Sodium 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:

Chlorine	(Cl)	3 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the PKD1 Domain From Vibrio Cholerae Metalloprotease Prtv, PDB code: 4l9d:
Jump to Sodium binding site number: 1; 2; 3;

Sodium 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 Sodium with other atoms in the Na 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:Na901 b:12.1 occ:0.90 O A:HOH1062 2.3 17.8 1.0 O A:ASP780 2.3 8.7 1.0 O A:GLY783 2.4 8.7 1.0 O A:HOH1043 2.4 19.2 1.0 O A:HOH1053 2.4 18.4 1.0 O A:HOH1108 2.4 24.2 1.0 C A:ASP780 3.5 6.8 1.0 C A:GLY783 3.6 7.4 1.0 O A:HOH1041 3.9 19.9 1.0 N A:GLY783 4.0 10.1 1.0 CB A:ASP780 4.2 6.6 1.0 OD1 A:ASN784 4.3 14.3 1.0 CA A:GLY783 4.3 8.8 1.0 CA A:ASP780 4.4 6.2 1.0 N A:SER781 4.5 7.7 1.0 N A:ASN784 4.5 6.0 1.0 C A:SER781 4.6 10.2 1.0 CA A:SER781 4.6 8.3 1.0 N A:ASP782 4.6 9.7 0.3 N A:ASP782 4.6 9.7 0.7 O A:HOH1135 4.7 11.5 1.0 N A:ASP780 4.7 6.2 1.0 CA A:ASN784 4.7 7.0 1.0 CG A:ASN784 4.8 10.4 1.0 O A:HOH1031 4.9 6.0 0.2 CG A:ASP780 4.9 6.8 1.0 O A:HOH1085 4.9 37.8 1.0

Sodium 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 Sodium with other atoms in the Na 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 B:Na902 b:16.5 occ:0.60 O B:HOH1061 1.9 28.2 1.0 O B:HOH1001 2.1 24.4 1.0 O B:ASP780 2.4 9.2 1.0 O B:GLY783 2.5 9.9 1.0 O B:HOH1105 2.5 39.0 1.0 O B:HOH1072 2.6 17.7 0.6 O B:HOH1127 2.6 38.3 1.0 C B:ASP780 3.5 7.0 1.0 C B:GLY783 3.6 7.9 1.0 O B:HOH1141 3.7 21.9 0.6 OD1 B:ASN784 4.1 14.9 1.0 O B:HOH1048 4.1 22.2 1.0 CB B:ASP780 4.2 6.8 1.0 N B:GLY783 4.2 11.7 1.0 CA B:ASP780 4.4 6.3 1.0 N B:SER781 4.4 7.2 1.0 CA B:GLY783 4.5 9.5 1.0 N B:ASN784 4.5 6.3 1.0 CA B:SER781 4.5 8.8 1.0 C B:SER781 4.6 8.7 1.0 N B:ASP782 4.6 9.1 1.0 CL B:CL904 4.6 15.7 0.8 CA B:ASN784 4.7 7.0 1.0 N B:ASP780 4.8 6.0 1.0 CG B:ASP780 4.8 6.5 1.0 CG B:ASN784 4.8 10.8 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na903 b:7.3 occ:1.00 O B:SER826 2.3 5.2 1.0 O B:HOH1124 2.4 12.0 1.0 O B:HOH1131 2.4 10.7 1.0 O B:HOH1010 2.5 7.2 1.0 O B:HOH1132 2.7 18.4 0.5 C B:SER826 3.4 4.2 1.0 CB B:ALA758 3.8 15.3 0.5 N B:SER826 4.1 4.3 1.0 O B:HOH1139 4.2 11.3 1.0 CA B:SER826 4.3 3.7 1.0 N B:ASP827 4.4 3.8 1.0 CA B:ASP827 4.5 3.7 1.0 OD1 B:ASP827 4.8 6.2 1.0 CB B:SER826 4.9 3.9 1.0 CB B:ASP827 4.9 4.0 1.0 O B:HOH1002 5.0 4.4 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