Atomistry » Copper » PDB 5wbd-5z85 » 5yt7
Atomistry »
  Copper »
    PDB 5wbd-5z85 »
      5yt7 »

Copper in PDB 5yt7: Crystal Structure of Circularly Permutated Azurin 3

Protein crystallography data

The structure of Crystal Structure of Circularly Permutated Azurin 3, PDB code: 5yt7 was solved by H.H.Chen, H.P.Liu, Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.02 / 1.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.888, 87.968, 66.096, 90.00, 110.22, 90.00
R / Rfree (%) 16.2 / 21.7

Other elements in 5yt7:

The structure of Crystal Structure of Circularly Permutated Azurin 3 also contains other interesting chemical elements:

Calcium (Ca) 3 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Circularly Permutated Azurin 3 (pdb code 5yt7). 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 Circularly Permutated Azurin 3, PDB code: 5yt7:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 5yt7

Go back to Copper Binding Sites List in 5yt7
Copper binding site 1 out of 4 in the Crystal Structure of Circularly Permutated Azurin 3


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 Circularly Permutated Azurin 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu201

b:19.2
occ:1.00
ND1 A:HIS65 2.1 19.2 1.0
ND1 A:HIS3 2.1 19.0 1.0
SG A:CYS131 2.2 17.7 1.0
O A:GLY64 2.7 18.6 1.0
CE1 A:HIS65 3.0 18.6 1.0
CG A:HIS3 3.1 18.1 1.0
CE1 A:HIS3 3.1 21.0 1.0
CG A:HIS65 3.1 17.9 1.0
SD A:MET7 3.3 17.7 1.0
CB A:CYS131 3.3 17.9 1.0
CA A:HIS65 3.3 18.0 1.0
CB A:HIS3 3.3 16.4 1.0
CB A:HIS65 3.5 18.2 1.0
C A:GLY64 3.7 19.0 1.0
CB A:PHE133 3.8 16.8 1.0
CE A:MET7 3.8 18.3 1.0
N A:HIS65 3.9 20.1 1.0
NE2 A:HIS65 4.1 17.6 1.0
NE2 A:HIS3 4.2 24.2 1.0
CD2 A:HIS3 4.2 21.8 1.0
CD2 A:HIS65 4.2 19.9 1.0
C A:HIS65 4.5 17.8 1.0
CG A:PHE133 4.6 18.2 1.0
N A:ASN66 4.6 17.6 1.0
CA A:CYS131 4.7 16.1 1.0
CG A:MET7 4.7 18.7 1.0
N A:PHE133 4.8 18.2 1.0
CA A:HIS3 4.9 17.1 1.0
CA A:PHE133 4.9 20.3 1.0
CD1 A:PHE133 5.0 19.9 1.0
CB A:MET7 5.0 17.7 1.0

Copper binding site 2 out of 4 in 5yt7

Go back to Copper Binding Sites List in 5yt7
Copper binding site 2 out of 4 in the Crystal Structure of Circularly Permutated Azurin 3


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 Circularly Permutated Azurin 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:15.2
occ:1.00
ND1 B:HIS3 2.1 15.7 1.0
ND1 B:HIS65 2.1 14.7 1.0
SG B:CYS131 2.2 14.8 1.0
O B:GLY64 2.8 14.0 1.0
CE1 B:HIS65 3.0 15.6 1.0
CE1 B:HIS3 3.1 16.9 1.0
CG B:HIS3 3.1 14.3 1.0
CG B:HIS65 3.1 13.4 1.0
CB B:CYS131 3.3 14.5 1.0
CB B:HIS3 3.3 13.3 1.0
CA B:HIS65 3.3 12.8 1.0
SD B:MET7 3.4 14.6 1.0
CB B:HIS65 3.5 13.2 1.0
C B:GLY64 3.7 14.0 1.0
CB B:PHE133 3.8 17.5 1.0
N B:HIS65 4.0 14.0 1.0
CE B:MET7 4.0 15.2 1.0
NE2 B:HIS65 4.2 15.9 1.0
NE2 B:HIS3 4.2 18.1 1.0
CD2 B:HIS3 4.2 15.7 1.0
CD2 B:HIS65 4.2 14.5 1.0
C B:HIS65 4.6 13.7 1.0
CG B:PHE133 4.6 17.4 1.0
N B:ASN66 4.6 14.1 1.0
CA B:CYS131 4.7 14.2 1.0
N B:PHE133 4.7 17.4 1.0
CG B:MET7 4.8 13.9 1.0
CA B:PHE133 4.8 19.5 1.0
CA B:HIS3 4.9 14.1 1.0

Copper binding site 3 out of 4 in 5yt7

Go back to Copper Binding Sites List in 5yt7
Copper binding site 3 out of 4 in the Crystal Structure of Circularly Permutated Azurin 3


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 Circularly Permutated Azurin 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu201

b:19.7
occ:1.00
ND1 C:HIS3 2.1 17.0 1.0
SG C:CYS131 2.1 17.9 1.0
ND1 C:HIS65 2.1 20.2 1.0
O C:GLY64 2.8 18.2 1.0
CE1 C:HIS3 3.0 17.5 1.0
CE1 C:HIS65 3.1 20.1 1.0
CG C:HIS3 3.1 16.7 1.0
CG C:HIS65 3.2 17.9 1.0
SD C:MET7 3.2 18.4 1.0
CB C:CYS131 3.3 17.2 1.0
CB C:HIS3 3.4 18.1 1.0
CA C:HIS65 3.4 18.8 1.0
CB C:HIS65 3.6 17.9 1.0
C C:GLY64 3.8 19.2 1.0
CB C:PHE133 3.8 20.2 1.0
CE C:MET7 3.9 19.3 1.0
N C:HIS65 4.0 18.5 1.0
NE2 C:HIS3 4.1 17.9 1.0
CD2 C:HIS3 4.2 19.0 1.0
NE2 C:HIS65 4.2 18.8 1.0
CD2 C:HIS65 4.3 18.5 1.0
C C:HIS65 4.5 17.8 1.0
N C:ASN66 4.6 16.7 1.0
CG C:PHE133 4.6 20.6 1.0
CA C:CYS131 4.7 17.5 1.0
CG C:MET7 4.7 18.7 1.0
N C:PHE133 4.8 20.0 1.0
CA C:PHE133 4.9 21.0 1.0
CA C:HIS3 4.9 18.5 1.0
CB C:MET7 5.0 17.4 1.0

Copper binding site 4 out of 4 in 5yt7

Go back to Copper Binding Sites List in 5yt7
Copper binding site 4 out of 4 in the Crystal Structure of Circularly Permutated Azurin 3


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 Circularly Permutated Azurin 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu201

b:20.0
occ:1.00
ND1 D:HIS65 2.1 18.3 1.0
ND1 D:HIS3 2.1 16.5 1.0
SG D:CYS131 2.2 17.9 1.0
O D:GLY64 2.8 21.8 1.0
CE1 D:HIS65 3.0 19.4 1.0
CG D:HIS3 3.1 18.1 1.0
CE1 D:HIS3 3.1 20.1 1.0
CG D:HIS65 3.1 19.9 1.0
SD D:MET7 3.2 18.1 1.0
CB D:CYS131 3.3 17.6 1.0
CA D:HIS65 3.3 18.8 1.0
CB D:HIS3 3.4 17.6 1.0
CB D:HIS65 3.5 19.4 1.0
C D:GLY64 3.7 19.1 1.0
CE D:MET7 3.8 17.6 1.0
CB D:PHE133 3.8 21.8 1.0
N D:HIS65 4.0 17.9 1.0
NE2 D:HIS65 4.1 21.7 1.0
NE2 D:HIS3 4.2 22.0 1.0
CD2 D:HIS3 4.2 20.9 1.0
CD2 D:HIS65 4.2 21.2 1.0
C D:HIS65 4.5 17.9 1.0
N D:ASN66 4.6 17.4 1.0
CG D:PHE133 4.6 21.1 1.0
CA D:CYS131 4.6 17.2 1.0
CG D:MET7 4.7 19.1 1.0
N D:PHE133 4.8 20.1 1.0
CA D:PHE133 4.9 21.6 1.0
CA D:HIS3 4.9 19.4 1.0

Reference:

H.H.Chen, B.Su, T.T.Zhang, A.Huang, H.P.Liu, Y.Yu, J.Wang. Engineering the Metal-Binding Loop of A Blue Copper Protein By Circular Permutation Rsc Adv 56093 2017.
ISSN: ESSN 2046-2069
DOI: 10.1039/C7RA11512A
Page generated: Mon Jul 14 05:35:52 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy