Chlorine in PDB 4l9d: Crystal Structure of the PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv

The structure of Crystal Structure of the PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv, PDB code: 4l9d was solved by A.Edwin, G.Stier, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 1.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.800, 50.833, 67.297, 90.00, 90.00, 90.00
R / Rfree (%)	10.9 / 14

The structure of Crystal Structure of the PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Sodium	(Na)	3 atoms

The binding sites of Chlorine atom in the Crystal Structure of the PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv (pdb code 4l9d). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of the PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv, PDB code: 4l9d:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of the PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv


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 PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl902 b:11.3 occ:1.00 O A:HOH1107 2.6 28.6 0.8 O A:HOH1056 2.9 16.4 1.0 O A:HOH1138 3.2 16.1 1.0 N B:LYS834 3.2 9.2 0.5 N A:LYS834 3.3 6.7 0.4 N A:LYS834 3.3 7.5 0.4 N A:LYS834 3.3 5.4 0.2 N B:LYS834 3.3 6.1 0.5 O A:HOH1057 3.6 32.7 1.0 CA B:ILE833 3.7 6.8 1.0 CA A:ILE833 3.8 6.3 1.0 CG B:LYS834 3.8 23.7 0.5 CB A:LYS834 3.9 7.2 0.4 CB B:LYS834 4.0 11.1 0.5 C B:ILE833 4.0 8.0 1.0 C A:ILE833 4.0 6.3 1.0 CB A:LYS834 4.1 11.8 0.4 CG A:LYS834 4.1 12.7 0.4 CA B:LYS834 4.1 9.4 0.5 CA A:LYS834 4.2 7.5 0.4 CB A:LYS834 4.2 5.0 0.2 CB B:ILE833 4.2 8.3 1.0 O B:LYS834 4.2 16.6 0.5 CA A:LYS834 4.2 8.9 0.4 O B:HOH1137 4.3 11.4 0.6 O A:THR832 4.3 8.7 1.0 O B:THR832 4.3 10.3 1.0 CA A:LYS834 4.3 5.4 0.2 O B:LYS834 4.3 12.1 0.5 O A:LYS834 4.3 9.9 0.4 CG2 B:ILE833 4.3 10.8 1.0 CA B:LYS834 4.4 9.0 0.5 CB B:LYS834 4.4 10.2 0.5 CB A:ILE833 4.4 7.6 1.0 O A:LYS834 4.4 7.8 0.2 O A:LYS834 4.5 8.3 0.4 O B:HOH1037 4.5 17.2 0.4 CG B:LYS834 4.5 14.7 0.5 O A:HOH1120 4.5 34.6 1.0 CG A:LYS834 4.5 14.5 0.4 CG2 A:ILE833 4.6 10.0 1.0 NZ A:LYS834 4.7 19.0 0.4 C B:LYS834 4.7 13.3 0.5 C B:LYS834 4.7 11.0 0.5 C A:LYS834 4.8 9.4 0.4 C A:LYS834 4.8 7.5 0.4 N B:ILE833 4.8 6.5 1.0 C A:LYS834 4.8 7.0 0.2 N A:ILE833 4.9 5.6 1.0 C A:THR832 5.0 6.0 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of the PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv


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 PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl903 b:9.5 occ:0.70 O A:HOH1009 2.7 6.5 1.0 O A:HOH1002 2.8 5.4 1.0 OH A:TYR813 2.8 5.2 1.0 N A:LYS809 3.0 5.9 1.0 N A:THR808 3.1 4.6 1.0 CA A:THR808 3.7 4.4 1.0 CZ A:TYR813 3.7 4.7 1.0 CB A:THR808 3.8 5.0 1.0 C A:THR808 3.8 5.2 1.0 CB A:LYS809 3.8 5.8 1.0 CA A:LYS809 3.8 5.8 1.0 CB A:TYR807 3.9 4.9 1.0 O A:LYS809 4.0 6.0 1.0 C A:TYR807 4.0 5.2 1.0 CE1 A:TYR813 4.1 4.2 1.0 O A:HOH1010 4.1 4.7 1.0 CA A:TYR807 4.1 5.2 1.0 C A:LYS809 4.4 5.7 1.0 CD1 A:TYR807 4.5 4.3 1.0 OG1 A:THR808 4.6 5.9 1.0 CE2 A:TYR813 4.7 4.8 1.0 CG A:TYR807 4.8 4.4 1.0 CG2 A:THR808 4.9 6.0 1.0 O A:THR808 5.0 7.2 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of the PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv


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 PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl904 b:15.7 occ:0.80 O B:HOH1067 2.8 33.5 1.0 O B:HOH1061 3.0 28.2 1.0 O B:HOH1098 3.1 38.3 1.0 N B:ILE785 3.1 6.1 1.0 O B:HOH1134 3.3 23.7 0.5 O B:HOH1048 3.7 22.2 1.0 CB B:ILE785 3.8 5.9 1.0 CG1 B:ILE785 3.8 6.4 1.0 CA B:ASN784 3.8 7.0 1.0 C B:ASN784 4.0 5.2 1.0 CB B:ASP780 4.0 6.8 1.0 CA B:ILE785 4.0 5.0 1.0 CD1 B:ILE785 4.1 7.0 1.0 N B:ASP780 4.3 6.0 1.0 O B:GLY783 4.4 9.9 1.0 NA B:NA902 4.6 16.5 0.6 CB B:ASN784 4.6 8.9 1.0 O B:ILE785 4.7 7.5 1.0 C B:SER779 4.7 5.5 1.0 O B:HOH1072 4.7 17.7 0.6 CA B:ASP780 4.7 6.3 1.0 OD1 B:ASN784 4.9 14.9 1.0 CA B:SER779 4.9 6.7 1.0 N B:ASN784 4.9 6.3 1.0 O B:ASP780 4.9 9.2 1.0 C B:ILE785 4.9 6.2 1.0

A.Edwin, P.Rompikuntal, E.Bjorn, G.Stier, S.N.Wai, A.E.Sauer-Eriksson. Calcium Binding By the PKD1 Domain Regulates Interdomain Flexibility in Vibrio Cholerae Metalloprotease Prtv. Febs Open Bio V. 3 263 2013.
ISSN: ESSN 2211-5463
PubMed: 23905008
DOI: 10.1016/J.FOB.2013.06.003