Chlorine in PDB 6z48: Crystal Structure of Thrombin in Complex with Macrocycle X1VE

The structure of Crystal Structure of Thrombin in Complex with Macrocycle X1VE, PDB code: 6z48 was solved by A.Angelini, S.Habeshian, C.Heinis, L.Cendron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.88 / 2.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.251, 100.573, 108.897, 90, 90.11, 90
R / Rfree (%)	18.9 / 24.3

The structure of Crystal Structure of Thrombin in Complex with Macrocycle X1VE also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Chlorine atom in the Crystal Structure of Thrombin in Complex with Macrocycle X1VE (pdb code 6z48). 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 Thrombin in Complex with Macrocycle X1VE, PDB code: 6z48:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Thrombin in Complex with Macrocycle X1VE


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 Thrombin in Complex with Macrocycle X1VE within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl302 b:14.3 occ:1.00 CL1 H:X1V302 0.0 14.3 1.0 C13 H:X1V302 1.7 15.9 1.0 C12 H:X1V302 2.7 15.0 1.0 S15 H:X1V302 3.0 17.5 1.0 O H:PHE227 3.4 17.0 1.0 CA H:GLY226 3.4 16.2 1.0 N H:PHE227 3.5 16.4 1.0 CZ H:TYR228 3.6 13.7 1.0 O H:TRP215 3.6 15.1 1.0 CG1 H:VAL213 3.7 14.5 1.0 CE1 H:TYR228 3.7 13.3 1.0 C H:GLY226 3.7 16.6 1.0 OH H:TYR228 3.7 12.4 1.0 C11 H:X1V302 4.0 14.7 1.0 C H:PHE227 4.1 16.3 1.0 CE2 H:TYR228 4.1 13.9 1.0 C10 H:X1V302 4.1 15.3 1.0 C H:TRP215 4.1 14.9 1.0 CB H:ALA190 4.2 17.0 1.0 CD1 H:TYR228 4.3 13.3 1.0 N H:TRP215 4.3 14.7 1.0 OD1 H:ASP189 4.3 20.5 1.0 N H:SER214 4.4 15.7 1.0 O H:HOH424 4.4 20.2 1.0 CA H:PHE227 4.4 17.1 1.0 CA H:VAL213 4.6 16.8 1.0 CB H:VAL213 4.6 15.7 1.0 CD2 H:TYR228 4.7 14.3 1.0 O H:GLY226 4.7 17.3 1.0 N H:GLY216 4.7 15.3 1.0 CA H:TRP215 4.7 15.2 1.0 CG H:TYR228 4.8 14.4 1.0 N H:GLY226 4.8 16.6 1.0 C H:VAL213 4.9 16.7 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Thrombin in Complex with Macrocycle X1VE


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 Thrombin in Complex with Macrocycle X1VE within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:14.3 occ:1.00 CL1 B:X1V302 0.0 14.3 1.0 C13 B:X1V302 1.7 15.9 1.0 C12 B:X1V302 2.7 15.0 1.0 S15 B:X1V302 3.0 17.5 1.0 CA B:GLY226 3.4 15.1 1.0 N B:PHE227 3.4 13.7 1.0 O B:PHE227 3.4 16.6 1.0 O B:TRP215 3.5 14.2 1.0 CZ B:TYR228 3.6 18.3 1.0 CG1 B:VAL213 3.7 10.9 1.0 C B:GLY226 3.7 15.2 1.0 OH B:TYR228 3.8 18.8 1.0 CE1 B:TYR228 3.9 17.3 1.0 CE2 B:TYR228 4.0 19.1 1.0 C11 B:X1V302 4.0 14.7 1.0 CB B:ALA190 4.1 16.1 1.0 C B:PHE227 4.1 16.6 1.0 C10 B:X1V302 4.1 15.3 1.0 C B:TRP215 4.1 14.5 1.0 N B:SER214 4.3 12.7 1.0 N B:TRP215 4.3 12.9 1.0 CA B:PHE227 4.4 15.4 1.0 CD1 B:TYR228 4.4 19.1 1.0 OD1 B:ASP189 4.4 16.2 1.0 O B:HOH414 4.5 31.4 1.0 CD2 B:TYR228 4.5 18.8 1.0 CA B:VAL213 4.6 12.4 1.0 CB B:VAL213 4.6 11.8 1.0 O B:GLY226 4.7 13.7 1.0 CA B:TRP215 4.7 13.5 1.0 CG B:TYR228 4.7 18.8 1.0 N B:GLY226 4.7 16.7 1.0 N B:GLY216 4.9 14.3 1.0 C B:VAL213 4.9 12.5 1.0 C B:SER214 4.9 11.8 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Thrombin in Complex with Macrocycle X1VE


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 Thrombin in Complex with Macrocycle X1VE within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl302 b:15.3 occ:1.00 CL1 D:X1V302 0.0 15.3 1.0 C13 D:X1V302 1.7 13.4 1.0 C12 D:X1V302 2.7 13.3 1.0 S15 D:X1V302 3.0 13.8 1.0 CA D:GLY226 3.3 19.7 1.0 O D:PHE227 3.5 20.2 1.0 CZ D:TYR228 3.5 13.2 1.0 N D:PHE227 3.6 17.6 1.0 O D:TRP215 3.6 12.6 1.0 OH D:TYR228 3.6 13.3 1.0 CG1 D:VAL213 3.8 11.1 1.0 C D:GLY226 3.8 19.6 1.0 CB D:ALA190 3.8 17.2 1.0 CE1 D:TYR228 3.8 13.6 1.0 CE2 D:TYR228 3.9 13.3 1.0 C11 D:X1V302 4.0 12.4 1.0 C10 D:X1V302 4.1 12.8 1.0 C D:PHE227 4.2 17.8 1.0 O D:HOH417 4.2 15.8 1.0 N D:TRP215 4.2 13.1 1.0 C D:TRP215 4.3 13.3 1.0 N D:SER214 4.4 12.8 1.0 OD1 D:ASP189 4.4 17.8 1.0 CD1 D:TYR228 4.4 13.4 1.0 CD2 D:TYR228 4.5 12.8 1.0 CA D:PHE227 4.5 17.8 1.0 CA D:VAL213 4.6 13.1 1.0 CB D:VAL213 4.6 12.5 1.0 N D:GLY226 4.7 18.7 1.0 O D:GLY226 4.7 21.4 1.0 CG D:TYR228 4.7 12.9 1.0 CA D:TRP215 4.8 12.5 1.0 C D:SER214 5.0 13.0 1.0 CG2 D:VAL213 5.0 11.0 1.0 C D:VAL213 5.0 13.9 1.0 CA D:ALA190 5.0 16.9 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Thrombin in Complex with Macrocycle X1VE


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 Thrombin in Complex with Macrocycle X1VE within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl302 b:14.3 occ:1.00 CL1 F:X1V302 0.0 14.3 1.0 C13 F:X1V302 1.7 15.9 1.0 C12 F:X1V302 2.7 15.0 1.0 S15 F:X1V302 3.0 17.5 1.0 CA F:GLY226 3.4 17.1 1.0 N F:PHE227 3.5 14.0 1.0 O F:PHE227 3.6 17.9 1.0 CZ F:TYR228 3.6 14.5 1.0 CG1 F:VAL213 3.6 9.0 1.0 O F:TRP215 3.7 18.5 1.0 OH F:TYR228 3.7 15.5 1.0 C F:GLY226 3.8 18.0 1.0 CE1 F:TYR228 3.8 15.0 1.0 C11 F:X1V302 4.1 14.7 1.0 CE2 F:TYR228 4.1 14.8 1.0 CB F:ALA190 4.1 10.3 1.0 C10 F:X1V302 4.1 15.3 1.0 C F:TRP215 4.2 16.7 1.0 OD1 F:ASP189 4.2 12.0 1.0 C F:PHE227 4.2 15.1 1.0 N F:TRP215 4.3 16.7 1.0 N F:SER214 4.4 13.3 1.0 O F:HOH413 4.4 13.0 1.0 CD1 F:TYR228 4.5 13.7 1.0 CA F:PHE227 4.5 14.8 1.0 CB F:VAL213 4.6 11.2 1.0 CD2 F:TYR228 4.6 14.6 1.0 CA F:VAL213 4.7 11.6 1.0 CA F:TRP215 4.7 17.0 1.0 N F:GLY226 4.8 18.9 1.0 N F:GLY216 4.8 17.3 1.0 O F:GLY226 4.8 18.2 1.0 CG F:TYR228 4.8 14.7 1.0 C F:SER214 5.0 16.1 1.0 C F:VAL213 5.0 12.4 1.0 CG2 F:VAL213 5.0 10.8 1.0

S.Habeshian, M.L.Merz, G.Sangouard, G.K.Mothukuri, M.Schuttel, Z.Bognar, C.Diaz-Perlas, J.Vesin, J.Bortoli Chapalay, G.Turcatti, L.Cendron, A.Angelini, C.Heinis. Synthesis and Direct Assay of Large Macrocycle Diversities By Combinatorial Late-Stage Modification at Picomole Scale. Nat Commun V. 13 3823 2022.
ISSN: ESSN 2041-1723
PubMed: 35780129
DOI: 10.1038/S41467-022-31428-8