Copper in PDB 1rkr: Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015

The structure of Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015, PDB code: 1rkr was solved by C.Li, T.Inoue, M.Gotowda, S.Suzuki, K.Yamaguchi, K.Kataoka, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.670, 54.260, 74.550, 90.00, 95.99, 90.00
R / Rfree (%)	17.3 / 23.6

The binding sites of Copper atom in the Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015 (pdb code 1rkr). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015, PDB code: 1rkr:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu200 b:13.2 occ:1.00 ND1 A:HIS117 1.9 18.8 1.0 ND1 A:HIS46 2.0 15.5 1.0 SG A:CYS112 2.1 4.6 1.0 O A:GLY45 2.5 22.7 1.0 CE1 A:HIS117 2.8 13.8 1.0 CE1 A:HIS46 3.0 14.4 1.0 CG A:HIS117 3.0 21.3 1.0 CG A:HIS46 3.1 8.8 1.0 SD A:MET121 3.1 24.5 1.0 CA A:HIS46 3.4 7.1 1.0 CB A:CYS112 3.4 11.8 1.0 CB A:HIS117 3.5 18.7 1.0 CB A:HIS46 3.6 9.9 1.0 C A:GLY45 3.6 11.9 1.0 CB A:PHE114 3.7 11.6 1.0 NE2 A:HIS117 3.9 12.8 1.0 N A:HIS46 4.0 10.8 1.0 NE2 A:HIS46 4.1 13.4 1.0 CD2 A:HIS117 4.1 19.8 1.0 CD2 A:HIS46 4.2 16.2 1.0 CE A:MET121 4.3 22.9 1.0 CG A:PHE114 4.4 14.8 1.0 C A:HIS46 4.6 6.9 1.0 CG A:MET121 4.6 17.5 1.0 N A:ASN47 4.7 6.5 1.0 CD1 A:PHE114 4.7 9.0 1.0 CA A:CYS112 4.8 10.2 1.0 CA A:PHE114 4.9 14.7 1.0 CA A:GLY45 4.9 12.1 1.0 N A:PHE114 4.9 9.9 1.0 CA A:HIS117 5.0 18.1 1.0

Copper binding site 2 out of 4 in the Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu201 b:17.1 occ:1.00 ND1 B:HIS46 2.0 5.8 1.0 ND1 B:HIS117 2.0 26.6 1.0 SG B:CYS112 2.1 8.9 1.0 O B:GLY45 2.5 17.4 1.0 CE1 B:HIS46 2.9 2.0 1.0 CE1 B:HIS117 2.9 22.4 1.0 CG B:HIS46 3.0 3.4 1.0 CG B:HIS117 3.0 22.6 1.0 SD B:MET121 3.2 12.0 1.0 CA B:HIS46 3.3 6.8 1.0 CB B:HIS117 3.4 19.6 1.0 CB B:CYS112 3.5 6.2 1.0 C B:GLY45 3.5 11.8 1.0 CB B:HIS46 3.5 3.0 1.0 N B:HIS46 3.9 12.0 1.0 CB B:PHE114 3.9 3.4 1.0 NE2 B:HIS46 4.0 6.2 1.0 NE2 B:HIS117 4.1 24.3 1.0 CD2 B:HIS46 4.2 8.6 1.0 CD2 B:HIS117 4.2 24.4 1.0 CE B:MET121 4.2 13.6 1.0 C B:HIS46 4.5 9.9 1.0 N B:ASN47 4.6 11.4 1.0 CG B:PHE114 4.6 5.9 1.0 CG B:MET121 4.7 9.0 1.0 CA B:CYS112 4.8 7.9 1.0 CA B:GLY45 4.9 9.1 1.0 N B:PHE114 4.9 11.0 1.0 CA B:HIS117 4.9 13.3 1.0 O B:PHE114 4.9 13.4 1.0 CA B:PHE114 5.0 10.0 1.0 CD1 B:PHE114 5.0 3.9 1.0

Copper binding site 3 out of 4 in the Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu202 b:18.8 occ:1.00 ND1 C:HIS117 1.9 2.0 1.0 ND1 C:HIS46 1.9 2.0 1.0 SG C:CYS112 2.2 11.8 1.0 O C:GLY45 2.5 15.7 1.0 CE1 C:HIS117 2.8 4.5 1.0 CE1 C:HIS46 2.8 6.3 1.0 CG C:HIS46 2.9 7.6 1.0 CG C:HIS117 2.9 12.0 1.0 SD C:MET121 3.1 10.5 1.0 CA C:HIS46 3.3 4.3 1.0 CB C:HIS117 3.4 15.9 1.0 CB C:HIS46 3.4 6.0 1.0 CB C:CYS112 3.5 17.3 1.0 C C:GLY45 3.6 8.3 1.0 CB C:PHE114 3.9 17.6 1.0 N C:HIS46 3.9 6.3 1.0 NE2 C:HIS46 3.9 6.5 1.0 NE2 C:HIS117 3.9 7.4 1.0 CE C:MET121 4.1 14.8 1.0 CD2 C:HIS46 4.1 9.4 1.0 CD2 C:HIS117 4.1 9.4 1.0 C C:HIS46 4.6 6.0 1.0 N C:ASN47 4.6 11.3 1.0 CG C:MET121 4.6 2.0 1.0 CG C:PHE114 4.6 16.7 1.0 CA C:CYS112 4.8 18.9 1.0 CA C:HIS117 4.9 9.1 1.0 CA C:GLY45 4.9 2.9 1.0 CD1 C:PHE114 5.0 14.7 1.0 N C:PHE114 5.0 14.2 1.0

Copper binding site 4 out of 4 in the Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Azurin-I From Alcaligenes Xylosoxidans Ncimb 11015 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu203 b:18.9 occ:1.00 ND1 D:HIS117 1.9 2.1 1.0 ND1 D:HIS46 2.0 9.9 1.0 SG D:CYS112 2.1 24.4 1.0 O D:GLY45 2.6 12.6 1.0 CE1 D:HIS117 2.9 2.0 1.0 CG D:HIS117 3.0 6.2 1.0 CE1 D:HIS46 3.0 5.5 1.0 CG D:HIS46 3.0 2.4 1.0 SD D:MET121 3.2 18.7 1.0 CA D:HIS46 3.3 7.0 1.0 CB D:CYS112 3.4 17.4 1.0 CB D:HIS46 3.4 3.4 1.0 CB D:HIS117 3.5 13.5 1.0 C D:GLY45 3.6 6.5 1.0 CB D:PHE114 3.9 4.9 1.0 N D:HIS46 3.9 6.0 1.0 NE2 D:HIS117 4.1 3.2 1.0 NE2 D:HIS46 4.1 9.8 1.0 CD2 D:HIS117 4.1 4.8 1.0 CE D:MET121 4.1 11.9 1.0 CD2 D:HIS46 4.2 5.7 1.0 C D:HIS46 4.4 13.5 1.0 N D:ASN47 4.4 10.0 1.0 CG D:PHE114 4.6 2.0 1.0 CG D:MET121 4.7 19.5 1.0 CA D:CYS112 4.7 16.4 1.0 CD1 D:PHE114 4.9 2.0 1.0 N D:PHE114 4.9 14.3 1.0

C.Li, T.Inoue, M.Gotowda, S.Suzuki, K.Yamaguchi, K.Kunishige, Y.Kai. Structure of Azurin I From the Denitrifying Bacterium Alcaligenes Xylosoxidans Ncimb 11015 at 2.45 A Resolution. Acta Crystallogr.,Sect.D V. 54 347 1998.
ISSN: ISSN 0907-4449
PubMed: 9761902
DOI: 10.1107/S0907444997010974