Copper in PDB 4yzw: Crystal Structure of AGPPO8

The structure of Crystal Structure of AGPPO8, PDB code: 4yzw was solved by Y.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.32 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.583, 106.583, 92.110, 90.00, 105.79, 90.00
R / Rfree (%)	18.8 / 23.3

The binding sites of Copper atom in the Crystal Structure of AGPPO8 (pdb code 4yzw). 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 AGPPO8, PDB code: 4yzw:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Crystal Structure of AGPPO8


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 AGPPO8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu801 b:72.3 occ:1.00 NE2 A:HIS227 2.0 30.4 1.0 NE2 A:HIS223 2.0 28.7 1.0 NE2 A:HIS252 2.0 26.6 1.0 CE1 A:HIS252 2.8 32.6 1.0 CE1 A:HIS223 2.8 24.6 1.0 CD2 A:HIS223 2.9 27.6 1.0 CE1 A:HIS227 3.0 28.6 1.0 CD2 A:HIS227 3.0 27.2 1.0 CD2 A:HIS252 3.2 30.4 1.0 ND1 A:HIS223 3.8 26.4 1.0 CG A:HIS223 3.9 27.3 1.0 ND1 A:HIS252 4.0 30.2 1.0 ND1 A:HIS227 4.1 36.9 1.0 CG A:HIS227 4.2 29.8 1.0 CE A:MET251 4.2 26.9 1.0 CG A:HIS252 4.2 27.0 1.0 CE1 A:HIS419 4.4 27.5 1.0 CU A:CU802 4.5 74.0 1.0 NE2 A:HIS419 4.6 30.8 1.0 CZ A:PHE415 4.6 26.4 1.0 CE1 A:PHE415 4.8 27.4 1.0 CE1 A:PHE248 5.0 31.0 1.0

Copper binding site 2 out of 4 in the Crystal Structure of AGPPO8


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 AGPPO8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu802 b:74.0 occ:1.00 NE2 A:HIS419 2.0 30.8 1.0 NE2 A:HIS379 2.1 28.2 1.0 NE2 A:HIS383 2.1 26.3 1.0 CE1 A:HIS419 2.8 27.5 1.0 CD2 A:HIS379 2.9 24.2 1.0 CD2 A:HIS383 3.0 25.7 1.0 CE1 A:HIS383 3.0 20.1 1.0 CE1 A:HIS379 3.1 26.7 1.0 CD2 A:HIS419 3.1 25.8 1.0 CE1 A:PHE415 3.9 27.4 1.0 ND1 A:HIS419 3.9 30.1 1.0 ND1 A:HIS383 4.1 20.8 1.0 CG A:HIS379 4.1 23.2 1.0 CG A:HIS383 4.1 20.1 1.0 CG A:HIS419 4.1 22.0 1.0 ND1 A:HIS379 4.1 27.3 1.0 CD1 A:PHE415 4.5 27.7 1.0 CU A:CU801 4.5 72.3 1.0 CZ A:PHE415 4.6 26.4 1.0 CD1 A:TRP418 4.7 21.2 1.0 CE1 A:PHE99 4.8 22.0 1.0 NE2 A:HIS252 4.9 26.6 1.0 CZ A:PHE99 5.0 18.4 1.0

Copper binding site 3 out of 4 in the Crystal Structure of AGPPO8


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 AGPPO8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu801 b:71.8 occ:1.00 NE2 B:HIS223 2.0 38.6 1.0 NE2 B:HIS227 2.0 25.8 1.0 NE2 B:HIS252 2.0 36.5 1.0 CE1 B:HIS223 2.8 32.1 1.0 CD2 B:HIS223 2.9 34.8 1.0 CE1 B:HIS252 3.0 35.1 1.0 CE1 B:HIS227 3.0 28.1 1.0 CD2 B:HIS227 3.0 32.3 1.0 CD2 B:HIS252 3.1 36.1 1.0 ND1 B:HIS223 3.8 32.2 1.0 CG B:HIS223 3.9 33.8 1.0 ND1 B:HIS252 4.1 37.2 1.0 ND1 B:HIS227 4.1 31.8 1.0 CG B:HIS227 4.2 33.8 1.0 CE B:MET251 4.2 27.0 1.0 CG B:HIS252 4.2 30.4 1.0 CZ B:PHE415 4.4 31.2 1.0 CE1 B:HIS419 4.5 31.4 1.0 CU B:CU802 4.5 63.0 1.0 NE2 B:HIS419 4.6 38.3 1.0 CE1 B:PHE415 4.7 33.5 1.0

Copper binding site 4 out of 4 in the Crystal Structure of AGPPO8


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 AGPPO8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu802 b:63.0 occ:1.00 NE2 B:HIS419 2.0 38.3 1.0 NE2 B:HIS379 2.1 28.3 1.0 NE2 B:HIS383 2.1 31.2 1.0 CE1 B:HIS419 2.8 31.4 1.0 CD2 B:HIS383 2.9 31.8 1.0 CD2 B:HIS379 3.0 28.4 1.0 CE1 B:HIS383 3.0 30.6 1.0 CE1 B:HIS379 3.0 27.7 1.0 CD2 B:HIS419 3.2 34.0 1.0 CE1 B:PHE415 3.8 33.5 1.0 ND1 B:HIS419 4.0 32.8 1.0 CG B:HIS383 4.0 28.8 1.0 ND1 B:HIS383 4.1 29.7 1.0 ND1 B:HIS379 4.1 32.3 1.0 CG B:HIS379 4.1 27.2 1.0 CG B:HIS419 4.2 27.7 1.0 CD1 B:PHE415 4.5 26.8 1.0 CZ B:PHE415 4.5 31.2 1.0 CU B:CU801 4.5 71.8 1.0 CZ B:PHE99 4.8 29.8 1.0 CE1 B:PHE99 4.9 27.7 1.0 CD1 B:TRP418 4.9 28.6 1.0 NE2 B:HIS252 4.9 36.5 1.0

Y.Hu, Y.Wang, J.Deng, H.Jiang. The Structure of A Prophenoloxidase (Ppo) From Anopheles Gambiae Provides New Insights Into the Mechanism of Ppo Activation. Bmc Biol. V. 14 2 2016.
ISSN: ESSN 1741-7007
PubMed: 26732497
DOI: 10.1186/S12915-015-0225-2