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Copper in PDB 3wky: Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean

Protein crystallography data

The structure of Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean, PDB code: 3wky was solved by T.Masuda, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.81 / 1.80
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 156.706, 156.706, 283.830, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 19.6

Other elements in 3wky:

The structure of Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 5 atoms
Sodium (Na) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean (pdb code 3wky). 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 Hemolymph Type Prophenoloxidase (Propob) From Crustacean, PDB code: 3wky:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 3wky

Go back to Copper Binding Sites List in 3wky
Copper binding site 1 out of 4 in the Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean


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 Hemolymph Type Prophenoloxidase (Propob) From Crustacean within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu708

b:26.5
occ:1.00
CU1 A:CUO708 0.0 26.5 1.0
O1 A:CUO708 2.0 34.5 1.0
NE2 A:HIS226 2.2 19.4 1.0
NE2 A:HIS199 2.2 20.4 1.0
O2 A:CUO708 2.3 28.9 1.0
NE2 A:HIS203 2.3 17.2 1.0
CE1 A:HIS199 3.0 18.0 1.0
CE1 A:HIS226 3.1 19.5 1.0
CD2 A:HIS199 3.2 20.5 1.0
CD2 A:HIS226 3.2 19.4 1.0
CE1 A:HIS203 3.2 18.3 1.0
CD2 A:HIS203 3.3 17.4 1.0
CU2 A:CUO708 3.6 20.8 1.0
ND1 A:HIS199 4.1 20.6 1.0
NE2 A:HIS397 4.2 17.5 1.0
CZ A:PHE393 4.2 13.0 1.0
CG A:HIS199 4.2 16.6 1.0
ND1 A:HIS226 4.2 15.8 1.0
CG A:HIS226 4.3 15.2 1.0
CE1 A:PHE393 4.3 15.2 1.0
ND1 A:HIS203 4.4 18.9 1.0
CG A:HIS203 4.4 14.8 1.0
CE1 A:HIS397 4.4 19.3 1.0
CE A:MET225 4.6 18.3 1.0
NE2 A:HIS357 4.8 13.8 1.0
CE1 A:PHE222 4.8 19.1 1.0

Copper binding site 2 out of 4 in 3wky

Go back to Copper Binding Sites List in 3wky
Copper binding site 2 out of 4 in the Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean


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 Hemolymph Type Prophenoloxidase (Propob) From Crustacean within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu708

b:20.8
occ:1.00
CU2 A:CUO708 0.0 20.8 1.0
O1 A:CUO708 2.0 34.5 1.0
NE2 A:HIS361 2.1 12.9 1.0
NE2 A:HIS357 2.1 13.8 1.0
O2 A:CUO708 2.2 28.9 1.0
NE2 A:HIS397 2.2 17.5 1.0
CE1 A:HIS397 3.0 19.3 1.0
CE1 A:HIS361 3.0 19.0 1.0
CD2 A:HIS361 3.1 16.9 1.0
CD2 A:HIS357 3.1 13.1 1.0
CE1 A:HIS357 3.1 13.1 1.0
CD2 A:HIS397 3.3 15.1 1.0
CU1 A:CUO708 3.6 26.5 1.0
CE1 A:PHE393 4.0 15.2 1.0
CE1 A:PHE72 4.1 19.3 1.0
ND1 A:HIS361 4.1 13.5 1.0
CG A:HIS361 4.2 13.4 1.0
ND1 A:HIS397 4.2 16.1 1.0
ND1 A:HIS357 4.2 14.2 1.0
CG A:HIS357 4.2 13.3 1.0
CG A:HIS397 4.3 14.8 1.0
CZ A:PHE72 4.4 20.4 1.0
CZ A:PHE393 4.5 13.0 1.0
NE2 A:HIS226 4.6 19.4 1.0
CD1 A:TRP396 4.6 15.8 1.0
CD2 A:HIS226 4.8 19.4 1.0
CD1 A:PHE393 4.8 16.0 1.0
NE2 A:HIS199 4.9 20.4 1.0
CE1 A:PHE222 5.0 19.1 1.0
CD1 A:PHE72 5.0 18.4 1.0

Copper binding site 3 out of 4 in 3wky

Go back to Copper Binding Sites List in 3wky
Copper binding site 3 out of 4 in the Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean


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 Hemolymph Type Prophenoloxidase (Propob) From Crustacean within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu708

b:26.7
occ:1.00
CU1 B:CUO708 0.0 26.7 1.0
O1 B:CUO708 2.2 34.5 1.0
NE2 B:HIS226 2.2 19.1 1.0
NE2 B:HIS199 2.2 22.4 1.0
O2 B:CUO708 2.2 27.3 1.0
NE2 B:HIS203 2.3 16.8 1.0
CE1 B:HIS199 3.0 15.5 1.0
CE1 B:HIS226 3.1 18.4 1.0
CD2 B:HIS226 3.2 18.7 1.0
CD2 B:HIS199 3.2 21.1 1.0
CD2 B:HIS203 3.2 16.8 1.0
CE1 B:HIS203 3.3 17.6 1.0
CU2 B:CUO708 3.6 20.5 1.0
ND1 B:HIS199 4.1 19.7 1.0
NE2 B:HIS397 4.2 18.0 1.0
CZ B:PHE393 4.2 13.6 1.0
ND1 B:HIS226 4.2 16.6 1.0
CG B:HIS199 4.2 16.9 1.0
CG B:HIS226 4.3 14.5 1.0
CE2 B:PHE393 4.3 14.7 1.0
CE1 B:HIS397 4.4 19.1 1.0
ND1 B:HIS203 4.4 17.9 1.0
CG B:HIS203 4.4 16.4 1.0
CE B:MET225 4.5 19.1 1.0
NE2 B:HIS357 4.8 13.6 1.0
CE1 B:PHE222 4.8 16.8 1.0

Copper binding site 4 out of 4 in 3wky

Go back to Copper Binding Sites List in 3wky
Copper binding site 4 out of 4 in the Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean


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 Hemolymph Type Prophenoloxidase (Propob) From Crustacean within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu708

b:20.5
occ:1.00
CU2 B:CUO708 0.0 20.5 1.0
O1 B:CUO708 1.8 34.5 1.0
NE2 B:HIS361 2.1 13.1 1.0
NE2 B:HIS357 2.2 13.6 1.0
NE2 B:HIS397 2.2 18.0 1.0
O2 B:CUO708 2.2 27.3 1.0
CE1 B:HIS397 3.0 19.1 1.0
CD2 B:HIS361 3.0 16.8 1.0
CD2 B:HIS357 3.1 13.2 1.0
CE1 B:HIS361 3.1 19.4 1.0
CE1 B:HIS357 3.2 14.7 1.0
CD2 B:HIS397 3.3 15.1 1.0
CU1 B:CUO708 3.6 26.7 1.0
CE2 B:PHE393 4.0 14.7 1.0
CE1 B:PHE72 4.1 19.4 1.0
CG B:HIS361 4.1 12.2 1.0
ND1 B:HIS397 4.2 16.2 1.0
ND1 B:HIS361 4.2 13.9 1.0
CG B:HIS357 4.2 12.8 1.0
ND1 B:HIS357 4.2 15.3 1.0
CG B:HIS397 4.3 14.6 1.0
CZ B:PHE72 4.4 19.1 1.0
CZ B:PHE393 4.5 13.6 1.0
NE2 B:HIS226 4.5 19.1 1.0
CD1 B:TRP396 4.6 15.3 1.0
CD2 B:HIS226 4.7 18.7 1.0
CD2 B:PHE393 4.8 14.8 1.0
NE2 B:HIS199 4.9 22.4 1.0
CE1 B:PHE222 5.0 16.8 1.0
CD1 B:PHE72 5.0 19.9 1.0

Reference:

T.Masuda, K.Momoji, T.Hirata, B.Mikami. Crystal Structure of A Crustacean Prophenoloxidase Provides A Clue to Understanding the Functionality of the Type 3 Copper Proteins. Febs J. 2014.
ISSN: ISSN 1742-464X
PubMed: 24720693
DOI: 10.1111/FEBS.12812
Page generated: Sun Dec 13 11:12:47 2020

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