Sodium in PDB 1xar: Crystal Structure of A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck).

The structure of Crystal Structure of A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck)., PDB code: 1xar was solved by H.Feinberg, Y.Guo, D.A.Mitchell, K.Drickamer, W.I.Weis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.73 / 2.25
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.050, 82.050, 110.260, 90.00, 90.00, 120.00
R / Rfree (%)	22.2 / 24.9

The binding sites of Sodium atom in the Crystal Structure of A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck). (pdb code 1xar). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck)., PDB code: 1xar:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck).


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 A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck). within 5.0Å range: probe atom residue distance (Å) B Occ A:Na100 b:64.8 occ:1.00 O A:GLU366 2.1 64.0 1.0 O A:HOH63 2.4 47.7 1.0 O A:HOH62 2.5 56.0 1.0 O A:ASN361 2.5 72.6 1.0 OD2 A:ASP378 2.8 52.7 1.0 C A:GLU366 3.3 64.8 1.0 C A:ASN361 3.7 73.6 1.0 CZ2 A:TRP339 3.7 47.6 1.0 CG A:ASP378 3.8 51.1 1.0 N A:ASN361 4.0 70.8 1.0 OD1 A:ASP367 4.0 63.3 1.0 CB A:GLU366 4.1 69.0 1.0 CB A:ASP378 4.1 48.5 1.0 CA A:GLU366 4.1 67.9 1.0 N A:ASP367 4.3 62.2 1.0 CA A:ASN361 4.3 72.6 1.0 N A:GLU366 4.3 69.9 1.0 CA A:ASP367 4.4 59.7 1.0 CH2 A:TRP339 4.4 49.6 1.0 CB A:ASN361 4.7 72.6 1.0 CE2 A:TRP339 4.7 48.3 1.0 N A:ASN362 4.8 75.8 1.0 CB A:PRO360 4.8 67.8 1.0 CG A:ASP367 4.9 62.1 1.0 OD1 A:ASP378 5.0 51.3 1.0 OD2 A:ASP332 5.0 57.1 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck).


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 A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck). within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:57.8 occ:1.00 OD1 A:ASP378 2.2 51.3 1.0 O A:ASP378 2.4 44.4 1.0 OE2 A:GLU359 2.7 65.7 1.0 OE1 A:GLU366 3.0 75.0 1.0 CG A:ASP378 3.1 51.1 1.0 OE2 A:GLU366 3.2 74.0 1.0 CD A:GLU366 3.3 73.0 1.0 C A:ASP378 3.4 45.0 1.0 OD2 A:ASP378 3.6 52.7 1.0 OD1 A:ASN361 3.7 72.3 1.0 N A:ASP378 3.8 44.9 1.0 CD A:GLU359 3.9 67.3 1.0 O A:HOH30 4.1 41.2 1.0 CA A:ASP378 4.1 45.2 1.0 CB A:ASP378 4.2 48.5 1.0 ND2 A:ASN377 4.2 48.2 1.0 N A:ASN379 4.4 46.2 1.0 CG A:GLU366 4.4 72.2 1.0 CB A:GLU366 4.5 69.0 1.0 CA A:ASN379 4.6 48.0 1.0 CG A:GLU359 4.6 67.6 1.0 CG A:ASN361 4.7 73.0 1.0 CG A:ASN377 4.8 48.8 1.0 OE1 A:GLU359 4.8 68.7 1.0 C A:ASN377 4.9 45.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck).


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 A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck). within 5.0Å range: probe atom residue distance (Å) B Occ B:Na200 b:51.2 occ:1.00 O B:ASN361 2.1 67.9 1.0 O B:GLU366 2.4 47.6 1.0 O B:HOH68 2.5 54.0 1.0 OD2 B:ASP378 2.7 44.9 1.0 C B:ASN361 3.2 67.8 1.0 C B:GLU366 3.4 49.1 1.0 N B:ASN361 3.8 62.5 1.0 CG B:ASP378 3.8 41.5 1.0 CZ2 B:TRP339 3.8 36.8 1.0 CA B:ASN361 3.9 65.5 1.0 CB B:GLU366 4.1 54.1 1.0 OD1 B:ASP367 4.2 46.8 1.0 CB B:ASP378 4.2 39.6 1.0 CB B:ASN361 4.2 65.7 1.0 CA B:GLU366 4.2 52.6 1.0 CH2 B:TRP339 4.3 36.3 1.0 N B:ASN362 4.3 70.8 1.0 N B:GLU366 4.4 55.3 1.0 O B:HOH77 4.4 53.4 1.0 N B:ASP367 4.4 45.7 1.0 CA B:ASP367 4.5 43.0 1.0 CA B:ASN362 4.6 73.7 1.0 N B:SER363 4.7 74.2 1.0 O B:SER363 4.8 71.7 1.0 OD1 B:ASP378 4.8 41.8 1.0 CE2 B:TRP339 4.9 36.5 1.0 OD1 B:ASP332 5.0 37.1 1.0 CB B:PRO360 5.0 55.8 1.0 C B:PRO360 5.0 59.7 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck).


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 A Fragment of Dc-Signr (Containing the Carbohydrate Recognition Domain and Two Repeats of the Neck). within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:49.9 occ:1.00 OD1 B:ASP378 2.1 41.8 1.0 O B:ASP378 2.4 38.8 1.0 O B:HOH75 2.4 56.0 1.0 OE1 B:GLU359 2.5 52.1 1.0 OE1 B:GLU366 2.6 61.0 1.0 OD1 B:ASN361 3.2 66.7 1.0 CD B:GLU366 3.2 58.3 1.0 CG B:ASP378 3.2 41.5 1.0 OE2 B:GLU366 3.3 61.1 1.0 CD B:GLU359 3.4 53.3 1.0 C B:ASP378 3.4 38.2 1.0 OE2 B:GLU359 3.5 53.7 1.0 N B:ASP378 3.6 36.9 1.0 CA B:ASP378 4.0 38.6 1.0 OD2 B:ASP378 4.0 44.9 1.0 CG B:ASN361 4.1 66.2 1.0 CB B:ASP378 4.2 39.6 1.0 N B:ASN379 4.4 38.8 1.0 CG B:GLU366 4.4 56.2 1.0 CB B:GLU366 4.5 54.1 1.0 C B:ASN377 4.7 36.2 1.0 CA B:ASN379 4.7 38.7 1.0 CG B:GLU359 4.8 52.0 1.0 CB B:ASN377 4.8 37.2 1.0 CB B:ASN361 4.9 65.7 1.0 ND2 B:ASN361 4.9 65.1 1.0

H.Feinberg, Y.Guo, D.A.Mitchell, K.Drickamer, W.I.Weis. Extended Neck Regions Stabilize Tetramers of the Receptors Dc-Sign and Dc-Signr J.Biol.Chem. V. 280 1327 2005.
ISSN: ISSN 0021-9258
PubMed: 15509576
DOI: 10.1074/JBC.M409925200