Sodium in PDB 3bkm: Structure of Anti-Amyloid-Beta Fab WO2 (Form A, P212121)

The structure of Structure of Anti-Amyloid-Beta Fab WO2 (Form A, P212121), PDB code: 3bkm was solved by L.A.Miles, K.S.Wun, G.A.Crespi, M.Fodero-Tavoletti, D.Galatis, C.J.Bageley, K.Beyreuther, C.L.Masters, R.Cappai, W.J.Mckinstry, K.J.Barnham, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.90 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.447, 90.496, 123.279, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.6

The structure of Structure of Anti-Amyloid-Beta Fab WO2 (Form A, P212121) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Structure of Anti-Amyloid-Beta Fab WO2 (Form A, P212121) (pdb code 3bkm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Anti-Amyloid-Beta Fab WO2 (Form A, P212121), PDB code: 3bkm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Anti-Amyloid-Beta Fab WO2 (Form A, P212121)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Anti-Amyloid-Beta Fab WO2 (Form A, P212121) within 5.0Å range: probe atom residue distance (Å) B Occ L:Na214 b:2.4 occ:1.00 OE1 H:GLU100C 1.9 22.0 1.0 NE2 L:HIS30 2.1 17.5 1.0 CD H:GLU100C 2.7 21.0 1.0 OE2 H:GLU100C 2.9 21.1 1.0 CD2 L:HIS30 3.0 15.8 1.0 CE1 L:HIS30 3.1 19.7 1.0 O H:HOH409 3.8 29.5 1.0 CG H:GLU100C 4.0 19.8 1.0 O L:HOH286 4.1 21.7 1.0 ND1 L:HIS30 4.2 15.9 1.0 CG L:HIS30 4.2 15.8 1.0 CB H:GLU100C 4.3 19.8 1.0 O L:ASN28 4.4 18.0 1.0

Sodium binding site 2 out of 2 in the Structure of Anti-Amyloid-Beta Fab WO2 (Form A, P212121)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Anti-Amyloid-Beta Fab WO2 (Form A, P212121) within 5.0Å range: probe atom residue distance (Å) B Occ L:Na215 b:3.7 occ:1.00 NE2 L:HIS188 2.0 12.8 1.0 OE1 L:GLU184 2.2 16.0 1.0 OE2 L:GLU184 2.2 17.7 1.0 CD L:GLU184 2.5 16.7 1.0 CD2 L:HIS188 3.0 12.7 1.0 CE1 L:HIS188 3.0 13.3 1.0 CG L:GLU184 4.1 13.9 1.0 NH2 L:ARG154 4.1 19.0 1.0 NE L:ARG187 4.1 21.6 1.0 ND1 L:HIS188 4.1 12.3 1.0 CG L:HIS188 4.1 12.1 1.0 O L:HOH372 4.2 30.9 1.0 NH2 L:ARG187 4.6 22.7 1.0 CB L:ARG187 4.8 12.8 1.0 O L:GLU184 4.8 13.8 1.0 CZ L:ARG187 4.9 22.8 1.0 CD L:ARG187 4.9 18.2 1.0 CB L:GLU184 4.9 13.0 1.0 CZ L:ARG154 5.0 17.4 1.0

L.A.Miles, K.S.Wun, G.A.Crespi, M.T.Fodero-Tavoletti, D.Galatis, C.J.Bagley, K.Beyreuther, C.L.Masters, R.Cappai, W.J.Mckinstry, K.J.Barnham, M.W.Parker. Amyloid-Beta-Anti-Amyloid-Beta Complex Structure Reveals An Extended Conformation in the Immunodominant B-Cell Epitope. J.Mol.Biol. V. 377 181 2008.
ISSN: ISSN 0022-2836
PubMed: 18237744
DOI: 10.1016/J.JMB.2007.12.036