Chlorine in PDB 5m6d: Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure

The structure of Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure, PDB code: 5m6d was solved by C.Gaboriaud, C.P.Moreau, A.M.Di Guilmi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.52 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.041, 130.237, 79.837, 90.00, 119.64, 90.00
R / Rfree (%)	19.5 / 21.5

The structure of Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Chlorine atom in the Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure (pdb code 5m6d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure, PDB code: 5m6d:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:41.2 occ:1.00 HG1 A:THR231 2.2 46.8 1.0 H A:LYS235 2.5 48.4 1.0 HZ3 A:LYS235 2.5 48.7 1.0 H A:ALA234 2.6 46.2 1.0 HB3 A:ALA234 2.7 45.2 1.0 HG3 A:LYS235 2.8 49.7 1.0 OG1 A:THR231 3.0 39.0 1.0 HA2 A:GLY232 3.2 47.5 1.0 N A:ALA234 3.2 38.5 1.0 H A:GLY250 3.3 44.4 1.0 N A:LYS235 3.3 40.3 1.0 NZ A:LYS235 3.3 40.6 1.0 HZ1 A:LYS235 3.4 48.7 1.0 CB A:ALA234 3.5 37.7 1.0 C A:GLY232 3.5 39.3 1.0 O A:THR231 3.5 40.4 1.0 C A:THR231 3.6 40.1 1.0 N A:GLY250 3.6 37.0 1.0 CA A:GLY232 3.6 39.6 1.0 HE2 A:LYS235 3.6 49.7 1.0 N A:GLY232 3.6 38.8 1.0 HE2 A:MET194 3.7 51.7 1.0 CG A:LYS235 3.7 41.4 1.0 N A:ALA233 3.7 39.4 1.0 CA A:ALA234 3.7 38.6 1.0 H A:ALA233 3.8 47.3 1.0 HA3 A:GLY250 3.8 43.7 1.0 HB2 A:LYS235 3.8 50.0 1.0 HB A:THR231 3.8 46.8 1.0 O A:GLY250 3.8 36.0 1.0 HB2 A:ALA234 3.9 45.2 1.0 CB A:THR231 3.9 39.0 1.0 HA A:ASP249 3.9 46.1 1.0 HZ2 A:LYS235 3.9 48.7 1.0 CE A:LYS235 3.9 41.4 1.0 HE1 A:MET194 3.9 51.7 1.0 O A:GLY232 4.0 40.0 1.0 C A:ALA234 4.0 39.4 1.0 CA A:GLY250 4.0 36.4 1.0 C A:GLY250 4.0 35.8 1.0 CB A:LYS235 4.1 41.7 1.0 H A:GLY232 4.1 46.6 1.0 OD1 A:ASP249 4.1 40.0 1.0 C A:ALA233 4.2 39.3 1.0 C A:ASP249 4.2 37.3 1.0 CE A:MET194 4.3 43.1 1.0 HB1 A:ALA234 4.3 45.2 1.0 HG2 A:LYS235 4.3 49.7 1.0 CA A:LYS235 4.3 41.1 1.0 CA A:THR231 4.3 39.7 1.0 CD A:LYS235 4.4 41.8 1.0 H A:THR231 4.5 47.6 1.0 CA A:ALA233 4.5 39.5 1.0 HA3 A:GLY232 4.5 47.5 1.0 CA A:ASP249 4.6 38.4 1.0 O A:HOH550 4.7 31.4 1.0 HA A:ALA234 4.7 46.3 1.0 HB3 A:ALA233 4.7 46.8 1.0 HE3 A:MET194 4.7 51.7 1.0 HA A:LYS235 4.8 49.3 1.0 HE3 A:LYS235 4.8 49.7 1.0 H A:ALA236 4.9 49.4 1.0 N A:SER251 4.9 35.6 1.0 HD3 A:LYS235 4.9 50.2 1.0 N A:THR231 4.9 39.7 1.0 HA2 A:GLY250 4.9 43.7 1.0

Chlorine binding site 2 out of 2 in the Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl404 b:59.0 occ:1.00 H B:LYS235 2.4 51.2 1.0 H B:ALA234 2.5 45.7 1.0 HB3 B:ALA234 2.6 45.5 1.0 HG1 B:THR231 2.6 48.9 1.0 HZ2 B:LYS235 2.7 54.4 1.0 HG3 B:LYS235 2.7 56.2 1.0 N B:LYS235 3.2 42.7 1.0 N B:ALA234 3.2 38.1 1.0 H B:GLY250 3.2 44.3 1.0 HA2 B:GLY232 3.3 50.5 1.0 CB B:ALA234 3.4 37.9 1.0 OG1 B:THR231 3.4 40.8 1.0 N B:GLY250 3.5 36.9 1.0 NZ B:LYS235 3.5 45.3 1.0 HE1 B:MET194 3.5 47.0 1.0 C B:GLY232 3.6 41.2 1.0 CA B:ALA234 3.6 38.6 1.0 CG B:LYS235 3.6 46.8 1.0 O B:THR231 3.7 44.5 1.0 CA B:GLY232 3.7 42.1 1.0 HA3 B:GLY250 3.7 42.7 1.0 HZ3 B:LYS235 3.7 54.4 1.0 C B:THR231 3.7 42.6 1.0 HB2 B:LYS235 3.8 56.3 1.0 N B:ALA233 3.8 38.6 1.0 HA B:ASP249 3.8 47.9 1.0 HB2 B:ALA234 3.8 45.5 1.0 N B:GLY232 3.8 40.2 1.0 H B:ALA233 3.8 46.3 1.0 HE2 B:LYS235 3.8 56.8 1.0 O B:GLY250 3.8 36.6 1.0 C B:ALA234 3.9 40.7 1.0 HE3 B:MET194 3.9 47.0 1.0 CA B:GLY250 3.9 35.6 1.0 O B:GLY232 4.0 42.8 1.0 OD1 B:ASP249 4.0 43.2 1.0 C B:GLY250 4.0 35.4 1.0 CB B:LYS235 4.0 46.9 1.0 HB B:THR231 4.1 47.8 1.0 CE B:MET194 4.1 39.1 1.0 HZ1 B:LYS235 4.1 54.4 1.0 CE B:LYS235 4.1 47.4 1.0 HB1 B:ALA234 4.1 45.5 1.0 C B:ALA233 4.2 38.6 1.0 C B:ASP249 4.2 37.1 1.0 CA B:LYS235 4.2 45.3 1.0 HG2 B:LYS235 4.2 56.2 1.0 CB B:THR231 4.2 39.8 1.0 H B:GLY232 4.3 48.3 1.0 HE2 B:MET194 4.3 47.0 1.0 CD B:LYS235 4.5 48.6 1.0 CA B:ASP249 4.5 39.9 1.0 CA B:ALA233 4.5 38.0 1.0 O B:HOH512 4.6 42.3 1.0 HA B:ALA234 4.6 46.4 1.0 CA B:THR231 4.6 40.8 1.0 HA3 B:GLY232 4.6 50.5 1.0 HB3 B:ALA233 4.7 44.1 1.0 HA B:LYS235 4.7 54.4 1.0 H B:THR231 4.7 49.2 1.0 H B:ALA236 4.8 53.1 1.0 HA2 B:GLY250 4.9 42.7 1.0 N B:SER251 4.9 34.8 1.0 HD3 B:LYS235 4.9 58.3 1.0 O B:ASP249 4.9 35.7 1.0 HB3 B:LYS235 5.0 56.3 1.0

C.Moreau, R.Terrasse, N.M.Thielens, T.Vernet, C.Gaboriaud, A.M.Di Guilmi. Deciphering Key Residues Involved in the Virulence-Promoting Interactions Between Streptococcus Pneumoniae and Human Plasminogen. J. Biol. Chem. V. 292 2217 2017.
ISSN: ESSN 1083-351X
PubMed: 28011643
DOI: 10.1074/JBC.M116.764209