Calcium 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:

Magnesium

(Mg)

1 atom

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the A New V27M Variant of Beta 2 Microglobulin Induced Amyloidosis in A Patient with Long-Term Hemodialysis, PDB code: 6m1b:

Calcium 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 Calcium with other atoms in the Ca 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:Ca104 b:68.2 occ:0.50 O A:HOH221 2.8 56.0 1.0 O3 A:PO4105 3.7 60.9 1.0 O A:HOH222 4.1 50.7 1.0 HH A:TYR10 4.2 41.3 1.0 HD22 A:LEU65 4.4 43.1 1.0 OH A:TYR10 4.4 34.4 1.0 O2 A:PO4105 4.5 68.3 1.0 CZ A:TYR26 4.6 35.2 1.0 P A:PO4105 4.6 81.1 1.0 CE2 A:TYR26 4.7 30.7 1.0 HD13 A:LEU65 4.7 38.9 1.0 OH A:TYR26 4.8 38.3 1.0 HE2 A:TYR26 4.8 36.8 1.0 CE1 A:TYR26 4.8 30.5 1.0 O A:HOH207 4.9 41.3 1.0 HH A:TYR26 4.9 46.0 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