Chlorine in PDB 4kem: Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site

The structure of Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site, PDB code: 4kem was solved by M.W.Vetting, D.Wichelecki, L.L.Morisco, S.R.Wasserman, S.Sojitra, M.Stead, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzymefunction Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.40 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.167, 82.925, 103.266, 90.00, 100.86, 90.00
R / Rfree (%)	16.4 / 18.6

The structure of Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site (pdb code 4kem). 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 A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site, PDB code: 4kem:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site


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 A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:10.7 occ:0.63 H A:ALA20 2.0 7.6 1.0 HB2 A:ASN19 2.5 8.6 1.0 HB3 A:LYS183 2.7 7.3 1.0 O A:ILE184 2.8 7.3 1.0 N A:ALA20 2.9 6.3 1.0 HB2 A:ASN214 2.9 9.5 1.0 OD1 A:ASN214 2.9 7.6 1.0 O A:ASP212 2.9 5.9 1.0 HD2 A:LYS183 3.0 9.9 1.0 HB2 A:ALA20 3.0 8.3 1.0 HB3 A:ALA20 3.1 8.3 1.0 H A:ILE184 3.3 7.3 1.0 HA A:ALA213 3.4 7.9 1.0 CB A:ALA20 3.4 6.9 1.0 CB A:ASN19 3.4 7.1 1.0 CB A:LYS183 3.6 6.1 1.0 HA A:ASN19 3.6 7.2 1.0 CG A:ASN214 3.6 7.5 1.0 CB A:ASN214 3.6 7.9 1.0 C A:ALA213 3.7 5.9 1.0 HA A:LYS183 3.7 7.1 1.0 CA A:ALA20 3.7 7.4 1.0 C A:ASN19 3.7 6.2 1.0 N A:ILE184 3.8 6.1 1.0 CA A:ASN19 3.8 6.0 1.0 CD A:LYS183 3.9 8.2 1.0 HE2 A:TYR156 3.9 8.4 1.0 O A:ALA213 3.9 6.4 1.0 C A:ASP212 3.9 7.4 1.0 CA A:ALA213 3.9 6.6 1.0 N A:ASN214 4.0 7.3 1.0 C A:ILE184 4.0 7.5 1.0 HB3 A:ASN19 4.0 8.6 1.0 CA A:LYS183 4.1 5.9 1.0 CG A:LYS183 4.1 7.1 1.0 HG3 A:LYS183 4.1 8.5 1.0 H A:ASN214 4.2 8.7 1.0 HA A:ALA20 4.3 8.9 1.0 HB2 A:LYS183 4.3 7.3 1.0 HB1 A:ALA20 4.3 8.3 1.0 CG A:ASN19 4.3 6.5 1.0 HB3 A:ASN214 4.3 9.5 1.0 C A:LYS183 4.3 6.3 1.0 N A:ALA213 4.4 6.9 1.0 CA A:ASN214 4.4 7.7 1.0 HD3 A:LYS183 4.4 9.9 1.0 H A:PHE21 4.5 8.7 1.0 HZ2 A:LYS183 4.5 15.8 1.0 CA A:ILE184 4.6 6.7 1.0 HE3 A:LYS183 4.6 9.4 1.0 OD1 A:ASN19 4.6 6.7 1.0 HB3 A:ASP212 4.7 7.3 1.0 CE A:LYS183 4.7 7.9 1.0 CE2 A:TYR156 4.8 7.0 1.0 HG13 A:ILE184 4.8 7.0 1.0 HA3 A:GLY185 4.9 9.9 1.0 C A:ALA20 4.9 7.1 1.0 O A:ASN19 4.9 9.1 1.0 ND2 A:ASN214 4.9 13.7 1.0 N A:PHE21 5.0 7.2 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site


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 A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:10.8 occ:0.62 H A:VAL179 2.1 9.0 1.0 H A:ARG178 2.2 10.4 1.0 HA3 A:GLY361 2.7 13.4 1.0 O A:VAL149 2.8 8.4 1.0 O A:HOH563 2.9 10.1 1.0 HA2 A:GLY361 2.9 13.4 1.0 N A:VAL179 3.0 7.5 1.0 N A:ARG178 3.0 8.7 1.0 HB3 A:ARG178 3.0 13.2 1.0 HB A:VAL179 3.1 9.9 1.0 HG23 A:VAL179 3.2 12.1 1.0 HA A:TYR150 3.3 8.4 1.0 CA A:GLY361 3.3 11.2 1.0 HE1 A:TRP148 3.3 13.7 1.0 CB A:ARG178 3.6 11.0 1.0 CA A:ARG178 3.6 11.4 1.0 HA A:TYR177 3.6 9.9 1.0 HB2 A:ARG178 3.7 13.2 1.0 CB A:VAL179 3.7 8.2 1.0 C A:ARG178 3.8 7.9 1.0 NE1 A:TRP148 3.8 11.4 1.0 CA A:VAL179 3.9 8.4 1.0 CG2 A:VAL179 3.9 10.1 1.0 HB3 A:TYR177 3.9 9.1 1.0 C A:VAL149 3.9 6.6 1.0 C A:TYR177 4.0 9.8 1.0 O A:VAL179 4.0 8.6 1.0 CA A:TYR150 4.1 7.0 1.0 HD1 A:TYR177 4.1 10.2 1.0 CA A:TYR177 4.2 8.2 1.0 HB3 A:TYR150 4.2 9.3 1.0 N A:GLY361 4.2 10.1 1.0 O A:GLY361 4.2 7.8 1.0 HG21 A:VAL179 4.2 12.1 1.0 C A:GLY361 4.3 9.5 1.0 HZ2 A:TRP148 4.4 10.6 1.0 C A:VAL179 4.4 7.2 1.0 CE2 A:TRP148 4.5 8.5 1.0 H A:GLY361 4.5 12.1 1.0 N A:TYR150 4.5 5.9 1.0 HB2 A:TYR150 4.5 9.3 1.0 HA A:ARG178 4.5 13.7 1.0 CB A:TYR150 4.5 7.8 1.0 CB A:TYR177 4.5 7.6 1.0 CD1 A:TRP148 4.5 11.4 1.0 H A:VAL149 4.6 8.6 1.0 HD1 A:TRP148 4.7 13.7 1.0 HG22 A:VAL179 4.7 12.1 1.0 CZ2 A:TRP148 4.7 8.8 1.0 HA A:VAL179 4.7 10.1 1.0 HG23 A:VAL149 4.8 9.4 1.0 O A:HOH664 4.9 16.3 1.0 C A:ASP360 4.9 11.7 1.0 CD1 A:TYR177 4.9 8.5 1.0 O A:ARG178 5.0 7.8 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site


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 A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:11.0 occ:0.63 H A:TYR56 2.3 6.7 1.0 H A:GLY54 2.5 8.9 1.0 HA A:ASN53 2.6 8.6 1.0 O A:THR28 2.7 6.8 1.0 H A:ARG55 2.8 7.1 1.0 O A:SER52 2.8 7.3 1.0 N A:TYR56 3.0 5.6 1.0 HD22 A:ASN51 3.0 8.8 1.0 N A:GLY54 3.0 7.4 1.0 HA A:TYR56 3.2 7.1 1.0 HD11 A:ILE13 3.3 12.6 1.0 CA A:ASN53 3.3 7.2 1.0 C A:ASN53 3.4 7.1 1.0 N A:ARG55 3.4 6.0 1.0 SD A:MET27 3.4 7.5 1.0 HD21 A:ASN51 3.5 8.8 1.0 CA A:TYR56 3.5 5.9 1.0 HB3 A:CYS29 3.5 9.7 1.0 ND2 A:ASN51 3.5 7.3 1.0 HG3 A:MET27 3.6 9.8 1.0 C A:SER52 3.7 6.0 1.0 C A:TYR56 3.9 6.0 1.0 HA A:CYS29 3.9 7.4 1.0 N A:ASN53 3.9 5.8 1.0 C A:THR28 3.9 6.0 1.0 C A:ARG55 4.0 6.3 1.0 O A:TYR56 4.0 7.2 1.0 CG A:MET27 4.0 8.2 1.0 C A:GLY54 4.1 6.2 1.0 CA A:GLY54 4.1 7.8 1.0 CA A:ARG55 4.2 5.3 1.0 HG2 A:MET27 4.2 9.8 1.0 H A:THR28 4.3 9.1 1.0 CB A:CYS29 4.3 8.1 1.0 CD1 A:ILE13 4.3 10.5 1.0 O A:ASN53 4.3 7.6 1.0 HB2 A:ARG55 4.3 8.3 1.0 CA A:CYS29 4.4 6.1 1.0 HB2 A:CYS29 4.5 9.7 1.0 HA2 A:GLY54 4.6 9.4 1.0 HD13 A:ILE13 4.6 12.6 1.0 HB2 A:ASN53 4.6 7.4 1.0 N A:CYS29 4.6 6.9 1.0 CB A:ASN53 4.6 6.2 1.0 HD12 A:ILE13 4.7 12.6 1.0 N A:ALA57 4.7 7.0 1.0 CG A:ASN51 4.7 6.6 1.0 H A:ASN53 4.7 7.0 1.0 O A:ASN51 4.7 6.4 1.0 HA3 A:GLY54 4.8 9.4 1.0 N A:THR28 4.8 7.6 1.0 CB A:ARG55 4.8 6.9 1.0 CB A:TYR56 5.0 6.1 1.0 H A:ALA57 5.0 8.4 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site


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 A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:10.3 occ:0.62 H B:ALA20 2.0 8.9 1.0 HB2 B:ASN19 2.5 8.5 1.0 HB3 B:LYS183 2.7 7.8 1.0 HB2 B:ASN214 2.8 10.3 1.0 N B:ALA20 2.8 7.4 1.0 O B:ILE184 2.9 6.7 1.0 OD1 B:ASN214 2.9 8.0 1.0 O B:ASP212 3.0 5.8 1.0 HD2 B:LYS183 3.0 8.5 1.0 HB2 B:ALA20 3.0 8.5 1.0 HB3 B:ALA20 3.1 8.5 1.0 H B:ILE184 3.3 6.7 1.0 CB B:ASN19 3.4 7.1 1.0 CB B:ALA20 3.4 7.1 1.0 HA B:ALA213 3.4 8.0 1.0 HA B:ASN19 3.6 7.8 1.0 CB B:ASN214 3.6 8.6 1.0 CG B:ASN214 3.6 6.6 1.0 CB B:LYS183 3.6 6.5 1.0 C B:ALA213 3.7 5.3 1.0 CA B:ALA20 3.7 8.2 1.0 HA B:LYS183 3.7 8.0 1.0 C B:ASN19 3.7 7.3 1.0 CA B:ASN19 3.7 6.5 1.0 N B:ILE184 3.8 5.5 1.0 CD B:LYS183 3.9 7.1 1.0 HE2 B:TYR156 3.9 8.3 1.0 O B:ALA213 3.9 5.6 1.0 HB3 B:ASN19 3.9 8.5 1.0 CA B:ALA213 3.9 6.7 1.0 C B:ASP212 4.0 7.5 1.0 C B:ILE184 4.0 6.0 1.0 N B:ASN214 4.0 5.4 1.0 CA B:LYS183 4.1 6.7 1.0 HG3 B:LYS183 4.1 6.9 1.0 CG B:LYS183 4.1 5.8 1.0 HA B:ALA20 4.2 9.8 1.0 CG B:ASN19 4.3 6.0 1.0 HB3 B:ASN214 4.3 10.3 1.0 HB1 B:ALA20 4.3 8.5 1.0 HB2 B:LYS183 4.3 7.8 1.0 H B:ASN214 4.3 6.5 1.0 C B:LYS183 4.4 5.8 1.0 N B:ALA213 4.4 6.7 1.0 CA B:ASN214 4.4 6.5 1.0 HD3 B:LYS183 4.4 8.5 1.0 H B:PHE21 4.5 8.6 1.0 HZ3 B:LYS183 4.5 13.9 1.0 CA B:ILE184 4.6 5.3 1.0 OD1 B:ASN19 4.6 6.6 1.0 HB3 B:ASP212 4.6 6.1 1.0 HE3 B:LYS183 4.6 8.3 1.0 CE2 B:TYR156 4.8 6.9 1.0 CE B:LYS183 4.8 6.9 1.0 HA3 B:GLY185 4.8 7.8 1.0 C B:ALA20 4.9 6.8 1.0 O B:ASN19 4.9 9.0 1.0 ND2 B:ASN214 4.9 13.5 1.0 HG13 B:ILE184 4.9 6.0 1.0 N B:PHE21 5.0 7.2 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site


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 A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl403 b:11.3 occ:0.62 H B:VAL179 2.1 8.7 1.0 H B:ARG178 2.2 10.6 1.0 HA3 B:GLY361 2.8 10.8 1.0 O B:VAL149 2.8 8.3 1.0 HA2 B:GLY361 2.8 10.8 1.0 O B:HOH570 2.9 11.9 1.0 HB3 B:ARG178 2.9 14.3 1.0 N B:VAL179 2.9 7.3 1.0 N B:ARG178 3.0 8.8 1.0 HB B:VAL179 3.2 11.8 1.0 HE1 B:TRP148 3.3 13.4 1.0 HG23 B:VAL179 3.3 12.0 1.0 CA B:GLY361 3.3 9.0 1.0 HA B:TYR150 3.3 8.3 1.0 CB B:ARG178 3.5 11.9 1.0 CA B:ARG178 3.6 8.7 1.0 HA B:TYR177 3.6 9.6 1.0 HB2 B:ARG178 3.7 14.3 1.0 C B:ARG178 3.7 6.9 1.0 CB B:VAL179 3.8 9.8 1.0 NE1 B:TRP148 3.8 11.2 1.0 CA B:VAL179 3.9 7.0 1.0 HB3 B:TYR177 3.9 7.6 1.0 CG2 B:VAL179 3.9 10.0 1.0 C B:VAL149 3.9 6.6 1.0 O B:VAL179 4.0 6.7 1.0 C B:TYR177 4.0 10.2 1.0 HD1 B:TYR177 4.1 9.9 1.0 CA B:TYR150 4.1 6.9 1.0 CA B:TYR177 4.2 8.0 1.0 HB3 B:TYR150 4.2 7.5 1.0 N B:GLY361 4.2 10.6 1.0 O B:GLY361 4.3 8.8 1.0 HG21 B:VAL179 4.3 12.0 1.0 C B:GLY361 4.3 7.6 1.0 HZ2 B:TRP148 4.4 11.4 1.0 C B:VAL179 4.4 6.3 1.0 H B:GLY361 4.5 12.8 1.0 CE2 B:TRP148 4.5 7.5 1.0 N B:TYR150 4.5 6.2 1.0 HA B:ARG178 4.5 10.4 1.0 CD1 B:TRP148 4.5 11.5 1.0 CB B:TYR177 4.5 6.4 1.0 HB2 B:TYR150 4.5 7.5 1.0 CB B:TYR150 4.6 6.2 1.0 HD1 B:TRP148 4.6 13.8 1.0 H B:VAL149 4.6 8.0 1.0 HA B:VAL179 4.7 8.4 1.0 HG22 B:VAL179 4.7 12.0 1.0 CZ2 B:TRP148 4.7 9.5 1.0 HG23 B:VAL149 4.8 10.8 1.0 O B:HOH623 4.9 15.9 1.0 HD2 B:ARG178 4.9 21.8 1.0 CD1 B:TYR177 4.9 8.3 1.0 CG B:ARG178 4.9 19.2 1.0 O B:ARG178 5.0 7.3 1.0 C B:ASP360 5.0 11.8 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site


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 A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl404 b:10.8 occ:0.63 H B:ASN265 2.1 6.7 1.0 H B:GLY263 2.3 6.3 1.0 HB3 B:PRO243 2.6 7.3 1.0 HB2 B:ASN265 2.8 7.2 1.0 OE2 B:GLU239 2.8 8.6 1.0 O B:HOH518 2.8 6.7 1.0 N B:ASN265 2.9 5.5 1.0 N B:GLY263 3.0 5.3 1.0 HA2 B:GLY263 3.0 7.6 1.0 H B:GLU264 3.1 6.6 1.0 N B:GLU264 3.1 5.5 1.0 C B:GLY263 3.2 6.2 1.0 CA B:GLY263 3.2 6.4 1.0 HG2 B:GLU264 3.3 9.4 1.0 OG1 B:THR262 3.4 6.7 1.0 CB B:PRO243 3.5 6.1 1.0 HG B:LEU266 3.5 7.9 1.0 HG3 B:GLU239 3.6 8.5 1.0 CB B:ASN265 3.6 6.0 1.0 HB2 B:PRO243 3.6 7.3 1.0 CA B:ASN265 3.6 4.1 1.0 CD B:GLU239 3.7 8.2 1.0 HD21 B:ASN265 3.7 8.6 1.0 HG1 B:THR262 3.7 8.0 1.0 HA B:PRO243 3.9 8.8 1.0 O B:GLY263 3.9 6.5 1.0 C B:GLU264 3.9 5.8 1.0 H B:LEU266 3.9 6.6 1.0 O B:HOH514 3.9 8.0 1.0 CA B:GLU264 4.0 5.1 1.0 C B:ASN265 4.1 5.9 1.0 CG B:GLU264 4.1 7.9 1.0 CG B:GLU239 4.2 7.1 1.0 HA3 B:GLY263 4.2 7.6 1.0 N B:LEU266 4.2 5.5 1.0 ND2 B:ASN265 4.2 7.2 1.0 C B:THR262 4.2 5.0 1.0 CA B:PRO243 4.2 7.3 1.0 HB3 B:ASN265 4.3 7.2 1.0 HG3 B:GLU264 4.3 9.4 1.0 CG B:ASN265 4.3 4.3 1.0 HA B:THR262 4.4 5.2 1.0 HG3 B:PRO243 4.5 7.5 1.0 CG B:LEU266 4.5 6.6 1.0 HA B:ASN265 4.5 5.0 1.0 OE1 B:GLU239 4.6 10.3 1.0 CB B:GLU264 4.6 6.2 1.0 CG B:PRO243 4.6 6.3 1.0 CB B:THR262 4.6 8.2 1.0 CA B:THR262 4.7 4.3 1.0 HG2 B:GLU239 4.8 8.5 1.0 HA B:GLU264 4.8 6.1 1.0 O B:ASN265 4.9 6.5 1.0 HB3 B:GLU264 4.9 7.4 1.0 HD21 B:LEU266 4.9 7.7 1.0 HG23 B:THR262 4.9 8.7 1.0 HB2 B:GLU239 4.9 6.1 1.0 HD22 B:ASN265 4.9 8.6 1.0 HD23 B:LEU266 4.9 7.7 1.0 HD11 B:LEU266 4.9 6.9 1.0 HD3 B:PRO243 5.0 6.2 1.0

M.W.Vetting, D.Wichelecki, L.L.Morisco, S.R.Wasserman, S.Sojitra, M.Stead, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of A Tartrate Dehydratase From Azospirillum, Target Efi-502395, with Bound Mg and A Putative Acrylate Ion, Ordered Active Site To Be Published.