Calcium in PDB 3zyg: NETRING2 Lam and EGF1 Domains

The structure of NETRING2 Lam and EGF1 Domains, PDB code: 3zyg was solved by E.Seiradake, C.H.Coles, P.V.Perestenko, K.Harlos, R.A.J.Mcilhinney, A.R.Aricescu, E.Y.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.500, 64.880, 120.080, 90.00, 103.06, 90.00
R / Rfree (%)	24.816 / 29.684

The binding sites of Calcium atom in the NETRING2 Lam and EGF1 Domains (pdb code 3zyg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the NETRING2 Lam and EGF1 Domains, PDB code: 3zyg:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the NETRING2 Lam and EGF1 Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of NETRING2 Lam and EGF1 Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1348 b:15.8 occ:1.00 O A:LEU94 2.2 14.0 1.0 O A:SER279 2.3 14.8 1.0 OE2 A:GLU99 2.3 19.6 1.0 OD1 A:ASP97 2.4 27.1 1.0 O A:THR105 2.4 17.2 1.0 O A:HOH2035 2.5 9.1 1.0 OG1 A:THR105 2.7 16.0 1.0 CD A:GLU99 3.3 27.0 1.0 C A:SER279 3.4 15.3 1.0 C A:LEU94 3.4 12.8 1.0 C A:THR105 3.4 18.4 1.0 CG A:ASP97 3.5 21.7 1.0 CG A:GLU99 3.7 20.1 1.0 CB A:THR105 3.8 16.3 1.0 N A:THR105 3.9 15.1 1.0 CA A:THR105 3.9 14.5 1.0 CA A:SER279 3.9 11.9 1.0 OD2 A:ASP97 4.0 21.2 1.0 CA A:LEU94 4.3 11.0 1.0 OE1 A:GLU99 4.3 19.4 1.0 CB A:SER279 4.3 15.0 1.0 N A:MET95 4.3 6.6 1.0 CA A:MET95 4.4 6.3 1.0 N A:TYR106 4.5 15.2 1.0 CB A:LEU94 4.6 10.3 1.0 C A:MET95 4.6 12.4 1.0 N A:ASN280 4.6 9.8 1.0 N A:ASP97 4.6 12.0 1.0 N A:PHE96 4.7 10.4 1.0 O A:ASP97 4.7 15.5 1.0 OD1 A:ASN280 4.8 14.4 1.0 CB A:ASP97 4.8 13.4 1.0 CA A:TYR106 4.9 14.0 1.0 CA A:ASN280 5.0 8.8 1.0 CG2 A:THR105 5.0 11.1 1.0

Calcium binding site 2 out of 2 in the NETRING2 Lam and EGF1 Domains


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of NETRING2 Lam and EGF1 Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1348 b:14.7 occ:1.00 O B:LEU94 2.2 17.9 1.0 O B:SER279 2.3 10.4 1.0 OE2 B:GLU99 2.3 12.6 1.0 O B:THR105 2.4 18.8 1.0 OD1 B:ASP97 2.4 20.1 1.0 O B:HOH2030 2.5 15.7 1.0 OG1 B:THR105 2.9 18.6 1.0 CD B:GLU99 3.3 10.7 1.0 C B:LEU94 3.4 16.7 1.0 C B:THR105 3.4 17.4 1.0 C B:SER279 3.4 13.2 1.0 CG B:ASP97 3.5 19.6 1.0 CG B:GLU99 3.7 15.3 1.0 N B:THR105 3.9 12.2 1.0 CA B:THR105 3.9 12.5 1.0 CB B:THR105 3.9 16.2 1.0 OD2 B:ASP97 4.0 21.1 1.0 CA B:SER279 4.0 10.3 1.0 CA B:LEU94 4.2 12.4 1.0 OE1 B:GLU99 4.3 9.7 1.0 N B:MET95 4.3 10.2 1.0 CB B:SER279 4.4 13.3 1.0 CA B:MET95 4.4 9.6 1.0 N B:TYR106 4.5 12.4 1.0 N B:ASP97 4.5 7.8 1.0 C B:MET95 4.5 13.7 1.0 CB B:LEU94 4.5 12.1 1.0 O B:ASP97 4.6 14.6 1.0 N B:ASN280 4.6 10.4 1.0 N B:PHE96 4.7 11.6 1.0 CB B:ASP97 4.8 9.8 1.0 CA B:TYR106 4.8 11.6 1.0 O B:MET95 5.0 11.8 1.0 CA B:ASN280 5.0 10.9 1.0 CA B:ASP97 5.0 8.4 1.0

E.Seiradake, C.H.Coles, P.V.Perestenko, K.Harlos, R.A.J.Mcilhinney, A.R.Aricescu, E.Y.Jones. Structural Basis For Cell Surface Patterning Through Netring-Ngl Interactions. Embo J. V. 30 4479 2011.
ISSN: ISSN 0261-4189
PubMed: 21946559
DOI: 10.1038/EMBOJ.2011.346