Calcium in PDB 4wnx: Netrin 4 Lacking the C-Terminal Domain

The structure of Netrin 4 Lacking the C-Terminal Domain, PDB code: 4wnx was solved by M.Mcdougall, T.Patel, R.Reuten, M.Meier, M.Koch, J.Stetefeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.49 / 2.72
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.755, 75.049, 74.672, 90.00, 96.07, 90.00
R / Rfree (%)	22 / 26.3

The binding sites of Calcium atom in the Netrin 4 Lacking the C-Terminal Domain (pdb code 4wnx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Netrin 4 Lacking the C-Terminal Domain, PDB code: 4wnx:

Calcium binding site 1 out of 1 in the Netrin 4 Lacking the C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Netrin 4 Lacking the C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:32.0 occ:1.00 OD1 A:ASP96 2.4 56.9 1.0 OG1 A:THR104 2.5 28.3 1.0 O A:TYR254 2.6 30.4 1.0 O A:ALA93 2.7 26.1 1.0 O A:THR104 2.7 30.5 1.0 O A:HOH605 2.7 30.8 1.0 H A:THR104 3.2 34.8 1.0 CG A:ASP96 3.2 56.4 1.0 OD2 A:ASP96 3.2 56.4 1.0 C A:THR104 3.4 28.2 1.0 OD1 A:ASP255 3.5 47.7 1.0 CB A:THR104 3.7 29.0 1.0 C A:TYR254 3.7 29.9 1.0 N A:THR104 3.8 29.0 1.0 CA A:THR104 3.8 28.9 1.0 C A:ALA93 3.9 45.5 1.0 HA A:MET94 3.9 49.3 1.0 HA A:TYR254 4.2 36.1 1.0 HB A:THR104 4.2 34.8 1.0 HA A:ASP255 4.2 37.9 1.0 HA A:TRP105 4.2 31.9 1.0 O A:SER97 4.3 59.4 1.0 N A:TRP105 4.4 60.0 1.0 HA A:SER98 4.4 78.5 1.0 H A:ASP96 4.5 62.1 1.0 HB1 A:ALA93 4.5 32.7 1.0 HD3 A:ARG100 4.5 81.8 1.0 CA A:TYR254 4.5 30.1 1.0 CG A:ASP255 4.5 47.1 1.0 HB3 A:TYR254 4.5 36.3 1.0 HD1 A:TYR254 4.6 38.0 1.0 CA A:MET94 4.6 41.1 1.0 O A:ASP96 4.7 55.8 1.0 CB A:ASP96 4.7 55.9 1.0 HG23 A:THR104 4.7 35.8 1.0 HA A:ALA93 4.7 32.0 1.0 N A:ASP255 4.7 29.0 1.0 N A:MET94 4.7 41.3 1.0 CG2 A:THR104 4.8 29.8 1.0 HA A:THR104 4.8 34.7 1.0 CA A:ASP255 4.8 31.6 1.0 CA A:TRP105 4.8 26.6 1.0 CA A:ALA93 4.8 26.7 1.0 C A:MET94 4.9 42.8 1.0 C A:ASP96 4.9 56.2 1.0 O A:MET94 4.9 38.7 1.0 HA A:ARG103 5.0 64.0 1.0

R.Reuten, T.R.Patel, M.Mcdougall, N.Rama, D.Nikodemus, B.Gibert, J.G.Delcros, C.Prein, M.Meier, S.Metzger, Z.Zhou, J.Kaltenberg, K.K.Mckee, T.Bald, T.Tuting, P.Zigrino, V.Djonov, W.Bloch, H.Clausen-Schaumann, E.Poschl, P.D.Yurchenco, M.Ehrbar, P.Mehlen, J.Stetefeld, M.Koch. Structural Decoding of Netrin-4 Reveals A Regulatory Function Towards Mature Basement Membranes. Nat Commun V. 7 13515 2016.
ISSN: ESSN 2041-1723
PubMed: 27901020
DOI: 10.1038/NCOMMS13515