Chlorine in PDB 4nte: Crystal Structure of Deph

The structure of Crystal Structure of Deph, PDB code: 4nte was solved by D.H.Scharf, M.Groll, A.Habel, T.Heinekamp, C.Hertweck, A.A.Brakhage, E.M.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.220, 78.220, 188.080, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 19.9

The structure of Crystal Structure of Deph also contains other interesting chemical elements:

Sodium

(Na)

7 atoms

The binding sites of Chlorine atom in the Crystal Structure of Deph (pdb code 4nte). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Deph, PDB code: 4nte:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of Deph


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 Deph within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl305 b:48.2 occ:1.00 CG A:HIS271 3.5 36.2 1.0 O A:HOH481 3.5 32.3 1.0 CB A:HIS271 3.6 35.0 1.0 CD2 A:HIS271 3.7 36.3 1.0 ND1 A:HIS271 4.0 37.1 1.0 OH A:TYR249 4.2 42.1 1.0 NE2 A:HIS271 4.3 36.8 1.0 CE1 A:HIS271 4.5 36.7 1.0 CE1 A:TYR249 4.6 38.4 1.0 CZ A:TYR249 4.8 39.1 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of Deph


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 Deph within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl306 b:26.3 occ:1.00 N A:HIS133 3.1 22.8 1.0 N A:CYS134 3.1 24.3 1.0 O A:HOH517 3.1 36.0 1.0 C6 A:FAD301 3.6 20.2 1.0 CB A:CYS134 3.6 26.8 1.0 C7 A:FAD301 3.7 20.4 1.0 CB A:PHE132 3.8 22.8 1.0 CA A:HIS133 3.8 24.8 1.0 CD2 A:HIS138 3.8 25.0 1.0 CB A:HIS133 3.8 26.1 1.0 CA A:CYS134 3.9 25.1 1.0 C5X A:FAD301 3.9 20.1 1.0 C A:HIS133 3.9 24.9 1.0 CA A:PHE132 4.1 21.8 1.0 C A:PHE132 4.1 22.5 1.0 C8 A:FAD301 4.1 20.6 1.0 O A:CYS134 4.2 22.7 1.0 CD1 A:PHE132 4.2 24.4 1.0 C7M A:FAD301 4.2 20.6 1.0 C9A A:FAD301 4.3 19.6 1.0 C9 A:FAD301 4.4 20.1 1.0 CB A:CYS137 4.5 24.1 1.0 CG A:PHE132 4.5 23.6 1.0 C A:CYS134 4.5 23.5 1.0 N5 A:FAD301 4.5 19.8 1.0 NE2 A:HIS138 4.6 25.6 1.0 CG A:HIS138 4.8 24.7 1.0 SG A:CYS137 4.9 25.5 1.0 C8M A:FAD301 4.9 21.4 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of Deph


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 Deph within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl307 b:45.9 occ:1.00 O A:ARG251 2.8 31.1 1.0 O A:ALA240 2.9 29.9 1.0 N A:ALA240 3.0 30.3 1.0 N A:SER259 3.0 29.1 1.0 CB A:THR258 3.4 28.1 1.0 OG A:SER259 3.5 29.7 1.0 CA A:ALA240 3.6 30.7 1.0 CB A:ARG251 3.6 37.5 1.0 CB A:ALA240 3.6 31.0 1.0 CA A:THR258 3.6 28.0 1.0 C A:ALA240 3.6 31.2 1.0 C A:ARG251 3.6 32.5 1.0 C A:CYS239 3.6 30.1 1.0 N A:ARG251 3.7 32.5 1.0 CB A:SER259 3.7 30.2 1.0 C A:THR258 3.8 28.6 1.0 CA A:ARG251 3.8 34.0 1.0 CB A:CYS239 3.9 29.6 1.0 CG1 A:VAL250 3.9 30.5 1.0 CA A:CYS239 3.9 29.9 1.0 CA A:SER259 4.0 30.0 1.0 CG2 A:THR258 4.2 27.6 1.0 OG1 A:THR258 4.4 28.5 1.0 C A:VAL250 4.5 31.0 1.0 O A:CYS239 4.6 30.6 1.0 N A:THR252 4.8 31.3 1.0 CG A:ARG251 4.9 41.1 1.0 O A:HOH511 4.9 32.6 1.0 N A:ILE241 4.9 32.4 1.0 O A:THR258 5.0 28.3 1.0 CA A:VAL250 5.0 30.4 1.0 SG A:CYS239 5.0 29.8 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of Deph


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 Deph within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl306 b:40.3 occ:1.00 O B:MET4 2.9 24.3 1.0 NH1 B:ARG103 2.9 27.8 1.0 CD B:ARG103 3.4 25.8 1.0 C B:MET4 3.6 25.8 1.0 N B:MET4 3.8 26.9 1.0 CB B:PRO3 3.9 27.3 1.0 CZ B:ARG103 4.0 27.7 1.0 NE B:ARG103 4.1 27.0 1.0 N B:LEU5 4.3 24.4 1.0 CA B:MET4 4.4 27.6 1.0 C B:PRO3 4.4 26.9 1.0 CB B:LEU5 4.4 25.0 1.0 CA B:PRO3 4.5 26.9 1.0 CB B:ARG103 4.5 23.1 1.0 CG B:ARG103 4.6 24.2 1.0 CA B:LEU5 4.6 24.3 1.0 O B:HOH420 4.8 24.3 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of Deph


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 Deph within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl307 b:34.6 occ:1.00 N B:HIS133 3.1 28.6 1.0 N B:CYS134 3.1 30.8 1.0 O B:HOH571 3.2 44.3 1.0 CB B:CYS134 3.6 33.1 1.0 C7 B:FAD301 3.6 23.4 1.0 CB B:HIS133 3.6 32.9 1.0 C6 B:FAD301 3.7 23.2 1.0 CA B:HIS133 3.7 30.5 1.0 CD2 B:HIS138 3.7 38.0 1.0 C8 B:FAD301 3.9 23.4 1.0 C5X B:FAD301 3.9 22.5 1.0 C B:HIS133 3.9 30.6 1.0 CA B:CYS134 3.9 32.1 1.0 CB B:PHE132 3.9 27.9 1.0 C9 B:FAD301 4.1 22.9 1.0 C B:PHE132 4.1 27.8 1.0 C9A B:FAD301 4.1 22.4 1.0 CA B:PHE132 4.2 27.6 1.0 C7M B:FAD301 4.2 24.1 1.0 O B:CYS134 4.2 29.8 1.0 NE2 B:HIS138 4.3 39.6 1.0 CB B:CYS137 4.5 30.4 1.0 CD1 B:PHE132 4.5 28.7 1.0 N5 B:FAD301 4.6 22.0 1.0 C B:CYS134 4.6 30.5 1.0 C8M B:FAD301 4.6 24.1 1.0 CG B:PHE132 4.7 28.3 1.0 SG B:CYS137 4.9 31.1 1.0 CG B:HIS133 4.9 35.7 1.0 CG B:HIS138 4.9 36.4 1.0 N10 B:FAD301 5.0 21.5 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of Deph


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Deph within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl308 b:62.9 occ:1.00 O A:HOH465 2.9 31.9 1.0 O B:HOH432 3.0 27.9 1.0 NH1 B:ARG29 3.4 26.1 1.0 CZ B:ARG29 3.5 26.4 1.0 NE B:ARG29 3.7 26.2 1.0 NH2 B:ARG29 4.0 27.2 1.0 CD B:ARG29 4.0 24.4 1.0 O B:HOH497 4.5 32.4 1.0 OD1 B:ASP7 4.6 22.9 1.0 O A:HOH472 4.9 36.3 1.0 OE2 A:GLU165 5.0 24.1 1.0 OD2 B:ASP7 5.0 22.2 1.0

D.H.Scharf, M.Groll, A.Habel, T.Heinekamp, C.Hertweck, A.A.Brakhage, E.M.Huber. Flavoenzyme-Catalyzed Formation of Disulfide Bonds in Natural Products Angew.Chem.Int.Ed.Engl. V. 53 2221 2014.
ISSN: ISSN 1433-7851
PubMed: 24446392
DOI: 10.1002/ANIE.201309302