Magnesium in PDB 6m1b: A New V27M Variant of Beta 2 Microglobulin Induced Amyloidosis in A Patient with Long-Term Hemodialysis

The structure of A New V27M Variant of Beta 2 Microglobulin Induced Amyloidosis in A Patient with Long-Term Hemodialysis, PDB code: 6m1b was solved by M.So, S.Nakahara, T.Nakaniwa, H.Tanaka, G.Kurisu, Y.Goto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.86 / 1.88
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.26, 28.9, 54.9, 90, 121.68, 90
R / Rfree (%)	20.5 / 24.6

The structure of A New V27M Variant of Beta 2 Microglobulin Induced Amyloidosis in A Patient with Long-Term Hemodialysis also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the A New V27M Variant of Beta 2 Microglobulin Induced Amyloidosis in A Patient with Long-Term Hemodialysis (pdb code 6m1b). 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 A New V27M Variant of Beta 2 Microglobulin Induced Amyloidosis in A Patient with Long-Term Hemodialysis, PDB code: 6m1b:

Magnesium binding site 1 out of 1 in the A New V27M Variant of Beta 2 Microglobulin Induced Amyloidosis in A Patient with Long-Term Hemodialysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A New V27M Variant of Beta 2 Microglobulin Induced Amyloidosis in A Patient with Long-Term Hemodialysis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:35.6 occ:1.00 O A:LEU87 2.1 31.9 1.0 O A:HOH203 2.2 32.6 1.0 O A:HIS84 2.3 28.1 1.0 O A:HOH212 2.4 39.7 1.0 H A:HIS84 3.1 29.3 1.0 C A:LEU87 3.3 32.1 1.0 HB2 A:LEU87 3.4 32.4 1.0 C A:HIS84 3.4 23.1 1.0 H A:LEU87 3.5 35.9 1.0 HA A:VAL85 3.6 30.4 1.0 N A:HIS84 3.8 24.4 1.0 HA A:SER88 4.0 35.9 1.0 CA A:LEU87 4.0 23.5 1.0 N A:LEU87 4.1 29.9 1.0 CB A:LEU87 4.2 27.0 1.0 HB3 A:ASN83 4.2 40.7 1.0 CA A:VAL85 4.2 25.3 1.0 N A:SER88 4.3 27.0 1.0 N A:VAL85 4.3 27.5 1.0 OD1 A:ASN83 4.3 45.5 1.0 CA A:HIS84 4.3 27.6 1.0 O A:SER88 4.4 35.1 1.0 HA A:ASN83 4.4 31.6 1.0 C A:SER88 4.4 34.1 1.0 CA A:SER88 4.4 29.9 1.0 C A:VAL85 4.4 29.9 1.0 O A:VAL85 4.5 27.7 1.0 HB3 A:LEU87 4.6 32.4 1.0 C A:ASN83 4.8 26.5 1.0 CB A:ASN83 4.9 33.9 1.0 CA A:ASN83 4.9 26.4 1.0 HA A:HIS84 4.9 33.1 1.0 HA A:LEU87 5.0 28.2 1.0 N A:GLN89 5.0 33.0 1.0

H.Mizuno, J.Hoshino, M.So, Y.Kogure, T.Fujii, Y.Ubara, K.Takaichi, T.Nakaniwa, H.Tanaka, G.Kurisu, F.Kametani, M.Nakagawa, T.Yoshinaga, Y.Sekijima, K.Higuchi, Y.Goto, M.Yazaki. Dialysis-Related Amyloidosis Associated with A Novel Beta 2 -Microglobulin Variant. Amyloid 1 2020.
ISSN: ISSN 1350-6129
PubMed: 32875920
DOI: 10.1080/13506129.2020.1813097