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

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

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

Magnesium	(Mg)	1 atom
Copper	(Cu)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean, PDB code: 3wky:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl715 b:25.0 occ:1.00 O B:HOH1103 3.0 30.4 1.0 N A:LEU288 3.2 20.8 1.0 O B:HOH862 3.6 29.7 1.0 CE1 B:HIS303 3.7 18.2 1.0 CA A:PRO287 3.8 24.2 1.0 CB A:LEU288 3.9 19.8 1.0 C A:PRO287 4.0 19.9 1.0 CA A:LEU288 4.1 20.6 1.0 NE2 B:HIS303 4.3 18.3 1.0 CB A:PRO287 4.4 23.9 1.0 CG2 B:VAL352 4.5 19.8 1.0 O B:HOH1157 4.5 30.4 1.0 O A:GLU285 4.6 20.5 1.0 ND1 B:HIS303 4.7 13.3 1.0 CA A:ILE286 4.7 19.8 1.0 CG2 A:ILE286 4.7 25.5 1.0 O B:HOH1302 4.8 35.2 1.0 N A:PRO287 5.0 23.2 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl716 b:65.5 occ:1.00 O A:HOH1243 2.4 51.2 1.0 O A:HOH1105 2.9 35.0 1.0 O A:HOH1081 3.1 40.5 1.0 NZ A:LYS56 3.2 52.6 1.0 CG1 A:VAL86 4.3 30.9 1.0 CG2 A:VAL99 4.3 38.5 1.0 CE A:LYS56 4.4 54.0 1.0 CD A:LYS56 4.4 45.5 1.0 CA A:ALA90 4.4 35.4 1.0 CG1 A:VAL95 4.5 38.4 1.0 O A:VAL86 4.5 31.2 1.0 CB A:ALA90 4.7 30.9 1.0 O A:HOH1281 4.8 48.0 1.0 N A:ALA90 4.9 35.0 1.0 O A:HOH1068 5.0 41.4 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl717 b:61.7 occ:1.00 O A:TRP170 3.5 47.2 1.0 N A:ASN478 3.6 31.6 1.0 CB A:SER477 3.8 29.4 1.0 NE1 A:TRP170 3.8 34.5 0.6 CE3 A:TRP170 3.9 33.9 0.4 CE2 A:TRP170 3.9 31.0 0.6 O A:ASN478 3.9 28.3 1.0 CA A:HIS171 4.0 52.7 0.5 O A:HOH969 4.0 32.9 1.0 CZ3 A:TRP170 4.0 31.0 0.4 CA A:HIS171 4.0 52.7 0.6 C A:TRP170 4.1 51.4 1.0 CD2 A:TRP170 4.2 34.7 0.4 CD1 A:TRP170 4.2 35.6 0.6 N A:SER172 4.2 54.5 1.0 CZ2 A:TRP170 4.3 32.3 0.6 C A:HIS171 4.3 56.8 1.0 N A:HIS171 4.3 47.0 1.0 CD2 A:TRP170 4.4 34.7 0.6 CH2 A:TRP170 4.4 31.7 0.4 CA A:SER477 4.4 33.0 1.0 CB A:ASN478 4.4 36.7 1.0 CA A:ASN478 4.4 30.8 1.0 C A:SER477 4.5 35.8 1.0 CE2 A:TRP170 4.5 33.7 0.4 CG A:TRP170 4.5 36.2 0.6 O A:HOH1142 4.5 35.5 1.0 C A:ASN478 4.6 31.6 1.0 CZ2 A:TRP170 4.6 31.3 0.4 OG A:SER477 4.7 35.3 1.0 CG A:TRP170 4.8 37.9 0.4 ND2 A:ASN478 4.8 50.2 1.0 CH2 A:TRP170 5.0 30.4 0.6

Chlorine binding site 4 out of 5 in the Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl718 b:42.1 occ:1.00 N A:ASP282 2.9 12.6 1.0 CA A:GLN281 3.4 14.1 1.0 CG A:ASP282 3.4 17.2 1.0 CB A:GLN281 3.5 16.1 1.0 OD1 A:ASP282 3.6 12.1 1.0 C A:GLN281 3.6 14.8 1.0 OD2 A:ASP282 3.7 17.0 1.0 CB A:ASP282 3.8 14.0 1.0 CA A:ASP282 3.9 14.5 1.0 CG A:GLN281 4.0 15.3 1.0 O A:HOH1149 4.2 31.5 1.0 CG2 A:VAL294 4.5 13.0 1.0 NH2 A:ARG284 4.6 20.6 1.0 O A:PHE280 4.6 14.4 1.0 N A:GLN281 4.7 13.5 1.0 O A:GLN281 4.9 13.8 1.0 O A:HOH1289 4.9 39.8 1.0 O A:ASP282 4.9 15.4 1.0 C A:ASP282 5.0 15.8 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Hemolymph Type Prophenoloxidase (Propob) From Crustacean within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl714 b:25.6 occ:1.00 O A:HOH1159 3.0 32.0 1.0 N B:LEU288 3.2 19.0 1.0 O A:HOH893 3.6 27.6 1.0 CE1 A:HIS303 3.7 18.4 1.0 CA B:PRO287 3.8 25.6 1.0 CB B:LEU288 3.9 21.4 1.0 C B:PRO287 4.0 20.2 1.0 CA B:LEU288 4.1 21.0 1.0 NE2 A:HIS303 4.3 18.6 1.0 CB B:PRO287 4.4 27.7 1.0 CG2 A:VAL352 4.5 19.4 1.0 O A:HOH935 4.5 40.0 1.0 O A:HOH959 4.5 29.1 1.0 O B:GLU285 4.6 20.5 1.0 ND1 A:HIS303 4.7 13.8 1.0 CA B:ILE286 4.7 22.1 1.0 O A:HOH975 4.8 36.2 1.0 CG2 B:ILE286 4.8 25.8 1.0 N B:PRO287 5.0 21.9 1.0

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