Calcium in PDB 2qqo: Crystal Structure of the A2B1B2 Domains From Human Neuropilin-2

The structure of Crystal Structure of the A2B1B2 Domains From Human Neuropilin-2, PDB code: 2qqo was solved by B.A.Appleton, C.Wiesmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.093, 192.909, 66.169, 90.00, 90.08, 90.00
R / Rfree (%)	18.5 / 23.9

The binding sites of Calcium atom in the Crystal Structure of the A2B1B2 Domains From Human Neuropilin-2 (pdb code 2qqo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the A2B1B2 Domains From Human Neuropilin-2, PDB code: 2qqo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the A2B1B2 Domains From Human Neuropilin-2


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 A2B1B2 Domains From Human Neuropilin-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:39.8 occ:1.00 OD1 A:ASP252 2.3 34.7 1.0 O A:HOH757 2.3 30.0 1.0 O A:ALA254 2.4 45.4 1.0 O A:VAL255 2.4 37.2 1.0 OE1 A:GLU197 2.6 29.8 1.0 OD2 A:ASP211 2.6 33.8 1.0 OD1 A:ASP211 2.7 37.2 1.0 CG A:ASP211 3.0 35.2 1.0 CG A:ASP252 3.4 38.9 1.0 C A:ALA254 3.4 41.7 1.0 C A:VAL255 3.5 37.4 1.0 CD A:GLU197 3.7 30.3 1.0 N A:ASP252 3.9 40.0 1.0 OD2 A:ASP252 4.0 40.6 1.0 O A:ASP252 4.0 40.5 1.0 CA A:VAL255 4.1 40.9 1.0 N A:VAL255 4.1 44.9 1.0 CB A:VAL255 4.2 41.9 1.0 C A:ASP252 4.3 44.8 1.0 N A:ALA254 4.3 40.0 1.0 OE2 A:GLU197 4.4 26.9 1.0 CA A:ASP252 4.4 43.5 1.0 CB A:ASP211 4.4 37.6 1.0 CA A:ALA254 4.5 41.5 1.0 CB A:ASP252 4.5 40.2 1.0 CB A:GLU197 4.6 35.9 1.0 ND1 A:HIS171 4.6 41.9 1.0 N A:ALA256 4.7 33.6 1.0 CE2 A:TYR169 4.7 27.8 1.0 OH A:TYR169 4.7 31.9 1.0 CG A:GLU197 4.8 32.2 1.0 C A:THR251 4.9 39.8 1.0 CB A:THR251 5.0 38.4 1.0 N A:ASP211 5.0 39.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the A2B1B2 Domains From Human Neuropilin-2


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 A2B1B2 Domains From Human Neuropilin-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1 b:39.9 occ:1.00 O B:HOH760 2.2 32.9 1.0 OE1 B:GLU197 2.3 31.0 1.0 O B:VAL255 2.4 40.0 1.0 OD1 B:ASP252 2.4 33.2 1.0 O B:ALA254 2.5 45.5 1.0 OD1 B:ASP211 2.7 41.2 1.0 OD2 B:ASP211 2.7 37.5 1.0 CG B:ASP211 3.0 40.1 1.0 C B:ALA254 3.4 40.9 1.0 NZ A:LYS326 3.4 45.8 1.0 C B:VAL255 3.5 39.0 1.0 CD B:GLU197 3.5 30.6 1.0 CG B:ASP252 3.5 40.8 1.0 N B:ASP252 4.1 42.4 1.0 CA B:VAL255 4.1 39.6 1.0 N B:VAL255 4.1 42.0 1.0 O B:ASP252 4.1 40.7 1.0 OE2 B:GLU197 4.2 32.9 1.0 CB B:VAL255 4.2 40.0 1.0 OD2 B:ASP252 4.2 45.4 1.0 N B:ALA254 4.3 42.1 1.0 C B:ASP252 4.4 44.5 1.0 CA B:ALA254 4.5 41.4 1.0 CB B:ASP211 4.5 40.3 1.0 CA B:ASP252 4.5 44.6 1.0 CB B:GLU197 4.5 34.4 1.0 ND1 B:HIS171 4.6 45.9 1.0 CB B:ASP252 4.6 41.4 1.0 N B:ALA256 4.6 38.8 1.0 CG B:GLU197 4.6 32.4 1.0 OH B:TYR169 4.7 29.3 1.0 CE2 B:TYR169 4.8 28.6 1.0 CE A:LYS326 4.9 46.1 1.0 CB B:THR251 4.9 32.9 1.0

B.A.Appleton, P.Wu, J.Maloney, J.Yin, W.C.Liang, S.Stawicki, K.Mortara, K.K.Bowman, J.M.Elliott, W.Desmarais, J.F.Bazan, A.Bagri, M.Tessier-Lavigne, A.W.Koch, Y.Wu, R.J.Watts, C.Wiesmann. Structural Studies of Neuropilin/Antibody Complexes Provide Insights Into Semaphorin and Vegf Binding Embo J. V. 26 4902 2007.
ISSN: ISSN 0261-4189
PubMed: 17989695
DOI: 10.1038/SJ.EMBOJ.7601906