Chlorine in PDB 8dak: Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3

The structure of Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3, PDB code: 8dak was solved by J.B.Thoden, M.K.Ghosh, D.F.Xiang, F.M.Raushel, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.10 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.534, 67.932, 96.125, 90, 90, 90
R / Rfree (%)	19.2 / 21.9

The binding sites of Chlorine atom in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3 (pdb code 8dak). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3, PDB code: 8dak:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3


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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:12.6 occ:1.00 NE2 A:HIS100 3.0 10.9 1.0 N A:ASP161 3.2 10.7 1.0 NE A:ARG102 3.2 12.1 1.0 CB A:ASP161 3.8 12.5 0.5 CB A:ASP161 3.8 13.6 0.5 CD A:ARG102 3.9 11.2 1.0 CD2 A:HIS100 3.9 10.6 1.0 CB A:ARG102 3.9 9.7 1.0 CA A:ILE160 3.9 8.9 1.0 CA A:ASP161 4.0 12.1 0.5 CA A:ASP161 4.0 11.6 0.5 C A:ILE160 4.1 9.4 1.0 CE1 A:HIS100 4.1 10.9 1.0 CG2 A:ILE160 4.1 9.1 1.0 CZ A:ARG102 4.2 12.9 1.0 NH1 A:ARG102 4.2 13.5 1.0 O A:ASP161 4.3 14.8 1.0 CG A:ASP161 4.4 15.7 0.5 CG A:ARG102 4.5 10.1 1.0 CB A:ILE160 4.6 8.5 1.0 C A:ASP161 4.6 11.7 1.0 OD2 A:ASP161 4.6 19.2 0.5 O A:GLY159 4.7 10.0 1.0 O A:HOH444 4.9 12.4 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3


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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:9.8 occ:1.00 O A:HOH441 2.9 16.0 1.0 NZ A:LYS74 3.1 4.0 1.0 O A:HOH306 3.2 14.5 1.0 ND2 A:ASN121 3.3 6.1 1.0 O A:HOH368 3.3 17.0 1.0 CB A:ASN121 3.7 5.2 1.0 CE A:LYS74 3.8 3.8 1.0 CD A:LYS74 3.9 3.8 1.0 CG A:ASN121 4.0 5.3 1.0 OH A:TYR134 4.1 8.4 1.0 CZ A:TYR134 4.2 7.0 1.0 CE1 A:TYR134 4.2 6.3 1.0 O A:HOH319 4.3 38.2 1.0 O A:HOH384 4.3 9.5 1.0 CB A:HIS67 4.4 6.4 1.0 O A:HOH474 4.4 9.8 1.0 O1B A:GDP201 4.4 14.6 0.5 O A:HIS67 4.4 4.9 1.0 O A:ASN121 4.7 4.9 1.0 O A:HOH404 4.8 7.0 1.0 CE2 A:TYR134 4.8 6.4 1.0 CD1 A:TYR134 4.9 5.9 1.0 CA A:ASN121 4.9 5.0 1.0 C A:ASN121 5.0 4.7 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3


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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:10.6 occ:1.00 O B:HOH439 3.0 16.1 1.0 O A:HOH389 3.0 22.5 1.0 NZ B:LYS74 3.1 5.6 1.0 O B:HOH456 3.2 33.7 1.0 ND2 B:ASN121 3.4 5.3 1.0 CE B:LYS74 3.8 5.1 1.0 CB B:ASN121 3.8 5.0 1.0 CD B:LYS74 3.9 4.9 1.0 CZ B:TYR134 4.0 4.8 1.0 OH B:TYR134 4.0 5.6 1.0 CE1 B:TYR134 4.1 4.6 1.0 CG B:ASN121 4.1 5.3 1.0 CB B:HIS67 4.1 6.2 1.0 O A:HOH395 4.4 24.4 1.0 O B:HIS67 4.4 5.5 1.0 O B:HOH447 4.5 20.1 1.0 O B:HOH373 4.5 8.2 1.0 O B:ASN121 4.6 5.5 1.0 ND1 B:HIS67 4.7 7.2 1.0 CE2 B:TYR134 4.7 4.7 1.0 CD1 B:TYR134 4.7 4.2 1.0 CG B:HIS67 4.9 6.7 1.0 C B:ASN121 4.9 5.0 1.0 CA B:ASN121 4.9 5.1 1.0 C B:HIS67 5.0 5.6 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3


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 the Gdp-D-Glycero-4-Keto-D-Lyxo-Heptose-3- Epimerase From Campylobacter Jejuni, Serotype Hs:3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:16.7 occ:1.00 NE2 B:HIS100 3.0 19.2 1.0 N B:ASP161 3.1 13.3 1.0 NE B:ARG102 3.2 12.2 1.0 O B:HOH488 3.2 40.6 1.0 O B:HOH455 3.4 39.2 1.0 CB B:ASP161 3.7 15.3 0.5 NH1 B:ARG102 3.7 15.7 1.0 CD2 B:HIS100 3.8 17.8 1.0 CB B:ASP161 3.9 15.4 0.5 CZ B:ARG102 3.9 14.6 1.0 CA B:ASP161 3.9 14.1 0.5 CA B:ASP161 4.0 14.1 0.5 CA B:ILE160 4.0 11.8 1.0 C B:ILE160 4.0 12.8 1.0 OD2 B:ASP161 4.0 17.5 0.5 CE1 B:HIS100 4.1 16.8 1.0 CG B:ASP161 4.1 16.4 0.5 CD B:ARG102 4.1 11.4 1.0 CB B:ARG102 4.1 9.5 1.0 CG2 B:ILE160 4.2 10.6 1.0 O B:ASP161 4.5 16.9 1.0 C B:ASP161 4.5 13.5 1.0 CB B:ILE160 4.6 10.8 1.0 CG B:ARG102 4.7 10.2 1.0 O B:GLY159 4.8 11.8 1.0 O B:HOH466 4.9 11.2 1.0 OD1 B:ASP161 4.9 17.6 0.5

M.K.Ghosh, D.F.Xiang, J.B.Thoden, H.M.Holden, F.M.Raushel. C3- and C3/C5-Epimerases Required For the Biosynthesis of the Capsular Polysaccharides From Campylobacter Jejuni . Biochemistry V. 61 2036 2022.
ISSN: ISSN 0006-2960
PubMed: 36093987
DOI: 10.1021/ACS.BIOCHEM.2C00364