Calcium in PDB 2h0b: Crystal Structure of the Second Lns/Lg Domain From Neurexin 1 Alpha

The structure of Crystal Structure of the Second Lns/Lg Domain From Neurexin 1 Alpha, PDB code: 2h0b was solved by L.R.Sheckler, L.Henry, S.Sugita, T.C.Sudhof, G.Rudenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.032, 61.586, 66.640, 78.47, 78.74, 84.68
R / Rfree (%)	18.4 / 23.3

The binding sites of Calcium atom in the Crystal Structure of the Second Lns/Lg Domain From Neurexin 1 Alpha (pdb code 2h0b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Second Lns/Lg Domain From Neurexin 1 Alpha, PDB code: 2h0b:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Second Lns/Lg Domain From Neurexin 1 Alpha


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 the Second Lns/Lg Domain From Neurexin 1 Alpha within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1000 b:27.3 occ:1.00 O A:MSE414 2.2 33.3 1.0 O B:HOH5317 2.3 34.8 1.0 O A:LEU346 2.3 30.8 1.0 O A:HOH5001 2.3 20.3 1.0 OD1 A:ASP329 2.4 28.9 1.0 O B:HOH5056 2.5 33.9 1.0 CG A:ASP329 3.3 31.1 1.0 OD2 A:ASP329 3.3 30.3 1.0 C A:LEU346 3.4 31.7 1.0 C A:MSE414 3.4 34.4 1.0 OE2 B:GLU290 3.7 42.4 1.0 CA A:LEU346 4.2 31.7 1.0 CA A:MSE414 4.3 35.5 1.0 N A:GLY347 4.3 31.4 1.0 N A:LEU415 4.3 33.7 1.0 N A:GLY416 4.3 33.4 1.0 CB A:MSE414 4.3 37.6 1.0 CA A:LEU415 4.4 33.8 1.0 CD2 A:TYR412 4.4 34.2 1.0 CA A:GLY347 4.4 31.6 1.0 CD B:GLU290 4.4 40.2 1.0 CB A:LEU346 4.5 31.2 1.0 N A:MSE414 4.5 34.5 1.0 CB B:LYS287 4.6 29.4 1.0 CB A:ASP329 4.7 31.6 1.0 O B:HOH5361 4.7 44.8 1.0 C A:LEU415 4.7 33.7 1.0 O B:VAL475 4.8 41.3 1.0 CB A:TYR412 4.8 33.4 1.0 OE1 B:GLU290 4.9 42.1 1.0 CG B:LYS287 4.9 28.4 1.0 O B:HOH5251 5.0 44.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Second Lns/Lg Domain From Neurexin 1 Alpha


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 the Second Lns/Lg Domain From Neurexin 1 Alpha within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2000 b:24.0 occ:1.00 O B:LEU346 2.3 31.5 1.0 O B:MSE414 2.3 33.9 1.0 O B:HOH5234 2.4 23.4 1.0 OD1 B:ASP329 2.4 30.4 1.0 O B:HOH5027 2.5 26.4 1.0 O B:HOH5179 2.6 39.5 1.0 OD2 B:ASP329 3.1 31.9 1.0 CG B:ASP329 3.2 34.3 1.0 C B:LEU346 3.3 32.3 1.0 C B:MSE414 3.5 34.2 1.0 N B:GLY347 4.2 31.5 1.0 CA B:LEU346 4.2 32.8 1.0 CA B:GLY347 4.2 32.2 1.0 CB B:MSE414 4.3 34.9 1.0 CA B:MSE414 4.4 34.3 1.0 N B:GLY416 4.4 33.5 1.0 CD2 B:TYR412 4.4 34.3 1.0 N B:LEU415 4.4 33.8 1.0 CA B:LEU415 4.5 34.3 1.0 CB B:LEU346 4.6 32.5 1.0 N B:MSE414 4.6 32.9 1.0 CB B:ASP329 4.6 34.7 1.0 C B:LEU415 4.8 34.6 1.0 CB B:TYR412 4.9 33.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Second Lns/Lg Domain From Neurexin 1 Alpha


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 the Second Lns/Lg Domain From Neurexin 1 Alpha within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3000 b:25.1 occ:1.00 O C:HOH5346 2.2 25.4 1.0 O C:MSE414 2.3 32.1 1.0 O C:HOH5054 2.3 22.1 1.0 OD1 C:ASP329 2.4 31.5 1.0 O C:LEU346 2.4 30.9 1.0 CG C:ASP329 3.3 33.6 1.0 C C:MSE414 3.4 32.2 1.0 OD2 C:ASP329 3.4 32.5 1.0 C C:LEU346 3.4 31.6 1.0 CA C:MSE414 4.1 33.1 1.0 CB C:MSE414 4.2 34.5 1.0 CA C:LEU346 4.2 31.6 1.0 N C:MSE414 4.2 32.5 1.0 N C:GLY416 4.3 31.6 1.0 CD2 C:TYR412 4.3 28.2 1.0 N C:LEU415 4.3 31.6 1.0 N C:GLY347 4.4 31.9 1.0 CA C:LEU415 4.5 31.2 1.0 CB C:LEU346 4.5 31.6 1.0 CA C:GLY347 4.6 31.9 1.0 OE1 C:GLN302 4.7 38.2 1.0 CB C:ASP329 4.7 33.8 1.0 CB C:TYR412 4.7 30.1 1.0 C C:LEU415 4.8 31.7 1.0 CG C:TYR412 5.0 29.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Second Lns/Lg Domain From Neurexin 1 Alpha


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 the Second Lns/Lg Domain From Neurexin 1 Alpha within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca4000 b:27.5 occ:1.00 O D:LEU346 2.2 30.0 1.0 O D:HOH5045 2.3 26.8 1.0 O D:MSE414 2.3 33.4 1.0 OD1 D:ASP329 2.4 29.7 1.0 O D:HOH5347 2.4 27.4 1.0 CG D:ASP329 3.3 33.4 1.0 C D:LEU346 3.4 30.3 1.0 OD2 D:ASP329 3.5 31.8 1.0 C D:MSE414 3.5 33.5 1.0 CB D:MSE414 4.2 34.4 1.0 CD2 D:TYR412 4.2 25.4 1.0 CA D:LEU346 4.2 30.3 1.0 CA D:MSE414 4.2 33.9 1.0 N D:GLY416 4.3 33.9 1.0 N D:MSE414 4.3 32.1 1.0 N D:GLY347 4.3 30.2 1.0 CA D:GLY347 4.4 31.1 1.0 CB D:LEU346 4.5 30.1 1.0 N D:LEU415 4.5 33.2 1.0 CA D:LEU415 4.6 33.3 1.0 CB D:ASP329 4.7 33.2 1.0 CB D:TYR412 4.7 27.8 1.0 C D:LEU415 4.8 33.8 1.0 CG D:TYR412 4.9 27.6 1.0 O D:HOH5423 4.9 41.7 1.0 CE2 D:TYR412 5.0 23.0 1.0

L.R.Sheckler, L.Henry, S.Sugita, T.C.Sudhof, G.Rudenko. Crystal Structure of the Second Lns/Lg Domain From Neurexin 1{Alpha}: CA2+ Binding and the Effects of Alternative Splicing J.Biol.Chem. V. 281 22896 2006.
ISSN: ISSN 0021-9258
PubMed: 16772286
DOI: 10.1074/JBC.M603464200