Magnesium in PDB 3r0n: Crystal Structure of the Immunoglobulin Variable Domain of Nectin-2

The structure of Crystal Structure of the Immunoglobulin Variable Domain of Nectin-2, PDB code: 3r0n was solved by U.A.Ramagopal, D.Samanta, S.G.Nathenson, S.C.Almo, New York Structuralgenomics Research Consortium (Nysgrc), Atoms-To-Animals: The Immunefunction Network (Ifn), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.90 / 1.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.964, 57.964, 67.544, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 17.3

The structure of Crystal Structure of the Immunoglobulin Variable Domain of Nectin-2 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Immunoglobulin Variable Domain of Nectin-2 (pdb code 3r0n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Immunoglobulin Variable Domain of Nectin-2, PDB code: 3r0n:

Magnesium binding site 1 out of 1 in the Crystal Structure of the Immunoglobulin Variable Domain of Nectin-2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Immunoglobulin Variable Domain of Nectin-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:15.1 occ:1.00 O A:HOH192 2.0 22.7 1.0 O A:HOH177 2.0 17.2 1.0 O A:PRO94 2.1 14.9 1.0 O A:HOH196 2.1 15.8 1.0 O A:HOH173 2.1 15.4 1.0 O A:HOH174 2.1 15.1 1.0 C A:PRO94 3.3 13.6 1.0 CA A:SER95 4.0 14.4 1.0 N A:SER95 4.1 14.2 1.0 ND1 A:HIS79 4.1 14.5 1.0 O A:ASN78 4.3 14.7 1.0 CA A:PRO94 4.4 12.7 1.0 CB A:SER95 4.4 14.8 1.0 CB A:PRO94 4.4 14.1 1.0 O A:ASN81 4.4 12.3 1.0 OG A:SER95 4.6 18.2 1.0 O A:HOH170 4.6 14.0 1.0 CE1 A:HIS79 4.7 14.0 1.0 CA A:HIS79 4.7 12.7 1.0

D.Samanta, U.A.Ramagopal, R.Rubinstein, V.Vigdorovich, S.G.Nathenson, S.C.Almo. Structure of Nectin-2 Reveals Determinants of Homophilic and Heterophilic Interactions That Control Cell-Cell Adhesion. Proc.Natl.Acad.Sci.Usa V. 109 14836 2012.
ISSN: ISSN 0027-8424
PubMed: 22927415
DOI: 10.1073/PNAS.1212912109