Chlorine in PDB 7lgp: Dape Enzyme From Shigella Flexneri

All present enzymatic activity of Dape Enzyme From Shigella Flexneri:
3.5.1.18;

The structure of Dape Enzyme From Shigella Flexneri, PDB code: 7lgp was solved by J.Osipiuk, M.Endres, D.P.Becker, A.Joachimiak, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.68 / 1.91
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.141, 180.141, 200.091, 90, 90, 120
R / Rfree (%)	15.9 / 18.7

The structure of Dape Enzyme From Shigella Flexneri also contains other interesting chemical elements:

Sodium	(Na)	3 atoms
Zinc	(Zn)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Chlorine atom in the Dape Enzyme From Shigella Flexneri (pdb code 7lgp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 15 binding sites of Chlorine where determined in the Dape Enzyme From Shigella Flexneri, PDB code: 7lgp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 15 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:45.0 occ:1.00 O A:HOH771 3.0 45.7 1.0 C A:CYS3 3.2 44.2 1.0 N A:VAL5 3.2 37.5 1.0 CA A:CYS3 3.2 48.7 1.0 NE2 A:GLN360 3.2 45.4 1.0 CB A:CYS3 3.4 51.6 1.0 N A:PRO4 3.5 42.1 1.0 N A:ILE6 3.5 35.6 1.0 CB A:VAL5 3.6 35.8 1.0 O A:CYS3 3.6 43.4 1.0 CG A:GLN360 3.6 38.8 1.0 CD A:PRO4 3.7 42.9 1.0 CA A:VAL5 3.8 35.9 1.0 CG1 A:ILE6 3.9 39.7 1.0 CD A:GLN360 3.9 42.5 1.0 CG2 A:VAL5 4.0 36.9 1.0 C A:VAL5 4.1 36.6 1.0 C A:PRO4 4.2 38.7 1.0 CB A:ILE6 4.4 38.2 1.0 CA A:PRO4 4.4 41.5 1.0 CG A:PRO4 4.5 43.6 1.0 CA A:ILE6 4.6 37.3 1.0 CD1 A:ILE6 4.6 40.3 1.0 SG A:CYS3 4.6 56.0 1.0 N A:CYS3 4.6 53.9 1.0 CB A:GLN360 4.8 36.2 1.0 CG1 A:VAL5 4.9 35.8 1.0

Chlorine binding site 2 out of 15 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:50.9 occ:1.00 O A:HOH895 3.0 57.4 1.0 OG1 A:THR48 3.0 42.1 1.0 N A:ASP47 3.3 50.2 1.0 ND2 A:ASN139 3.5 48.4 1.0 N A:THR48 3.7 46.3 1.0 CB A:ALA46 3.7 50.5 1.0 CB A:ASP47 3.7 54.5 1.0 CA A:ASP47 3.8 51.1 1.0 C A:ASP47 3.9 48.8 1.0 CB A:ASN139 4.0 43.3 1.0 O A:HOH691 4.0 36.2 1.0 O A:HOH636 4.1 49.2 1.0 CB A:THR48 4.1 42.1 1.0 O A:PHE45 4.1 46.0 1.0 CG A:ASN139 4.2 47.1 1.0 C A:ALA46 4.3 49.1 1.0 CG A:PRO20 4.4 39.5 1.0 CA A:THR48 4.5 42.5 1.0 CB A:PRO20 4.5 39.0 1.0 CA A:ALA46 4.6 50.8 1.0 CG A:ASP47 4.6 57.3 1.0 O A:ASP47 4.7 46.6 1.0 OD2 A:ASP47 4.8 63.5 1.0

Chlorine binding site 3 out of 15 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:57.8 occ:1.00 N A:ASN120 3.1 48.1 1.0 CA A:HIS118 3.4 47.4 1.0 C A:HIS118 3.5 49.5 1.0 C A:ASN120 3.5 48.5 1.0 N A:PRO119 3.6 49.3 1.0 CA A:ASN120 3.6 49.8 1.0 CD A:PRO119 3.7 49.3 1.0 N A:HIS121 3.8 46.9 1.0 O A:ASN120 3.9 46.2 1.0 CB A:ASN120 3.9 54.4 1.0 CB A:HIS118 4.0 46.9 1.0 O A:HIS118 4.1 48.3 1.0 C A:PRO119 4.2 49.1 1.0 CG A:PRO119 4.3 50.6 1.0 CA A:PRO119 4.4 48.1 1.0 ND1 A:HIS118 4.5 50.5 1.0 OD1 A:ASN120 4.5 61.3 1.0 CA A:HIS121 4.6 45.0 1.0 O A:GLN117 4.7 51.4 1.0 N A:HIS118 4.7 48.8 1.0 CG A:ASN120 4.7 57.0 1.0 CG A:HIS118 4.7 48.4 1.0 CB A:PRO119 5.0 50.5 1.0

Chlorine binding site 4 out of 15 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:36.0 occ:1.00 NH1 A:ARG178 3.1 29.0 1.0 O A:HOH882 3.2 30.4 1.0 O B:HOH849 3.3 36.5 1.0 O A:HOH831 3.4 48.2 1.0 CD B:PRO197 3.6 29.1 1.0 CG B:PRO197 3.8 28.7 1.0 CG A:PRO227 3.9 32.7 1.0 CZ A:ARG178 4.2 28.7 1.0 O B:ALA195 4.2 28.0 1.0 CB A:PRO227 4.4 33.3 1.0 O A:HOH746 4.4 32.4 1.0 CE1 B:HIS198 4.4 46.6 1.0 NH2 A:ARG178 4.6 27.9 1.0 ND1 B:HIS198 4.6 46.5 1.0 O B:HOH707 4.7 27.9 1.0 N B:PRO197 4.9 28.2 1.0 O B:HOH856 4.9 51.8 1.0

Chlorine binding site 5 out of 15 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:52.4 occ:1.00 O A:HOH900 3.0 46.3 1.0 NE2 A:GLN367 3.1 43.1 1.0 CD2 A:HIS118 3.7 49.3 1.0 CG A:GLU371 3.7 48.1 1.0 CG A:GLN367 3.7 39.7 1.0 CB A:GLU371 3.7 43.8 1.0 NE2 A:HIS118 3.8 52.0 1.0 CD A:GLN367 3.9 40.9 1.0 CD1 A:PHE114 3.9 38.6 1.0 CB A:GLN117 4.0 58.2 1.0 CG A:GLN117 4.1 63.6 1.0 CA A:PHE114 4.3 40.2 1.0 O A:GLN367 4.4 35.2 1.0 CB A:PHE114 4.6 39.4 1.0 CA A:GLU371 4.7 41.5 1.0 CE1 A:PHE114 4.7 39.5 1.0 CG A:PHE114 4.7 37.8 1.0 O A:PHE114 4.9 43.3 1.0 O A:HOH896 4.9 54.4 1.0

Chlorine binding site 6 out of 15 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:54.0 occ:1.00 N A:GLN291 3.1 33.1 1.0 CG A:ARG328 3.6 37.0 1.0 NH2 A:ARG332 3.6 66.4 1.0 CA A:GLY290 3.7 35.0 1.0 CB A:GLN291 3.8 38.5 1.0 CB A:ARG328 3.9 34.6 1.0 O A:ARG328 3.9 36.4 1.0 C A:GLY290 3.9 34.2 1.0 CG A:GLN291 3.9 43.0 1.0 CD A:ARG328 4.0 39.4 1.0 CE1 A:PHE329 4.0 38.8 1.0 CA A:GLN291 4.0 35.4 1.0 CD1 A:PHE329 4.1 37.5 1.0 C A:ARG328 4.1 33.8 1.0 NE A:ARG332 4.2 63.1 1.0 NE A:ARG328 4.2 41.5 1.0 O A:GLN291 4.3 34.1 1.0 CZ A:ARG332 4.4 65.8 1.0 O A:HOH692 4.4 41.8 1.0 CA A:ARG328 4.6 32.8 1.0 N A:PHE329 4.6 31.9 1.0 C A:GLN291 4.7 34.3 1.0 N A:GLY290 4.8 36.7 1.0 CZ A:PHE329 4.9 39.6 1.0 CA A:PHE329 5.0 33.5 1.0

Chlorine binding site 7 out of 15 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl508 b:68.9 occ:1.00 O A:HOH753 3.1 36.4 1.0 N A:GLY248 3.3 37.1 1.0 CA A:PRO247 3.6 36.7 1.0 CB A:PRO247 3.8 35.6 1.0 C A:PRO247 4.0 36.5 1.0 OE1 A:GLN191 4.0 69.1 1.0 CD A:GLN191 4.1 62.3 1.0 CG2 A:THR240 4.2 43.4 1.0 CA A:GLY248 4.3 38.9 1.0 N A:GLU249 4.4 36.3 1.0 CA A:GLY239 4.4 36.0 1.0 NE2 A:GLN191 4.5 63.8 1.0 N A:GLY239 4.5 34.8 1.0 C A:GLY239 4.6 39.1 1.0 CG A:GLN191 4.7 56.7 1.0 O A:HOH601 4.9 40.0 0.6 N A:PRO247 4.9 37.1 1.0 C A:GLY248 4.9 38.4 1.0 N A:THR240 4.9 39.6 1.0 O A:GLU249 4.9 34.7 1.0

Chlorine binding site 8 out of 15 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:39.8 occ:1.00 O B:HOH778 3.1 35.8 1.0 N B:VAL5 3.1 34.2 1.0 C B:CYS3 3.2 39.9 1.0 NE2 B:GLN360 3.3 42.6 1.0 CA B:CYS3 3.3 41.1 1.0 N B:ILE6 3.4 37.5 1.0 N B:PRO4 3.5 37.4 1.0 O B:CYS3 3.5 39.6 1.0 CB B:VAL5 3.6 34.8 1.0 CG B:GLN360 3.6 40.2 1.0 CB B:CYS3 3.6 44.7 1.0 CG1 B:ILE6 3.7 41.1 1.0 CA B:VAL5 3.7 34.6 1.0 CD B:PRO4 3.9 37.9 1.0 CG2 B:VAL5 3.9 34.8 1.0 CD B:GLN360 3.9 41.9 1.0 C B:VAL5 4.1 36.7 1.0 C B:PRO4 4.1 35.4 1.0 SG B:CYS3 4.3 52.0 1.0 CB B:ILE6 4.3 39.2 1.0 CD1 B:ILE6 4.4 42.9 1.0 CA B:PRO4 4.4 36.0 1.0 CA B:ILE6 4.4 38.1 1.0 O B:HOH652 4.5 43.9 1.0 N B:CYS3 4.6 42.0 1.0 CG B:PRO4 4.7 36.0 1.0 O B:SER2 4.8 44.2 1.0 CB B:GLN360 4.8 38.9 1.0 CG1 B:VAL5 4.8 34.9 1.0

Chlorine binding site 9 out of 15 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:41.1 occ:1.00 O B:HOH647 2.7 66.2 1.0 O B:HOH823 3.0 49.1 1.0 NE2 B:GLN367 3.3 38.1 1.0 CD2 B:HIS118 3.5 42.1 1.0 NE2 B:HIS118 3.6 43.6 1.0 CD B:GLU371 3.8 39.6 0.4 CB B:GLU371 3.8 41.2 0.6 OE2 B:GLU371 3.8 41.6 0.4 CG B:GLN367 3.8 36.4 1.0 CB B:GLN117 3.8 43.9 1.0 CB B:GLU371 3.8 37.6 0.4 CG B:GLU371 3.9 39.4 0.4 CG B:GLU371 3.9 45.8 0.6 CG B:GLN117 4.0 46.1 1.0 CD B:GLN367 4.0 38.0 1.0 CD1 B:PHE114 4.1 35.0 1.0 CA B:PHE114 4.1 35.3 1.0 OE1 B:GLU371 4.3 39.6 0.4 O B:GLN367 4.5 33.1 1.0 CB B:PHE114 4.6 34.0 1.0 O B:PHE114 4.7 35.8 1.0 CA B:GLU371 4.8 36.9 0.4 CA B:GLU371 4.8 38.4 0.6 CG B:HIS118 4.8 43.0 1.0 CG B:PHE114 4.8 35.5 1.0 O B:ARG113 4.9 34.1 1.0 N B:PHE114 4.9 33.9 1.0 CE1 B:HIS118 4.9 42.9 1.0 CE1 B:PHE114 5.0 36.3 1.0 C B:PHE114 5.0 36.6 1.0

Chlorine binding site 10 out of 15 in the Dape Enzyme From Shigella Flexneri


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Dape Enzyme From Shigella Flexneri within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl504 b:47.0 occ:1.00 O B:HOH666 3.0 32.4 1.0 N B:GLY248 3.1 28.7 1.0 NE2 B:GLN191 3.2 37.4 1.0 CA B:PRO247 3.7 27.5 1.0 C B:PRO247 3.9 29.1 1.0 CB B:PRO247 4.0 28.1 1.0 CA B:GLY248 4.0 28.6 1.0 N B:GLU249 4.1 27.8 1.0 CD B:GLN191 4.2 38.4 1.0 CG B:GLN191 4.3 34.4 1.0 CG2 B:THR240 4.4 33.6 1.0 C B:GLY248 4.5 28.6 1.0 N B:GLY239 4.7 27.6 1.0 O B:GLU249 4.7 27.6 1.0 CA B:GLY239 4.7 29.2 1.0 CB B:GLN191 4.7 31.4 1.0 C B:GLY239 4.8 30.9 1.0 O B:GLY239 5.0 32.9 1.0

J.Osipiuk, M.Endres, D.P.Becker, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Dape Enzyme From Shigella Flexneri To Be Published.