Atomistry » Copper » PDB 1rju-1tl4 » 1rkr
Atomistry »
  Copper »
    PDB 1rju-1tl4 »
      1rkr »

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

Protein crystallography data

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

Copper Binding Sites:

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 1rkr

Go back to Copper Binding Sites List in 1rkr
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 1rkr

Go back to Copper Binding Sites List in 1rkr
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 1rkr

Go back to Copper Binding Sites List in 1rkr
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 1rkr

Go back to Copper Binding Sites List in 1rkr
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

Reference:

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
Page generated: Tue Jul 30 22:43:07 2024

Last articles

Br in 19GS
Br in 1D07
Br in 1CS7
Br in 1BA3
Br in 1CIJ
Br in 1C4U
Br in 1BSO
Br in 1BK9
Br in 1AZF
Br in 1AWC
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy