Sodium in PDB 2d4d: The Crystal Structure of Human BETA2-Microglobulin, L39W W60F W95F Mutant

The structure of The Crystal Structure of Human BETA2-Microglobulin, L39W W60F W95F Mutant, PDB code: 2d4d was solved by K.Iwata, T.Matsuura, A.Nakagawa, Y.Goto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.423, 28.776, 57.241, 90.00, 123.56, 90.00
R / Rfree (%)	21.6 / 26.5

The binding sites of Sodium atom in the The Crystal Structure of Human BETA2-Microglobulin, L39W W60F W95F Mutant (pdb code 2d4d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the The Crystal Structure of Human BETA2-Microglobulin, L39W W60F W95F Mutant, PDB code: 2d4d:

Sodium binding site 1 out of 1 in the The Crystal Structure of Human BETA2-Microglobulin, L39W W60F W95F Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Human BETA2-Microglobulin, L39W W60F W95F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:29.6 occ:1.00 O A:LEU87 2.2 19.8 1.0 O A:HOH107 2.4 29.4 1.0 O A:HOH132 2.4 29.6 1.0 O A:HOH123 2.5 27.0 1.0 O A:HIS84 2.7 13.9 1.0 O A:HOH140 2.8 38.0 1.0 C A:LEU87 3.4 19.4 1.0 C A:HIS84 3.7 13.2 1.0 N A:HIS84 4.1 14.0 1.0 CA A:LEU87 4.2 18.2 1.0 N A:LEU87 4.2 16.4 1.0 CA A:VAL85 4.3 13.7 1.0 N A:SER88 4.4 21.1 1.0 N A:VAL85 4.4 13.6 1.0 CB A:LEU87 4.4 17.6 1.0 C A:SER88 4.5 23.6 1.0 C A:VAL85 4.5 14.2 1.0 O A:VAL85 4.5 13.8 1.0 CA A:SER88 4.5 22.7 1.0 O A:SER88 4.5 24.1 1.0 CA A:HIS84 4.5 13.1 1.0 OD1 A:ASN83 4.6 28.3 1.0 N A:GLN89 5.0 23.9 1.0 C A:ASN83 5.0 15.6 1.0

M.Kihara, E.Chatani, K.Iwata, K.Yamamoto, T.Matsuura, A.Nakagawa, H.Naiki, Y.Goto. Conformation of Amyloid Fibrils of BETA2-Microglobulin Probed By Tryptophan Mutagenesis J.Biol.Chem. V. 281 31061 2006.
ISSN: ISSN 0021-9258
PubMed: 16901902
DOI: 10.1074/JBC.M605358200