.0

Copper binding site 6 out of 12 in 1jvo

Go back to Copper Binding Sites List in 1jvo
Copper binding site 6 out of 12 in the Azurin Dimer, Crosslinked Via Disulfide Bridge


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Azurin Dimer, Crosslinked Via Disulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu129

b:47.6
occ:1.00
ND1 F:HIS46 2.0 48.8 1.0
ND1 F:HIS117 2.2 99.3 1.0
SG F:CYS112 2.3 44.5 1.0
O F:GLY45 2.7 46.7 1.0
CG F:HIS46 2.9 47.0 1.0
CE1 F:HIS46 3.0 41.7 1.0
CE1 F:HIS117 3.1 98.0 1.0
CB F:CYS112 3.2 43.7 1.0
CA F:HIS46 3.2 34.3 1.0
CG F:HIS117 3.2 99.3 1.0
CB F:HIS46 3.2 41.7 1.0
SD F:MET121 3.3 99.3 1.0
CB F:HIS117 3.5 98.0 1.0
C F:GLY45 3.6 41.5 1.0
CB F:PHE114 3.7 77.5 1.0
N F:HIS46 3.8 35.5 1.0
CE F:MET121 4.0 99.3 1.0
NE2 F:HIS46 4.0 41.7 1.0
CD2 F:HIS46 4.1 45.6 1.0
NE2 F:HIS117 4.3 99.3 1.0
CD2 F:HIS117 4.3 99.3 1.0
C F:HIS46 4.5 37.3 1.0
CG F:PHE114 4.6 76.6 1.0
N F:ASN47 4.6 41.5 1.0
CA F:CYS112 4.7 98.6 1.0
N F:PHE114 4.8 99.3 1.0
CA F:PHE114 4.8 99.3 1.0
CG F:MET121 4.9 99.3 1.0
CA F:GLY45 4.9 50.8 1.0

Copper binding site 7 out of 12 in 1jvo

Go back to Copper Binding Sites List in 1jvo
Copper binding site 7 out of 12 in the Azurin Dimer, Crosslinked Via Disulfide Bridge


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Azurin Dimer, Crosslinked Via Disulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu129

b:47.6
occ:1.00
ND1 G:HIS46 2.0 38.8 1.0
SG G:CYS112 2.1 36.4 1.0
ND1 G:HIS117 2.2 46.6 1.0
CE1 G:HIS46 2.9 31.7 1.0
O G:GLY45 3.0 35.3 1.0
SD G:MET121 3.0 38.3 1.0
CG G:HIS46 3.1 37.1 1.0
CE1 G:HIS117 3.2 42.6 1.0
CG G:HIS117 3.2 44.5 1.0
CB G:CYS112 3.3 35.6 1.0
CA G:HIS46 3.4 34.5 1.0
CB G:HIS117 3.5 42.6 1.0
CB G:HIS46 3.5 31.7 1.0
CE G:MET121 3.7 33.7 1.0
C G:GLY45 3.9 30.1 1.0
CB G:PHE114 3.9 50.1 1.0
NE2 G:HIS46 4.0 31.7 1.0
N G:HIS46 4.1 35.7 1.0
CD2 G:HIS46 4.1 35.6 1.0
NE2 G:HIS117 4.3 48.5 1.0
CD2 G:HIS117 4.3 49.7 1.0
CG G:MET121 4.6 36.6 1.0
C G:HIS46 4.6 37.5 1.0
CA G:CYS112 4.7 40.6 1.0
N G:ASN47 4.7 49.6 1.0
CG G:PHE114 4.7 49.3 1.0
N G:PHE114 4.8 37.7 1.0
CA G:PHE114 4.9 37.9 1.0
CB G:MET121 4.9 33.7 1.0
CA G:HIS117 5.0 34.5 1.0

Copper binding site 8 out of 12 in 1jvo

Go back to Copper Binding Sites List in 1jvo
Copper binding site 8 out of 12 in the Azurin Dimer, Crosslinked Via Disulfide Bridge


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Azurin Dimer, Crosslinked Via Disulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu129

b:47.6
occ:1.00
ND1 H:HIS46 2.0 41.5 1.0
ND1 H:HIS117 2.1 37.0 1.0
SG H:CYS112 2.3 38.9 1.0
CE1 H:HIS46 2.9 34.4 1.0
O H:GLY45 3.0 44.2 1.0
CE1 H:HIS117 3.0 33.0 1.0
SD H:MET121 3.1 41.7 1.0
CG H:HIS46 3.1 39.7 1.0
CG H:HIS117 3.1 34.9 1.0
CB H:CYS112 3.3 38.1 1.0
CA H:HIS46 3.4 34.2 1.0
CB H:HIS117 3.5 33.0 1.0
CB H:HIS46 3.5 34.4 1.0
C H:GLY45 3.8 39.0 1.0
CE H:MET121 3.9 37.2 1.0
CB H:PHE114 3.9 35.9 1.0
N H:HIS46 4.0 35.5 1.0
NE2 H:HIS46 4.1 34.4 1.0
NE2 H:HIS117 4.2 38.9 1.0
CD2 H:HIS46 4.2 38.3 1.0
CD2 H:HIS117 4.2 40.1 1.0
C H:HIS46 4.5 37.2 1.0
N H:ASN47 4.6 39.0 1.0
CG H:MET121 4.7 40.1 1.0
CG H:PHE114 4.7 35.0 1.0
CA H:CYS112 4.7 43.2 1.0
N H:PHE114 4.9 50.9 1.0
CA H:HIS117 5.0 30.1 1.0

Copper binding site 9 out of 12 in 1jvo

Go back to Copper Binding Sites List in 1jvo
Copper binding site 9 out of 12 in the Azurin Dimer, Crosslinked Via Disulfide Bridge


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Azurin Dimer, Crosslinked Via Disulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu129

b:47.6
occ:1.00
ND1 I:HIS117 2.0 46.6 1.0
ND1 I:HIS46 2.1 41.0 1.0
SG I:CYS112 2.2 37.5 1.0
O I:GLY45 2.8 42.9 1.0
CE1 I:HIS117 3.0 42.5 1.0
CG I:HIS117 3.0 44.5 1.0
CE1 I:HIS46 3.0 33.9 1.0
SD I:MET121 3.1 40.5 1.0
CG I:HIS46 3.2 39.2 1.0
CB I:CYS112 3.3 36.7 1.0
CB I:HIS117 3.4 42.5 1.0
CA I:HIS46 3.4 32.3 1.0
CB I:HIS46 3.5 33.9 1.0
C I:GLY45 3.7 37.7 1.0
CB I:PHE114 3.8 29.7 1.0
CE I:MET121 3.9 36.0 1.0
N I:HIS46 4.0 33.5 1.0
NE2 I:HIS117 4.1 48.4 1.0
CD2 I:HIS117 4.1 49.6 1.0
NE2 I:HIS46 4.2 33.9 1.0
CD2 I:HIS46 4.3 37.8 1.0
C I:HIS46 4.6 35.2 1.0
CG I:MET121 4.6 38.9 1.0
CA I:CYS112 4.7 31.9 1.0
CG I:PHE114 4.7 28.8 1.0
N I:ASN47 4.7 29.0 1.0
N I:PHE114 4.8 37.2 1.0
CA I:HIS117 4.9 43.8 1.0
CA I:PHE114 4.9 37.3 1.0
CB I:MET121 5.0 36.0 1.0

Copper binding site 10 out of 12 in 1jvo

Go back to Copper Binding Sites List in 1jvo
Copper binding site 10 out of 12 in the Azurin Dimer, Crosslinked Via Disulfide Bridge


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Azurin Dimer, Crosslinked Via Disulfide Bridge within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cu129

b:47.6
occ:1.00
ND1 J:HIS46 2.0 28.2 1.0
ND1 J:HIS117 2.1 50.5 1.0
SG J:CYS112 2.3 37.2 1.0
O J:GLY45 2.8 28.6 1.0
CE1 J:HIS46 2.9 21.1 1.0
CE1 J:HIS117 3.0 46.4 1.0
CG J:HIS46 3.1 26.4 1.0
CG J:HIS117 3.1 48.3 1.0
SD J:MET121 3.2 47.9 1.0
CB J:CYS112 3.3 36.4 1.0
CA J:HIS46 3.4 34.6 1.0
CB J:HIS117 3.5 46.4 1.0
CB J:HIS46 3.5 21.1 1.0
C J:GLY45 3.8 23.4 1.0
CB J:PHE114 3.8 34.1 1.0
CE J:MET121 4.0 43.3 1.0
NE2 J:HIS46 4.0 21.1 1.0
N J:HIS46 4.0 35.8 1.0
NE2 J:HIS117 4.1 52.3 1.0
CD2 J:HIS46 4.1 25.0 1.0
CD2 J:HIS117 4.2 53.5 1.0
CG J:PHE114 4.6 33.3 1.0
C J:HIS46 4.6 37.6 1.0
CA J:CYS112 4.7 33.4 1.0
N J:ASN47 4.7 20.8 1.0
CG J:MET121 4.8 46.2 1.0
N J:PHE114 4.8 41.8 1.0
CA J:PHE114 4.9 42.0 1.0
CA J:HIS117 4.9 43.0 1.0

Reference:

I.M.C.Van Amsterdam, M.Ubbink, O.Einsle, A.Messerschmidt, A.Merli, D.Cavazzini, G.L.Rossi, G.W.Canters. Dramatic Modulation of Electron Transfer in Protein Complexes By Crosslinking Nat.Struct.Biol. V. 9 48 2002.
ISSN: ISSN 1072-8368
PubMed: 11740504
DOI: 10.1038/NSB736
Page generated: Sun Dec 13 10:59:45 2020

Last articles

Zn in 7O75
Zn in 7O73
Zn in 7O4I
Zn in 7O72
Zn in 7O4J
Zn in 7NVR
Zn in 7NVY
Zn in 7NVZ
Zn in 7NW0
Zn in 7O4K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy