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

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

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 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 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 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 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 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 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 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 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 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 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

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