Chlorine in PDB 6ix5: The Structure of Lepi Complex with Sam and Its Substrate Analogue

The structure of The Structure of Lepi Complex with Sam and Its Substrate Analogue, PDB code: 6ix5 was solved by Y.Cai, M.Ohashi, Y.Hai, Y.Tang, J.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.99 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.051, 62.239, 114.150, 90.00, 113.15, 90.00
R / Rfree (%)	16.3 / 18.9

The structure of The Structure of Lepi Complex with Sam and Its Substrate Analogue also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the The Structure of Lepi Complex with Sam and Its Substrate Analogue (pdb code 6ix5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the The Structure of Lepi Complex with Sam and Its Substrate Analogue, PDB code: 6ix5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the The Structure of Lepi Complex with Sam and Its Substrate Analogue


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Structure of Lepi Complex with Sam and Its Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl412 b:19.8 occ:1.00 O B:HOH614 2.9 18.3 1.0 NE2 B:GLN107 3.2 11.7 1.0 N A:ALA331 3.3 7.0 1.0 NH1 B:ARG97 3.4 19.4 1.0 N A:GLY330 3.4 8.9 1.0 CB A:ALA331 3.6 11.6 1.0 CA A:LYS329 3.7 10.2 1.0 OE1 B:GLN107 3.7 9.7 1.0 C A:LYS329 3.8 7.8 1.0 CG B:ARG97 3.8 16.1 1.0 CD B:GLN107 3.9 11.1 1.0 O A:HOH537 4.0 26.8 1.0 CB B:ARG97 4.0 11.2 1.0 CA A:ALA331 4.0 9.8 1.0 CD B:ARG97 4.2 20.1 1.0 C A:GLY330 4.2 9.1 1.0 CA A:GLY330 4.3 9.1 1.0 O A:GLU328 4.3 14.8 1.0 N A:LYS329 4.4 8.1 1.0 CZ B:ARG97 4.6 26.6 1.0 CA B:ARG97 4.6 9.1 1.0 C A:GLU328 4.6 12.2 1.0 O A:LYS329 4.6 10.5 1.0 O A:PRO327 4.7 9.8 1.0 CB A:LYS329 4.8 12.0 1.0 O A:HOH798 4.8 19.5 1.0 NE B:ARG97 4.9 25.6 1.0 O A:ALA331 4.9 12.7 1.0 O B:ARG97 4.9 7.2 1.0 C A:ALA331 5.0 12.1 1.0

Chlorine binding site 2 out of 8 in the The Structure of Lepi Complex with Sam and Its Substrate Analogue


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Structure of Lepi Complex with Sam and Its Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl413 b:15.2 occ:1.00 N A:ASN243 3.2 14.4 1.0 O A:HOH715 3.3 29.1 1.0 CA A:TYR241 3.4 11.8 1.0 C A:TYR241 3.4 8.8 1.0 CB A:ASN243 3.6 11.8 1.0 N A:GLN244 3.6 12.2 1.0 N A:PRO242 3.7 13.4 1.0 CA A:ASN243 3.7 16.0 1.0 CG A:GLN244 3.7 12.7 1.0 CB A:TYR241 3.8 9.4 1.0 C A:ASN243 3.8 23.8 1.0 CD A:PRO242 3.9 13.1 1.0 O A:TYR241 3.9 10.2 1.0 CD1 A:TYR241 4.0 9.9 1.0 C A:PRO242 4.3 17.9 1.0 CG A:TYR241 4.4 8.7 1.0 CB A:GLN244 4.5 9.5 1.0 CA A:GLN244 4.5 8.6 1.0 CG A:ASN243 4.5 23.1 1.0 CA A:PRO242 4.6 14.2 1.0 O A:LYS240 4.6 13.3 1.0 NE2 A:GLN244 4.7 13.2 1.0 CD A:GLN244 4.7 14.1 1.0 N A:TYR241 4.7 10.2 1.0 O A:ASN243 4.7 20.8 1.0 CG A:PRO242 4.7 16.0 1.0

Chlorine binding site 3 out of 8 in the The Structure of Lepi Complex with Sam and Its Substrate Analogue


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Structure of Lepi Complex with Sam and Its Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl414 b:53.0 occ:1.00 NE A:ARG132 3.7 13.1 1.0 CZ A:ARG132 3.8 14.9 1.0 NH1 A:ARG132 3.8 13.1 1.0 CD A:ARG132 3.8 10.7 1.0 O A:HOH764 4.0 32.0 1.0 OG A:SER61 4.2 13.3 1.0 OE1 A:GLU128 4.2 17.6 1.0 O A:HOH548 4.2 20.7 1.0 O A:HOH541 4.3 32.6 1.0 CD A:GLU128 4.4 18.0 1.0 OE2 A:GLU128 4.4 19.2 1.0 NH2 A:ARG132 4.4 18.3 1.0 O A:SER61 4.9 14.2 1.0 O A:HOH870 4.9 25.7 1.0 O A:HOH587 4.9 15.4 1.0

Chlorine binding site 4 out of 8 in the The Structure of Lepi Complex with Sam and Its Substrate Analogue


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Structure of Lepi Complex with Sam and Its Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl415 b:57.3 occ:1.00 O A:HOH846 2.7 38.3 1.0 O A:HOH616 2.9 20.4 1.0 O A:HOH789 3.2 20.2 1.0 O A:THR198 3.6 15.0 1.0 CD2 B:PHE41 3.7 16.7 1.0 CE2 B:PHE41 3.7 18.3 1.0 NE A:ARG197 3.8 17.7 0.5 CB A:ARG197 3.8 11.7 0.5 CB A:ARG197 3.9 11.1 0.5 CZ A:ARG197 3.9 18.5 0.5 CG A:ARG197 3.9 17.1 0.5 NH1 A:ARG197 4.0 14.9 0.5 CG B:PHE41 4.2 12.7 1.0 CZ B:PHE41 4.2 17.4 1.0 CD A:ARG197 4.2 23.8 0.5 O A:HOH829 4.3 31.1 1.0 CG A:ARG197 4.4 19.9 0.5 N A:THR198 4.4 12.2 1.0 O A:HOH580 4.4 30.6 1.0 CD A:ARG197 4.5 23.9 0.5 O B:HOH577 4.5 21.2 1.0 C A:THR198 4.5 11.1 1.0 NH2 A:ARG197 4.5 16.4 0.5 CA A:ARG197 4.6 10.6 0.5 CD1 B:PHE41 4.6 20.5 1.0 CA A:ARG197 4.6 10.6 0.5 CE1 B:PHE41 4.6 21.7 1.0 C A:ARG197 4.9 13.3 1.0 CB B:PHE41 4.9 12.7 1.0 O A:HOH809 5.0 27.6 1.0

Chlorine binding site 5 out of 8 in the The Structure of Lepi Complex with Sam and Its Substrate Analogue


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Structure of Lepi Complex with Sam and Its Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl416 b:99.3 occ:1.00 O A:HOH663 3.2 14.6 1.0 CA A:ALA144 3.5 8.0 1.0 CB A:ALA144 3.7 11.9 1.0 NZ A:LYS167 3.8 16.2 0.4 O A:MET143 3.8 12.1 1.0 N A:ALA144 3.8 8.9 1.0 C A:MET143 4.0 10.3 1.0 CG A:MET143 4.1 13.1 0.6 CE A:LYS167 4.5 28.5 0.6 O A:HOH588 4.6 14.4 1.0 C A:ALA144 4.8 11.5 1.0 CB A:MET143 4.8 6.6 0.6 CD A:LYS167 4.8 19.6 0.6 CB A:MET143 4.8 6.7 0.4 CE A:LYS167 4.8 30.4 0.4 CE A:MET143 4.8 14.2 0.6

Chlorine binding site 6 out of 8 in the The Structure of Lepi Complex with Sam and Its Substrate Analogue


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Structure of Lepi Complex with Sam and Its Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl410 b:53.6 occ:1.00 O B:PHE205 3.5 16.7 1.0 C B:THR204 3.8 22.2 1.0 O B:THR204 3.9 18.5 1.0 C B:PHE205 3.9 17.3 1.0 O B:SER203 3.9 21.0 1.0 CA B:THR204 4.0 14.8 1.0 N B:PHE205 4.1 18.1 1.0 NZ B:LYS240 4.3 44.2 1.0 N B:PRO206 4.3 17.7 1.0 O B:HOH533 4.3 19.1 1.0 CA B:PRO206 4.3 20.7 1.0 C B:SER203 4.4 17.7 1.0 O B:LEU202 4.5 17.4 1.0 N B:THR204 4.5 14.3 1.0 CA B:PHE205 4.7 15.5 1.0 OH B:TYR241 5.0 22.6 1.0

Chlorine binding site 7 out of 8 in the The Structure of Lepi Complex with Sam and Its Substrate Analogue


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Structure of Lepi Complex with Sam and Its Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl411 b:55.5 occ:1.00 CD B:ARG132 3.7 8.4 1.0 NE B:ARG132 3.7 10.1 1.0 NH1 B:ARG132 3.8 12.9 1.0 CZ B:ARG132 3.8 15.5 1.0 OG B:SER61 4.0 12.3 1.0 OE1 B:GLU128 4.1 16.7 1.0 O B:HOH597 4.1 20.4 1.0 OE2 B:GLU128 4.1 15.5 1.0 CD B:GLU128 4.1 16.1 1.0 O B:HOH717 4.2 30.6 1.0 NH2 B:ARG132 4.6 17.0 1.0 O B:HOH605 4.7 13.4 1.0 O B:HOH561 4.8 27.6 1.0 O B:SER61 4.8 12.2 1.0 CG B:GLU128 5.0 9.9 1.0

Chlorine binding site 8 out of 8 in the The Structure of Lepi Complex with Sam and Its Substrate Analogue


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The Structure of Lepi Complex with Sam and Its Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl412 b:61.7 occ:1.00 O B:ASP62 3.6 13.4 1.0 N B:GLY64 3.8 9.3 1.0 O B:HOH917 3.8 31.6 1.0 CA B:GLY64 3.8 10.7 1.0 C B:LEU63 4.0 17.0 1.0 O B:LEU63 4.1 18.6 1.0 O B:HOH561 4.3 27.6 1.0 O B:SER61 4.4 12.2 1.0 C B:ASP62 4.5 12.8 1.0 CA B:LEU63 4.8 12.7 1.0 O B:HOH520 4.9 19.0 1.0

Y.Cai, Y.Hai, M.Ohashi, C.S.Jamieson, M.Garcia-Borras, K.N.Houk, J.Zhou, Y.Tang. Structural Basis For Stereoselective Dehydration and Hydrogen-Bonding Catalysis By the Sam-Dependent Pericyclase Lepi. Nat.Chem. V. 11 812 2019.
ISSN: ESSN 1755-4349
PubMed: 31332284
DOI: 10.1038/S41557-019-0294-X