Sodium in PDB 2i1n: Crystal Structure of the 1ST Pdz Domain of Human DLG3

The structure of Crystal Structure of the 1ST Pdz Domain of Human DLG3, PDB code: 2i1n was solved by A.P.Turnbull, C.Phillips, G.Bunkoczi, J.Debreczeni, E.Ugochukwu, A.C.W.Pike, F.Gorrec, C.Umeano, J.Elkins, G.Berridge, P.Savitsky, O.Gileadi, F.Von Delft, J.Weigelt, A.Edwards, C.Arrowsmith, M.Sundstrom, D.Doyle, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.16 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.817, 80.545, 67.693, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.8

The binding sites of Sodium atom in the Crystal Structure of the 1ST Pdz Domain of Human DLG3 (pdb code 2i1n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the 1ST Pdz Domain of Human DLG3, PDB code: 2i1n:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of the 1ST Pdz Domain of Human DLG3


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 1ST Pdz Domain of Human DLG3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:28.7 occ:1.00 N A:VAL195 3.3 27.1 1.0 CA A:VAL194 3.7 26.6 1.0 CG2 A:VAL195 3.8 28.4 1.0 CB A:VAL194 3.9 26.2 1.0 C A:VAL194 4.0 26.8 1.0 CG1 A:VAL195 4.1 29.0 1.0 CG1 A:VAL194 4.2 26.5 1.0 CB A:VAL195 4.3 27.6 1.0 CB A:ARG198 4.3 29.2 1.0 CA A:VAL195 4.3 27.6 1.0 CG A:ARG198 4.5 33.8 1.0 CD1 A:ILE149 4.7 21.5 0.5 O A:GLU193 4.9 26.2 1.0 N A:VAL194 5.0 25.9 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of the 1ST Pdz Domain of Human DLG3


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 1ST Pdz Domain of Human DLG3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:59.4 occ:1.00 CB B:TYR129 4.2 30.4 1.0 CG1 B:VAL213 4.2 28.3 1.0 N B:GLU131 4.3 29.9 1.0 C B:GLU130 4.4 30.8 1.0 N B:GLU130 4.4 30.3 1.0 C B:TYR129 4.5 30.6 1.0 CA B:GLU130 4.6 30.8 1.0 O B:TYR129 4.6 29.9 1.0 O B:HOH321 4.6 25.4 1.0 CB B:GLU131 4.8 30.3 1.0 O B:GLU130 4.9 31.5 1.0 O B:HOH364 4.9 50.1 1.0 CG2 B:VAL213 5.0 27.8 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the 1ST Pdz Domain of Human DLG3


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 1ST Pdz Domain of Human DLG3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:40.0 occ:1.00 O B:HOH315 3.4 28.8 1.0 O B:HOH312 3.6 23.7 1.0 CB B:ASP190 4.1 29.6 1.0 OD2 B:ASP190 4.6 34.1 1.0 CG B:ASP190 4.9 31.0 1.0 O B:GLU188 4.9 28.2 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the 1ST Pdz Domain of Human DLG3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the 1ST Pdz Domain of Human DLG3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:49.3 occ:1.00 O B:ILE165 3.8 30.7 1.0 O B:HOH391 3.9 39.8 1.0 CB B:ALA172 4.4 27.6 1.0 CG2 B:ILE165 4.5 29.3 1.0 C B:ILE165 4.7 30.8 1.0 CG B:PRO167 4.7 30.9 1.0 N B:PRO167 4.7 30.4 1.0 CD B:PRO167 4.9 30.4 1.0 CB B:ILE165 4.9 30.1 1.0 C B:ILE166 4.9 30.4 1.0 CA B:PRO167 5.0 29.5 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the 1ST Pdz Domain of Human DLG3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the 1ST Pdz Domain of Human DLG3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:52.2 occ:1.00 NE2 A:HIS153 3.9 28.6 1.0 CE1 A:HIS153 3.9 30.2 1.0 OD1 B:ASN180 4.1 31.6 1.0 CG2 B:VAL154 4.1 30.4 1.0 CD1 B:PHE161 4.1 30.8 1.0 O B:HOH367 4.2 40.5 1.0 CE1 B:PHE161 4.2 30.8 1.0 CB B:ASN180 4.2 29.9 1.0 CG B:ASN180 4.2 30.5 1.0 O A:HOH344 4.3 37.1 1.0 O B:ASN180 4.5 27.9 1.0 CD2 B:HIS153 4.5 31.2 1.0 CD2 A:HIS153 4.6 29.0 1.0 O A:HOH313 4.6 22.2 1.0 ND1 A:HIS153 4.7 29.8 1.0 NE2 B:HIS153 4.7 30.2 1.0 OD1 A:ASN180 4.7 32.2 1.0 CA B:ASN180 4.7 29.3 1.0 O B:HOH343 4.7 31.9 1.0 CG B:PHE161 4.7 29.8 1.0 CZ B:PHE161 4.9 32.1 1.0 O A:HIS153 4.9 28.2 1.0 ND2 B:ASN180 5.0 31.6 1.0

J.M.Elkins, E.Papagrigoriou, G.Berridge, X.Yang, C.Phillips, C.Gileadi, P.Savitsky, D.A.Doyle. Structure of PICK1 and Other Pdz Domains Obtained with the Help of Self-Binding C-Terminal Extensions. Protein Sci. V. 16 683 2007.
ISSN: ISSN 0961-8368
PubMed: 17384233
DOI: 10.1110/PS.062657507