Calcium in PDB 1sl6: Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.

The structure of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X., PDB code: 1sl6 was solved by Y.Guo, H.Feinberg, E.Conroy, D.A.Mitchell, R.Alvarez, O.Blixt, M.E.Taylor, W.I.Weis, K.Drickamer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.96 / 2.25
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	153.750, 153.750, 128.702, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 25.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. (pdb code 1sl6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 24 binding sites of Calcium where determined in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X., PDB code: 1sl6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:49.0 occ:1.00 OD1 A:ASP367 2.2 49.1 1.0 OE2 A:GLU336 2.2 55.6 1.0 OD1 A:ASN362 2.4 58.0 1.0 O A:GLU366 2.4 49.4 1.0 O A:HOH400 2.4 40.8 1.0 OD2 A:ASP332 2.5 50.7 1.0 OE1 A:GLU336 2.6 56.5 1.0 OD1 A:ASP332 2.7 53.0 1.0 CD A:GLU336 2.7 57.6 1.0 CG A:ASP332 2.9 52.5 1.0 CG A:ASN362 3.2 56.1 1.0 C A:GLU366 3.3 49.4 1.0 CG A:ASP367 3.4 50.3 1.0 CA A:ASP367 3.7 46.7 1.0 N A:ASP367 3.9 47.5 1.0 CA A:CA3 3.9 56.9 1.0 CB A:ASP367 4.0 47.4 1.0 CB A:ASN362 4.0 54.9 1.0 ND2 A:ASN362 4.0 54.7 1.0 N A:GLU366 4.2 53.3 1.0 CG A:GLU336 4.2 56.3 1.0 OD2 A:ASP367 4.4 51.8 1.0 CA A:GLU366 4.4 50.5 1.0 CB A:ASP332 4.4 51.8 1.0 CZ2 A:TRP339 4.5 48.7 1.0 OD1 A:ASN365 4.6 55.9 1.0 CA A:ASN362 4.6 56.0 1.0 O A:ASP332 4.7 52.4 1.0 OD2 A:ASP378 4.7 45.2 1.0 N A:GLY337 4.8 59.7 1.0 CA A:GLU336 4.9 61.0 1.0 CH2 A:TRP339 4.9 47.2 1.0 O A:HOH401 5.0 60.2 1.0 C A:ASN365 5.0 55.0 1.0 CB A:GLU336 5.0 59.3 1.0 C A:ASP367 5.0 46.0 1.0

Calcium binding site 2 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:48.4 occ:1.00 OD1 A:ASP378 2.3 44.5 1.0 O4 A:FUC13 2.4 60.6 1.0 OE1 A:GLU366 2.5 55.2 1.0 O3 A:FUC13 2.5 65.7 1.0 O A:ASP378 2.5 45.2 1.0 OD1 A:ASN377 2.5 41.6 1.0 OD1 A:ASN361 2.6 48.3 1.0 OE1 A:GLU359 2.9 50.3 1.0 C4 A:FUC13 3.2 66.9 1.0 CG A:ASP378 3.3 44.5 1.0 C3 A:FUC13 3.3 67.6 1.0 CD A:GLU366 3.3 53.2 1.0 CG A:ASN361 3.5 50.3 1.0 CG A:ASN377 3.6 45.4 1.0 OE2 A:GLU366 3.6 52.9 1.0 C A:ASP378 3.6 45.1 1.0 CD A:GLU359 3.6 50.0 1.0 ND2 A:ASN361 3.8 50.9 1.0 N A:ASP378 3.8 42.0 1.0 OE2 A:GLU359 3.9 49.4 1.0 OD2 A:ASP378 3.9 45.2 1.0 C2 A:FUC13 4.0 71.4 1.0 ND2 A:ASN377 4.0 45.8 1.0 CA A:ASP378 4.2 44.3 1.0 CB A:ASP378 4.3 41.9 1.0 N A:ASN361 4.3 52.4 1.0 N A:ASN362 4.6 53.6 1.0 CG A:GLU366 4.6 51.0 1.0 C5 A:FUC13 4.6 68.7 1.0 CB A:ASN361 4.7 49.1 1.0 N A:SER363 4.7 58.9 1.0 N A:ASN379 4.8 45.8 1.0 O2 A:FUC13 4.8 72.0 1.0 C A:ASN377 4.8 42.7 1.0 CB A:GLU366 4.8 50.3 1.0 CG A:GLU359 4.8 46.7 1.0 CB A:SER363 4.9 60.8 1.0 CB A:ASN377 4.9 43.4 1.0 CA A:ASN361 4.9 51.9 1.0

Calcium binding site 3 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:56.9 occ:1.00 OE1 A:GLU336 2.2 56.5 1.0 OD1 A:ASN365 2.4 55.9 1.0 O A:HOH401 2.4 60.2 1.0 OD2 A:ASP367 2.5 51.8 1.0 O A:HOH402 2.5 54.6 1.0 OD1 A:ASP367 2.6 49.1 1.0 CG A:ASP367 2.8 50.3 1.0 CG A:ASN365 3.4 55.9 1.0 CD A:GLU336 3.4 57.6 1.0 ND2 A:ASN365 3.8 53.7 1.0 CA A:CA1 3.9 49.0 1.0 CB A:GLU336 4.2 59.3 1.0 CG A:GLU336 4.2 56.3 1.0 CB A:ASP367 4.3 47.4 1.0 OE2 A:GLU336 4.3 55.6 1.0 OD1 A:ASN362 4.4 58.0 1.0 O A:ASP332 4.5 52.4 1.0 CA A:GLU336 4.6 61.0 1.0 CB A:ASN365 4.7 54.8 1.0 OD1 A:ASP332 4.9 53.0 1.0 ND2 A:ASN362 4.9 54.7 1.0 OD2 A:ASP332 4.9 50.7 1.0

Calcium binding site 4 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4 b:62.3 occ:1.00 OD2 A:ASP256 2.5 62.7 1.0 O E:HOH422 2.6 52.7 1.0 OE1 A:GLU253 2.7 79.2 1.0 CG A:ASP256 3.5 63.1 1.0 CD A:GLU253 3.5 78.7 1.0 OE2 A:GLU253 3.6 79.5 1.0 CB A:ASP256 3.8 60.6 1.0 OG E:SER350 4.1 46.2 1.0 OG E:SER348 4.3 51.5 1.0 OD1 A:ASP256 4.6 64.3 1.0 CB E:SER348 4.7 47.5 1.0 CG A:GLU253 4.9 77.6 1.0 CB E:SER350 5.0 40.8 1.0 CA A:GLU253 5.0 76.0 1.0

Calcium binding site 5 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1 b:40.1 occ:1.00 OD1 B:ASP367 2.2 46.6 1.0 O B:HOH400 2.3 39.6 1.0 OD2 B:ASP332 2.4 40.2 1.0 OD1 B:ASN362 2.5 45.3 1.0 O B:GLU366 2.5 43.6 1.0 OD1 B:ASP332 2.5 39.9 1.0 OE1 B:GLU336 2.6 49.1 1.0 OE2 B:GLU336 2.6 50.1 1.0 CG B:ASP332 2.8 41.0 1.0 CD B:GLU336 2.9 49.4 1.0 CG B:ASN362 3.2 47.9 1.0 C B:GLU366 3.3 44.3 1.0 CG B:ASP367 3.4 47.7 1.0 CA B:ASP367 3.7 43.9 1.0 N B:ASP367 3.8 43.2 1.0 CA B:CA3 3.9 46.6 1.0 CB B:ASN362 3.9 47.6 1.0 CB B:ASP367 4.0 45.0 1.0 N B:GLU366 4.1 47.8 1.0 ND2 B:ASN362 4.1 46.4 1.0 O B:HOH424 4.2 51.7 1.0 CB B:ASP332 4.3 40.1 1.0 CA B:GLU366 4.3 46.2 1.0 CG B:GLU336 4.4 48.6 1.0 OD2 B:ASP367 4.4 48.9 1.0 CZ2 B:TRP339 4.5 43.1 1.0 CA B:ASN362 4.5 49.9 1.0 O B:ASP332 4.5 43.0 1.0 O B:HOH401 4.7 37.2 1.0 OD2 B:ASP378 4.7 42.8 1.0 OD1 B:ASN365 4.7 48.1 1.0 CH2 B:TRP339 4.9 40.7 1.0 N B:GLY337 4.9 49.0 1.0 C B:ASP367 4.9 43.0 1.0 C B:ASN365 4.9 49.9 1.0

Calcium binding site 6 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2 b:44.1 occ:1.00 OD1 B:ASP378 2.2 42.4 1.0 OD1 B:ASN377 2.4 40.1 1.0 O3 B:FUC13 2.4 47.3 0.5 O B:ASP378 2.4 39.1 1.0 O4 B:FUC13 2.5 48.0 0.5 OD1 B:ASN361 2.5 46.9 1.0 OE1 B:GLU366 2.5 51.7 1.0 OE1 B:GLU359 2.5 47.5 1.0 C4 B:FUC13 3.2 50.7 0.5 C3 B:FUC13 3.2 51.0 0.5 CG B:ASP378 3.3 41.5 1.0 CD B:GLU359 3.3 50.4 1.0 CG B:ASN361 3.3 49.2 1.0 CG B:ASN377 3.4 40.0 1.0 C B:ASP378 3.5 41.6 1.0 OE2 B:GLU359 3.6 50.3 1.0 CD B:GLU366 3.6 50.2 1.0 N B:ASP378 3.7 41.3 1.0 ND2 B:ASN361 3.7 48.8 1.0 ND2 B:ASN377 3.8 41.6 1.0 C2 B:FUC13 3.8 55.2 0.5 OD2 B:ASP378 3.9 42.8 1.0 CA B:ASP378 4.0 41.5 1.0 OE2 B:GLU366 4.1 49.0 1.0 CB B:ASP378 4.2 41.5 1.0 N B:ASN361 4.3 48.6 1.0 O2 B:FUC13 4.5 56.4 0.5 CG B:GLU359 4.6 48.5 1.0 C B:ASN377 4.6 40.7 1.0 CB B:ASN361 4.6 49.0 1.0 C5 B:FUC13 4.7 52.1 0.5 CB B:ASN377 4.7 39.4 1.0 N B:ASN379 4.7 42.5 1.0 N B:ASN362 4.7 49.0 1.0 CG B:GLU366 4.8 45.9 1.0 CA B:ASN361 4.9 49.4 1.0 CA B:ASN377 4.9 40.7 1.0 CB B:GLU366 4.9 47.3 1.0 N B:SER363 5.0 54.1 1.0

Calcium binding site 7 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:46.6 occ:1.00 OD1 B:ASN365 2.2 48.1 1.0 O B:HOH402 2.3 44.2 1.0 OE1 B:GLU336 2.4 49.1 1.0 O B:HOH401 2.4 37.2 1.0 OD1 B:ASP367 2.5 46.6 1.0 OD2 B:ASP367 2.6 48.9 1.0 CG B:ASP367 2.9 47.7 1.0 CG B:ASN365 3.3 46.0 1.0 CD B:GLU336 3.6 49.4 1.0 ND2 B:ASN365 3.8 46.5 1.0 CA B:CA1 3.9 40.1 1.0 OD1 B:ASN362 4.2 45.3 1.0 CB B:GLU336 4.2 48.5 1.0 CG B:GLU336 4.3 48.6 1.0 CB B:ASP367 4.3 45.0 1.0 O B:ASP332 4.5 43.0 1.0 OE2 B:GLU336 4.5 50.1 1.0 CB B:ASN365 4.6 47.9 1.0 OD1 B:ASP332 4.6 39.9 1.0 ND2 B:ASN362 4.7 46.4 1.0 CA B:GLU336 4.8 49.1 1.0 CA B:ASN365 4.8 50.9 1.0 CG B:ASN362 4.8 47.9 1.0 OD2 B:ASP332 5.0 40.2 1.0

Calcium binding site 8 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4 b:76.8 occ:1.00 OE1 B:GLU253 2.2 83.1 1.0 O F:HOH424 2.3 66.6 1.0 OD2 B:ASP256 2.7 72.9 1.0 CD B:GLU253 3.0 83.2 1.0 OE2 B:GLU253 3.1 83.6 1.0 CG B:ASP256 3.5 71.5 1.0 CB B:ASP256 3.8 69.2 1.0 OG F:SER350 3.9 48.4 1.0 OG F:SER348 4.3 48.7 1.0 CG B:GLU253 4.5 81.7 1.0 OD1 B:ASP256 4.5 75.0 1.0 CB F:SER348 4.6 42.7 1.0 CA B:GLU253 4.9 80.8 1.0 CB F:SER350 4.9 45.2 1.0 O F:HOH440 4.9 49.1 1.0

Calcium binding site 9 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1 b:46.9 occ:1.00 OD2 C:ASP332 2.4 43.4 1.0 O C:HOH17 2.4 39.7 1.0 O C:GLU366 2.4 41.9 1.0 OD1 C:ASN362 2.4 54.0 1.0 OD1 C:ASP367 2.5 42.1 1.0 OE2 C:GLU336 2.6 51.8 1.0 OE1 C:GLU336 2.6 49.8 1.0 OD1 C:ASP332 2.7 48.2 1.0 CG C:ASP332 2.9 45.1 1.0 CD C:GLU336 2.9 52.4 1.0 CG C:ASN362 3.3 54.2 1.0 C C:GLU366 3.3 42.0 1.0 CG C:ASP367 3.5 44.5 1.0 CA C:ASP367 3.7 42.7 1.0 CA C:CA3 3.8 41.9 1.0 N C:ASP367 3.9 40.5 1.0 CB C:ASN362 3.9 52.4 1.0 CB C:ASP367 4.1 43.3 1.0 N C:GLU366 4.2 44.3 1.0 ND2 C:ASN362 4.3 53.9 1.0 CZ2 C:TRP339 4.3 39.7 1.0 CB C:ASP332 4.4 44.3 1.0 CA C:GLU366 4.4 42.8 1.0 CG C:GLU336 4.4 51.8 1.0 OD1 C:ASN365 4.5 43.2 1.0 CA C:ASN362 4.5 52.1 1.0 OD2 C:ASP367 4.5 47.0 1.0 OD2 C:ASP378 4.6 42.3 1.0 O C:ASP332 4.7 45.4 1.0 CH2 C:TRP339 4.8 41.8 1.0 O C:HOH18 4.9 39.5 1.0 C C:ASP367 4.9 43.8 1.0 N C:GLY337 5.0 52.6 1.0 CA C:GLU336 5.0 53.0 1.0

Calcium binding site 10 out of 24 in the Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Fragment of Dc-Signr (Containg the Carbohydrate Recognition Domain and Two Repeats of the Neck) Complexed with Lewis-X. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2 b:47.3 occ:1.00 OD1 C:ASP378 2.1 41.9 1.0 OE1 C:GLU359 2.4 58.9 1.0 O4 C:FUC13 2.4 77.1 1.0 OD1 C:ASN377 2.4 40.6 1.0 O C:ASP378 2.5 42.2 1.0 O3 C:FUC13 2.5 76.6 1.0 OD1 C:ASN361 2.6 46.5 1.0 OE1 C:GLU366 2.6 45.1 1.0 CG C:ASP378 3.2 41.5 1.0 CD C:GLU359 3.3 58.6 1.0 C4 C:FUC13 3.3 79.2 1.0 C3 C:FUC13 3.3 79.3 1.0 CD C:GLU366 3.5 47.0 1.0 CG C:ASN377 3.5 43.6 1.0 CG C:ASN361 3.5 48.3 1.0 OE2 C:GLU359 3.6 59.1 1.0 C C:ASP378 3.6 44.5 1.0 N C:ASP378 3.7 42.9 1.0 OE2 C:GLU366 3.8 50.5 1.0 C2 C:FUC13 3.9 82.2 1.0 ND2 C:ASN361 3.9 47.4 1.0 ND2 C:ASN377 3.9 41.4 1.0 OD2 C:ASP378 4.0 42.3 1.0 CA C:ASP378 4.1 42.7 1.0 CB C:ASP378 4.3 41.8 1.0 N C:ASN361 4.3 49.8 1.0 CG C:GLU359 4.5 56.9 1.0 C C:ASN377 4.6 43.0 1.0 O2 C:FUC13 4.6 80.4 1.0 C5 C:FUC13 4.7 80.7 1.0 CG C:GLU366 4.7 44.2 1.0 N C:ASN379 4.7 46.6 1.0 CB C:ASN377 4.8 43.1 1.0 N C:ASN362 4.8 51.1 1.0 CB C:ASN361 4.8 48.0 1.0 CB C:GLU366 4.8 42.9 1.0 CA C:ASN377 4.9 44.1 1.0 N C:SER363 4.9 53.0 1.0 CA C:ASN361 4.9 50.0 1.0 O5 C:FUC13 5.0 82.1 1.0

Y.Guo, H.Feinberg, E.Conroy, D.A.Mitchell, R.Alvarez, O.Blixt, M.E.Taylor, W.I.Weis, K.Drickamer. Structural Basis For Distinct Ligand-Binding and Targeting Properties of the Receptors Dc-Sign and Dc-Signr Nat.Struct.Mol.Biol. V. 11 591 2004.
ISSN: ISSN 1545-9993
PubMed: 15195147
DOI: 10.1038/NSMB784