Chlorine in PDB 6k4r: Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A

The structure of Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A, PDB code: 6k4r was solved by S.Y.Ouyang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.09 / 3.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.846, 159.178, 135.032, 90.00, 101.78, 90.00
R / Rfree (%)	23.9 / 27.9

The structure of Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A (pdb code 6k4r). 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 Sidj-Cam-Amp Ternary Complex at 3.11 A, PDB code: 6k4r:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A


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 Sidj-Cam-Amp Ternary Complex at 3.11 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl902 b:57.5 occ:1.00 CE A:LYS260 3.5 55.7 1.0 N A:PHE587 3.6 51.0 1.0 CB A:LEU586 3.8 50.4 1.0 CA A:PHE587 3.9 51.5 1.0 CD A:LYS260 4.0 54.8 1.0 CB A:PHE587 4.1 50.4 1.0 C A:LEU586 4.1 53.3 1.0 NZ A:LYS260 4.1 58.9 1.0 CA A:LEU586 4.5 52.8 1.0 CG A:LYS260 4.5 54.3 1.0 OD2 A:ASP307 4.6 48.9 1.0 CE A:LYS590 4.6 47.1 1.0 CD1 A:LEU586 4.7 47.9 1.0 O A:LEU586 4.7 54.1 1.0 CD2 A:PHE587 4.7 51.3 1.0 NZ A:LYS590 4.8 49.0 1.0 CG A:LEU586 4.9 48.4 1.0 N A:LEU586 4.9 53.3 1.0 CG A:PHE587 4.9 50.9 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A


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 Sidj-Cam-Amp Ternary Complex at 3.11 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl903 b:80.2 occ:1.00 OE1 A:GLN167 3.8 73.8 1.0 O A:ALA240 4.0 62.3 1.0 C A:ALA240 4.1 63.6 1.0 CD1 A:ILE163 4.2 74.7 1.0 CB A:ALA240 4.3 59.2 1.0 N A:LEU241 4.3 63.5 1.0 CA A:LEU241 4.4 62.6 1.0 CG1 A:ILE163 4.4 75.4 1.0 CB A:GLU244 4.4 71.2 1.0 CD1 A:LEU241 4.5 63.7 1.0 CG A:GLU244 4.6 70.9 1.0 CD A:GLN167 4.6 72.6 1.0 NE2 A:GLN167 4.7 71.7 1.0 CA A:ALA240 4.9 60.2 1.0 CE1 A:TYR245 4.9 69.4 1.0 CB A:LEU241 5.0 62.6 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A


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 Sidj-Cam-Amp Ternary Complex at 3.11 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl904 b:61.1 occ:1.00 N B:PHE587 3.3 52.5 1.0 CB B:LEU586 3.6 50.4 1.0 CA B:PHE587 3.8 51.0 1.0 CB B:PHE587 3.8 51.8 1.0 C B:LEU586 3.9 53.6 1.0 CE B:LYS260 4.0 51.5 1.0 CA B:LEU586 4.1 51.3 1.0 CD B:LYS260 4.1 49.6 1.0 N B:LEU586 4.3 52.8 1.0 NZ B:LYS260 4.5 56.1 1.0 CD1 B:LEU586 4.5 49.0 1.0 CG B:LEU586 4.6 50.5 1.0 CG B:LYS260 4.7 48.5 1.0 O B:LEU586 4.7 53.1 1.0 CG B:PHE587 4.9 52.7 1.0 CD2 B:PHE587 4.9 53.4 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A


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 Sidj-Cam-Amp Ternary Complex at 3.11 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl905 b:57.6 occ:1.00 OE2 B:GLU605 3.0 51.7 1.0 OE1 B:GLU605 3.2 55.0 1.0 OG1 B:THR602 3.2 47.8 1.0 CD B:GLU605 3.3 53.7 1.0 NH2 B:ARG505 3.5 63.4 1.0 ND2 B:ASN601 3.5 50.8 1.0 CA B:THR602 4.1 47.5 1.0 CZ B:PHE558 4.2 57.8 1.0 CE2 B:PHE558 4.2 57.9 1.0 CB B:THR602 4.2 47.4 1.0 N B:THR602 4.3 46.9 1.0 CZ B:PHE563 4.4 54.1 1.0 O B:LEU598 4.5 47.5 1.0 CG B:GLU605 4.6 49.9 1.0 C B:ASN601 4.7 47.4 1.0 CG B:ASN601 4.7 49.3 1.0 CE2 B:PHE563 4.7 54.1 1.0 CG2 B:THR602 4.8 47.1 1.0 CB B:GLU605 4.8 47.7 1.0 CZ B:ARG505 4.8 60.9 1.0 CD2 B:LEU552 4.8 47.9 1.0 O B:ASN601 4.9 46.5 1.0 CB B:ASN601 5.0 48.0 1.0

N.Gan, X.Zhen, Y.Liu, X.Xu, C.He, J.Qiu, Y.Liu, G.M.Fujimoto, E.S.Nakayasu, B.Zhou, L.Zhao, K.Puvar, C.Das, S.Ouyang, Z.Q.Luo. Regulation of Phosphoribosyl Ubiquitination By A Calmodulin-Dependent Glutamylase. Nature V. 572 387 2019.
ISSN: ESSN 1476-4687
PubMed: 31330531
DOI: 10.1038/S41586-019-1439-1