Chlorine 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:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the APOBEC3B Antibody 5G7 Fv-Clasp (pdb code 7km6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the APOBEC3B Antibody 5G7 Fv-Clasp, PDB code: 7km6:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the APOBEC3B Antibody 5G7 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of APOBEC3B Antibody 5G7 Fv-Clasp within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl203 b:41.0 occ:0.87 N L:VAL15 3.3 37.7 1.0 O L:HOH319 3.4 46.1 1.0 CD1 L:ILE112 3.7 34.2 0.7 CG1 L:ILE112 3.7 34.9 1.0 CA L:SER14 3.7 38.3 1.0 CG2 L:VAL15 3.8 41.4 0.9 CB L:VAL15 4.0 42.2 1.0 C L:SER14 4.0 37.5 1.0 CB L:SER14 4.1 40.4 1.0 CA L:VAL15 4.3 38.2 1.0 CD2 L:PHE120 4.4 38.7 1.0 CE2 L:PHE120 4.5 36.1 1.0 O L:VAL13 4.6 37.0 1.0 OG L:SER14 4.8 41.1 0.6 N L:SER14 4.9 39.1 1.0 CZ2 L:TRP124 5.0 35.1 1.0

Chlorine binding site 2 out of 3 in the APOBEC3B Antibody 5G7 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of APOBEC3B Antibody 5G7 Fv-Clasp within 5.0Å range: probe atom residue distance (Å) B Occ l:Cl201 b:77.5 occ:1.00 OE2 l:GLU145 3.4 52.9 1.0 CB l:ARG148 3.9 24.9 1.0 CD l:GLU145 4.3 49.0 1.0 O l:ARG148 4.4 28.3 1.0 C l:ARG148 4.4 25.9 1.0 OE1 l:GLN152 4.4 38.6 0.6 CD l:ARG148 4.6 27.8 1.0 O l:HOH378 4.6 43.9 1.0 OE1 l:GLU145 4.7 46.8 1.0 N l:GLN149 4.7 27.7 1.0 CG l:GLN149 4.8 37.3 1.0 CA l:ARG148 4.8 25.6 1.0 CD l:GLN152 4.8 37.1 0.7 CG l:ARG148 4.9 24.6 1.0 CA l:GLN149 4.9 28.8 1.0

Chlorine binding site 3 out of 3 in the APOBEC3B Antibody 5G7 Fv-Clasp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of APOBEC3B Antibody 5G7 Fv-Clasp within 5.0Å range: probe atom residue distance (Å) B Occ l:Cl202 b:35.2 occ:1.00 O l:HOH339 3.1 42.7 1.0 N l:VAL15 3.2 33.9 1.0 CA l:SER14 3.7 37.6 0.5 CA l:SER14 3.7 37.6 0.5 CD1 l:ILE112 3.7 32.3 0.8 CG1 l:ILE112 3.8 32.4 1.0 CB l:SER14 3.8 40.1 0.5 CB l:SER14 3.8 40.0 0.5 CG2 l:VAL15 3.9 37.2 1.0 C l:SER14 3.9 36.4 0.5 C l:SER14 3.9 36.4 0.5 CB l:VAL15 4.0 37.5 1.0 CA l:VAL15 4.2 34.7 1.0 OG l:SER14 4.4 41.2 0.5 CD2 l:PHE120 4.6 37.3 1.0 CE2 l:PHE120 4.7 36.8 1.0 O l:VAL13 4.8 34.6 1.0 N l:SER14 5.0 37.0 0.5 N l:SER14 5.0 37.0 0.5

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