Chlorine in PDB 6pc3: Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp

The structure of Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp, PDB code: 6pc3 was solved by H.Song, C.Wang, G.X.Shaw, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.43 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.312, 90.856, 105.238, 90.00, 106.74, 90.00
R / Rfree (%)	17.9 / 22.5

The structure of Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Potassium	(K)	2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp (pdb code 6pc3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp, PDB code: 6pc3:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp


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 Helicobacter Pylori Ppx/Gppa in Complex with Gsp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:36.0 occ:1.00 O B:HOH751 3.2 41.8 1.0 O B:HOH683 3.2 32.6 1.0 NH2 A:ARG16 3.3 29.3 1.0 NH1 A:ARG205 3.3 32.2 1.0 CD A:ARG205 3.5 29.1 1.0 CE A:LYS35 3.6 37.4 1.0 H1' B:GSP501 3.7 49.7 1.0 CA A:GLY202 3.8 33.6 1.0 HN21 B:GSP501 4.0 38.5 1.0 NZ A:LYS35 4.1 38.7 1.0 N3 B:GSP501 4.1 35.9 1.0 HO3' B:GSP501 4.2 61.8 1.0 CB A:ARG205 4.2 30.7 1.0 CZ A:ARG16 4.3 33.2 1.0 CZ A:ARG205 4.3 31.7 1.0 NE A:ARG205 4.3 35.2 1.0 CG A:ARG205 4.3 34.5 1.0 N A:GLY202 4.4 28.1 1.0 NE A:ARG16 4.4 31.3 1.0 CD A:LYS35 4.4 35.9 1.0 HO2' B:GSP501 4.4 49.1 1.0 N2 B:GSP501 4.5 32.2 1.0 O A:GLY201 4.6 29.3 1.0 C1' B:GSP501 4.7 41.5 1.0 C A:GLY201 4.7 35.0 1.0 C2 B:GSP501 4.7 35.6 1.0 O A:HOH631 4.7 42.1 1.0 C A:GLY202 4.9 31.4 1.0 NH2 A:ARG256 4.9 28.7 1.0 C4 B:GSP501 4.9 40.4 1.0 O A:GLY202 4.9 28.5 1.0 O3' B:GSP501 4.9 51.6 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp


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 Helicobacter Pylori Ppx/Gppa in Complex with Gsp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:39.5 occ:1.00 NH2 A:ARG205 2.9 38.8 1.0 NH1 A:ARG205 3.1 32.2 1.0 O A:HOH692 3.1 34.8 1.0 O A:HOH694 3.3 31.1 1.0 O B:HOH731 3.4 39.8 1.0 CZ A:ARG205 3.4 31.7 1.0 NE A:ARG16 3.9 31.3 1.0 CA A:GLY285 3.9 32.0 1.0 CZ A:ARG16 4.0 33.2 1.0 CD A:ARG16 4.0 31.2 1.0 N A:GLY285 4.1 27.5 1.0 CG1 A:VAL200 4.2 28.5 1.0 NH1 A:ARG16 4.3 28.2 1.0 N A:GLY201 4.3 32.8 1.0 O A:HOH650 4.3 28.1 1.0 CA A:GLY201 4.4 28.4 1.0 N A:VAL286 4.4 31.3 1.0 HN22 B:GSP501 4.5 38.5 1.0 C A:VAL284 4.5 30.8 1.0 NH2 A:ARG16 4.6 29.3 1.0 C A:GLY285 4.6 33.8 1.0 O A:VAL284 4.7 28.0 1.0 HN21 B:GSP501 4.7 38.5 1.0 NE A:ARG205 4.8 35.2 1.0 N2 B:GSP501 4.9 32.2 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Helicobacter Pylori Ppx/Gppa in Complex with Gsp


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 Helicobacter Pylori Ppx/Gppa in Complex with Gsp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl506 b:33.8 occ:1.00 O A:HOH774 2.8 44.4 1.0 O B:HOH719 3.1 37.2 1.0 NH2 B:ARG16 3.2 29.8 1.0 NE B:ARG205 3.2 45.1 1.0 NH2 B:ARG205 3.5 34.0 1.0 H1' A:GSP501 3.6 53.0 1.0 NZ B:LYS35 3.6 43.0 1.0 CA B:GLY202 3.7 29.6 1.0 CE B:LYS35 3.8 36.5 1.0 CZ B:ARG205 3.8 42.2 1.0 HN21 A:GSP501 4.2 39.5 1.0 N3 A:GSP501 4.2 38.2 1.0 CD B:ARG205 4.2 32.0 1.0 CB B:ARG205 4.2 30.6 1.0 CZ B:ARG16 4.2 36.0 1.0 N B:GLY202 4.3 26.9 1.0 CD B:LYS35 4.3 30.0 1.0 NE B:ARG16 4.4 31.6 1.0 C1' A:GSP501 4.5 44.3 1.0 O B:HOH694 4.6 32.7 1.0 CG B:ARG205 4.6 38.2 1.0 HO2' A:GSP501 4.6 52.8 1.0 C B:GLY201 4.6 34.1 1.0 O B:HOH746 4.6 42.8 1.0 O B:GLY201 4.7 32.9 1.0 N2 A:GSP501 4.7 33.0 1.0 C B:GLY202 4.8 34.6 1.0 NH2 B:ARG256 4.8 36.0 1.0 O B:GLY202 4.9 32.6 1.0 C2 A:GSP501 4.9 36.6 1.0 C4 A:GSP501 4.9 37.2 1.0

H.Song, M.N.Dharmasena, C.Wang, G.X.Shaw, S.Cherry, J.E.Tropea, D.J.Jin, X.Ji. Structure and Activity of Ppx/Gppa Homologs From Escherichia Coli and Helicobacter Pylori. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31679177
DOI: 10.1111/FEBS.15120