Sodium in PDB 7km6: APOBEC3B Antibody 5G7 Fv-Clasp

The structure of APOBEC3B Antibody 5G7 Fv-Clasp, PDB code: 7km6 was solved by H.Tang, K.Shi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.86 / 1.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.074, 68.823, 88.759, 90, 107.05, 90
R / Rfree (%)	18.9 / 23.8

The structure of APOBEC3B Antibody 5G7 Fv-Clasp also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the APOBEC3B Antibody 5G7 Fv-Clasp (pdb code 7km6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the APOBEC3B Antibody 5G7 Fv-Clasp, PDB code: 7km6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the APOBEC3B Antibody 5G7 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of APOBEC3B Antibody 5G7 Fv-Clasp within 5.0Å range: probe atom residue distance (Å) B Occ H:Na202 b:45.8 occ:1.00 OE1 H:GLU167 2.3 72.3 1.0 CD H:GLU167 3.2 68.8 0.6 O H:HOH322 3.4 66.4 1.0 OE2 H:GLU167 3.5 69.9 0.5 CB H:HIS170 4.3 98.0 1.0 CD2 H:HIS170 4.4 95.8 1.0 CG H:GLU167 4.6 64.2 0.8 CG H:HIS170 4.7 96.2 1.0 O H:GLU167 4.8 65.0 1.0 CB H:GLU167 4.8 62.9 1.0 CA H:GLU167 4.9 59.9 0.9

Sodium binding site 2 out of 2 in the APOBEC3B Antibody 5G7 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of APOBEC3B Antibody 5G7 Fv-Clasp within 5.0Å range: probe atom residue distance (Å) B Occ l:Na203 b:77.5 occ:1.00 O l:HOH350 2.4 35.3 1.0 OD2 l:ASP128 2.4 43.2 0.5 CG l:ASP128 3.2 40.8 1.0 CB l:ASP128 3.3 37.1 1.0 CA l:TRP124 3.8 38.6 1.0 CG l:TRP124 3.9 34.6 1.0 CB l:TRP124 3.9 35.6 1.0 N l:THR125 4.1 40.2 1.0 CD1 l:TRP124 4.3 35.9 1.0 CD2 l:TRP124 4.3 36.0 1.0 OD1 l:ASP128 4.4 43.4 0.7 C l:TRP124 4.5 40.0 1.0 OG1 l:THR125 4.6 40.3 1.0 CG1 l:VAL15 4.6 40.8 0.9 O l:SER123 4.7 44.3 1.0 O l:HOH356 4.7 30.1 1.0 CE3 l:TRP124 4.8 31.4 1.0 NE1 l:TRP124 4.8 35.0 1.0 CE2 l:TRP124 4.8 37.4 1.0 CA l:ASP128 4.9 33.5 1.0 N l:TRP124 4.9 41.1 1.0

H.Tang, O.Demir, F.Kurniawan, W.L.Brown, K.Shi, N.H.Moeller, M.A.Carpenter, C.Belica, K.Orellana, G.Du, A.M.Lebeau, R.E.Amaro, R.S.Harris, H.Aihara. Structural Characterization of A Minimal Antibody Against Human APOBEC3B. Viruses V. 13 2021.
ISSN: ESSN 1999-4915
PubMed: 33921405
DOI: 10.3390/V13040663