Sodium in PDB 3l88: Crystal Structure of the Human Adenovirus Type 21 Fiber Knob

The structure of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob, PDB code: 3l88 was solved by K.Cupelli, M.Jost, B.D.Persson, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.45 / 2.50
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.000, 63.920, 209.350, 90.00, 91.70, 90.00
R / Rfree (%)	23.4 / 25.9

The structure of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob (pdb code 3l88). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob, PDB code: 3l88:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:23.7 occ:1.00 OD2 B:ASP199 2.9 22.4 1.0 O B:LEU204 3.1 14.8 1.0 CB B:ASN203 3.7 18.7 1.0 O B:ASN203 3.7 13.3 1.0 CD2 B:LEU205 3.8 11.8 1.0 C B:LEU204 3.9 14.4 1.0 CG B:ASP199 3.9 20.4 1.0 C B:ASN203 3.9 14.2 1.0 N B:LEU205 4.4 15.2 1.0 N B:LEU204 4.4 13.1 1.0 CA B:ASN203 4.4 16.4 1.0 CA B:LEU205 4.5 15.0 1.0 CG B:LEU205 4.5 14.5 1.0 CB B:ASP199 4.5 17.3 1.0 OD1 B:ASP199 4.7 21.9 1.0 CA B:LEU204 4.8 12.9 1.0 CG B:ASN203 4.9 22.6 1.0

Sodium binding site 2 out of 11 in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3 b:22.2 occ:1.00 O B:VAL285 4.2 23.0 1.0 CD2 B:PHE242 4.5 16.3 1.0 CE2 B:PHE242 4.6 14.7 1.0 CA B:ALA286 4.9 16.8 1.0

Sodium binding site 3 out of 11 in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob within 5.0Å range: probe atom residue distance (Å) B Occ F:Na2 b:22.6 occ:1.00 ND2 F:ASN182 3.5 11.9 1.0 OD1 F:ASP179 3.7 31.7 1.0 CD1 F:ILE305 3.8 30.9 1.0 O F:VAL177 4.0 20.3 1.0 CG1 F:ILE305 4.4 28.2 1.0 CG F:ASN182 4.5 14.9 1.0 CB F:ASN182 4.6 14.3 1.0 CG F:ASP179 4.8 31.8 1.0

Sodium binding site 4 out of 11 in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob within 5.0Å range: probe atom residue distance (Å) B Occ F:Na7 b:38.0 occ:1.00 OD1 F:ASP264 2.4 43.0 1.0 OG1 F:THR261 3.1 24.7 1.0 CG F:ASP264 3.4 38.6 1.0 CB F:THR261 3.4 19.5 1.0 N F:ASP264 3.7 25.1 1.0 CB F:TYR263 3.8 27.1 1.0 CG2 F:THR261 3.9 17.9 1.0 OD2 F:ASP264 4.0 40.2 1.0 O F:PRO301 4.2 23.5 1.0 N F:TYR263 4.3 24.3 1.0 CB F:ASP264 4.3 31.7 1.0 CA F:TYR263 4.4 26.4 1.0 C1 F:GOL3 4.4 44.6 1.0 CA F:ASP264 4.6 27.3 1.0 C F:TYR263 4.6 26.4 1.0 CA F:THR261 4.8 18.7 1.0 CG F:TYR263 4.9 26.4 1.0 CB F:SER266 5.0 17.4 1.0 C F:THR261 5.0 17.9 1.0

Sodium binding site 5 out of 11 in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob within 5.0Å range: probe atom residue distance (Å) B Occ H:Na6 b:32.2 occ:1.00 N H:ASP207 3.2 25.0 1.0 CG H:ASP207 3.4 46.3 1.0 N H:THR206 3.5 19.7 1.0 CB H:ASP207 3.6 38.5 1.0 OD2 H:ASP207 3.6 51.2 1.0 OD1 H:ASP207 3.8 47.4 1.0 OE1 H:GLU208 3.9 43.8 1.0 CA H:ASP207 4.0 29.2 1.0 C H:LEU205 4.1 17.3 1.0 CA H:THR206 4.1 20.6 1.0 C H:THR206 4.1 21.7 1.0 CB H:THR206 4.2 22.6 1.0 CA H:LEU205 4.4 15.0 1.0 CD2 H:LEU205 4.7 12.0 1.0 CG2 H:THR206 4.8 25.6 1.0 CB H:LEU205 4.8 14.4 1.0 O H:LEU205 4.8 18.2 1.0

Sodium binding site 6 out of 11 in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob within 5.0Å range: probe atom residue distance (Å) B Occ I:Na11 b:19.5 occ:1.00 ND2 I:ASN182 2.8 11.8 1.0 O I:VAL177 3.1 20.1 1.0 OD1 I:ASP179 3.3 31.8 1.0 CG I:ASN182 3.8 14.9 1.0 CD1 I:ILE305 3.9 30.9 1.0 O I:SER178 4.0 23.3 1.0 CB I:ASN182 4.0 14.2 1.0 C I:SER178 4.1 20.4 1.0 C I:VAL177 4.1 17.6 1.0 N I:ASP179 4.3 22.1 1.0 CA I:ASP179 4.3 23.1 1.0 CG I:ASP179 4.5 31.8 1.0 CG1 I:ILE305 4.6 28.4 1.0 CA I:SER178 4.8 18.1 1.0 N I:SER178 4.9 17.2 1.0 OD1 I:ASN182 4.9 16.6 1.0

Sodium binding site 7 out of 11 in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob within 5.0Å range: probe atom residue distance (Å) B Occ J:Na8 b:52.6 occ:1.00 N J:THR206 3.1 19.7 1.0 N J:ASP207 3.3 25.1 1.0 C J:LEU205 3.7 17.3 1.0 CA J:THR206 3.8 20.7 1.0 CG J:ASP207 3.8 46.3 1.0 CD1 G:TYR263 3.9 27.8 1.0 CB J:THR206 3.9 22.8 1.0 CB J:ASP207 4.0 38.5 1.0 CA J:LEU205 4.0 15.1 1.0 C J:THR206 4.0 21.7 1.0 CE1 G:TYR263 4.0 23.5 1.0 OD1 J:ASP207 4.1 47.5 1.0 OE1 J:GLU208 4.1 43.8 1.0 OD2 J:ASP207 4.1 51.1 1.0 CA J:ASP207 4.2 29.2 1.0 CD2 J:LEU205 4.5 11.9 1.0 CB J:LEU205 4.5 14.5 1.0 CG2 J:THR206 4.6 25.7 1.0 O J:LEU205 4.6 18.2 1.0 O J:LEU204 5.0 14.6 1.0

Sodium binding site 8 out of 11 in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob within 5.0Å range: probe atom residue distance (Å) B Occ J:Na9 b:20.3 occ:1.00 O J:ASN149 3.2 38.6 0.6 O J:ASN149 3.6 41.8 0.4 ND2 J:ASN149 4.1 33.2 0.4 CB J:ASN149 4.2 35.9 0.4 CB J:ASN149 4.3 25.1 0.6 C J:ASN149 4.3 36.4 0.6 C J:ASN149 4.4 39.6 0.4 OD1 J:ASP151 4.4 51.8 1.0 OD1 J:ASN149 4.5 13.3 0.6 CG J:ASN149 4.7 34.5 0.4 CG J:ASN149 4.8 18.9 0.6 CA J:ASN149 4.9 31.5 0.6 O I:THR244 4.9 27.3 1.0 CA J:ASN149 4.9 37.3 0.4

Sodium binding site 9 out of 11 in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob within 5.0Å range: probe atom residue distance (Å) B Occ K:Na4 b:25.5 occ:1.00 NA K:NA5 2.5 26.4 1.0 OD2 K:ASP207 3.7 51.2 1.0 CG K:ASP207 4.7 46.2 1.0

Sodium binding site 10 out of 11 in the Crystal Structure of the Human Adenovirus Type 21 Fiber Knob


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Human Adenovirus Type 21 Fiber Knob within 5.0Å range: probe atom residue distance (Å) B Occ K:Na5 b:26.4 occ:1.00 NA K:NA4 2.5 25.5 1.0 OD2 K:ASP207 4.4 51.2 1.0 CG K:ASP207 4.8 46.2 1.0 OD1 K:ASP207 4.9 47.4 1.0

K.Cupelli, S.Muller, B.D.Persson, M.Jost, N.Arnberg, T.Stehle. Structure of Adenovirus Type 21 Knob in Complex with CD46 Reveals Key Differences in Receptor Contacts Among Species B Adenoviruses. J.Virol. V. 84 3189 2010.
ISSN: ISSN 0022-538X
PubMed: 20071571
DOI: 10.1128/JVI.01964-09