Sodium in PDB 4irl: X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein

The structure of X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein, PDB code: 4irl was solved by T.Jin, M.Huang, P.Smith, T.Xiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.43 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.749, 124.750, 178.044, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.4

The binding sites of Sodium atom in the X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein (pdb code 4irl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein, PDB code: 4irl:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:19.6 occ:1.00 O A:HOH1181 2.3 28.9 1.0 O A:ALA240 2.3 16.3 1.0 O A:HOH1178 2.5 37.0 1.0 C A:ALA240 3.4 14.4 1.0 CB A:ALA240 3.7 13.9 1.0 O A:HOH996 3.9 30.5 1.0 CA A:ALA240 4.1 13.4 1.0 N A:VAL241 4.4 14.2 1.0 O A:HOH652 4.4 23.0 1.0 CA A:VAL241 4.6 14.1 1.0 O A:HOH889 4.7 23.3 1.0 N A:ASN242 4.7 13.9 1.0 C A:VAL241 4.9 12.6 1.0

Sodium binding site 2 out of 4 in the X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na507 b:20.1 occ:1.00 O B:ALA240 2.3 16.7 1.0 O B:HOH924 2.3 25.7 1.0 O B:HOH954 2.4 30.7 1.0 O B:HOH713 2.4 25.2 1.0 C B:ALA240 3.4 16.1 1.0 CB B:ALA240 3.6 20.1 1.0 O B:HOH851 3.7 43.5 1.0 O B:HOH836 3.9 27.7 1.0 CA B:ALA240 4.0 14.4 1.0 N B:VAL241 4.4 15.0 1.0 O B:HOH894 4.4 22.2 1.0 O B:HOH1144 4.5 24.8 1.0 CA B:VAL241 4.6 16.2 1.0 O B:HOH832 4.7 27.0 1.0 N B:ASN242 4.8 13.6 1.0 C B:VAL241 4.9 13.3 1.0

Sodium binding site 3 out of 4 in the X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na508 b:44.7 occ:1.00 O B:HOH1205 2.3 36.9 1.0 OD1 B:ASN13 2.6 17.3 1.0 O B:HOH628 2.6 20.3 1.0 O B:HOH891 2.6 46.3 1.0 O B:HOH705 2.6 20.9 1.0 O B:HOH669 2.7 17.9 1.0 CG B:ASN13 3.5 17.2 1.0 ND2 B:ASN13 3.7 19.1 1.0 O B:HOH633 3.8 19.6 1.0 O B:HOH952 3.9 29.8 1.0 N B:LYS43 4.2 16.2 1.0 CH2 B:TRP63 4.7 15.6 1.0 CA B:LYS43 4.9 16.7 1.0 CZ3 B:TRP63 4.9 17.0 1.0 CB B:ASN13 4.9 13.1 1.0 O B:PRO41 5.0 16.6 1.0

Sodium binding site 4 out of 4 in the X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of the Card Domain of Zebrafish Gbp-NLRP1 Like Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Na506 b:25.1 occ:1.00 O C:ALA240 2.4 19.5 1.0 O C:HOH971 2.4 37.8 1.0 O C:HOH920 2.6 31.8 1.0 C C:ALA240 3.5 16.7 1.0 CB C:ALA240 3.8 22.8 1.0 O C:HOH986 4.1 53.3 1.0 O C:HOH858 4.2 38.5 1.0 CA C:ALA240 4.2 14.4 1.0 O C:HOH856 4.2 46.6 1.0 O C:HOH634 4.4 22.4 1.0 O C:HOH812 4.4 30.8 1.0 N C:VAL241 4.5 14.9 1.0 CA C:VAL241 4.7 14.9 1.0 N C:ASN242 4.9 14.6 1.0 C C:VAL241 5.0 15.0 1.0

T.Jin, M.Huang, P.Smith, J.Jiang, T.S.Xiao. Structure of the Caspase-Recruitment Domain From A Zebrafish Guanylate-Binding Protein. Acta Crystallogr.,Sect.F V. 69 855 2013.
ISSN: ESSN 1744-3091
PubMed: 23908027
DOI: 10.1107/S1744309113015558