Calcium in PDB 3tbd: Crystal Structure of Domain VI and LE1 of Human Netrin-G2

The structure of Crystal Structure of Domain VI and LE1 of Human Netrin-G2, PDB code: 3tbd was solved by J.Brasch, Q.Liu, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.27 / 1.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	63.134, 63.134, 190.640, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 22.7

The structure of Crystal Structure of Domain VI and LE1 of Human Netrin-G2 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Domain VI and LE1 of Human Netrin-G2 (pdb code 3tbd). 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 Crystal Structure of Domain VI and LE1 of Human Netrin-G2, PDB code: 3tbd:

Calcium binding site 1 out of 1 in the Crystal Structure of Domain VI and LE1 of Human Netrin-G2


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 Domain VI and LE1 of Human Netrin-G2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:17.9 occ:1.00 OE2 A:GLU82 2.3 18.6 1.0 O A:LEU77 2.3 17.5 1.0 OD1 A:ASP80 2.4 20.7 1.0 O A:SER262 2.4 15.6 1.0 O A:THR88 2.4 18.2 1.0 O A:HOH433 2.5 16.8 1.0 OG1 A:THR88 2.5 17.6 1.0 CD A:GLU82 3.2 17.9 1.0 C A:THR88 3.4 18.8 1.0 CG A:ASP80 3.5 24.1 1.0 C A:LEU77 3.5 17.9 1.0 C A:SER262 3.5 16.2 1.0 CG A:GLU82 3.6 20.8 1.0 CB A:THR88 3.7 19.4 1.0 N A:THR88 3.8 19.2 1.0 CA A:THR88 3.9 19.2 1.0 OD2 A:ASP80 3.9 23.1 1.0 CA A:SER262 4.1 16.0 1.0 OE1 A:GLU82 4.2 17.5 1.0 CA A:LEU77 4.3 17.3 1.0 CB A:SER262 4.3 16.6 1.0 N A:MET78 4.5 16.6 1.0 N A:ASP80 4.5 18.7 1.0 N A:TYR89 4.5 18.3 1.0 CB A:LEU77 4.5 17.7 1.0 C A:MET78 4.5 16.6 1.0 CA A:MET78 4.5 15.3 1.0 O A:ASP80 4.6 19.8 1.0 N A:ASN263 4.6 15.9 1.0 N A:PHE79 4.7 17.3 1.0 CB A:ASP80 4.8 22.3 1.0 CA A:TYR89 4.8 17.9 1.0 CA A:ASN263 4.8 14.6 1.0 CG2 A:THR88 4.8 20.1 1.0 O A:MET78 5.0 16.6 1.0 CA A:ASP80 5.0 19.0 1.0

J.Brasch, O.J.Harrison, G.Ahlsen, Q.Liu, L.Shapiro. Crystal Structure of the Ligand Binding Domain of Netrin G2. J.Mol.Biol. V. 414 723 2011.
ISSN: ISSN 0022-2836
PubMed: 22041449
DOI: 10.1016/J.JMB.2011.10.030