Sodium in PDB 3o79: Crystal Structure of Wild-Type Rabbit Prp 126-230

The structure of Crystal Structure of Wild-Type Rabbit Prp 126-230, PDB code: 3o79 was solved by B.Sweeting, A.Chakrabartty, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.44 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	29.530, 86.170, 87.140, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 21.8

The structure of Crystal Structure of Wild-Type Rabbit Prp 126-230 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Wild-Type Rabbit Prp 126-230 (pdb code 3o79). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Wild-Type Rabbit Prp 126-230, PDB code: 3o79:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Wild-Type Rabbit Prp 126-230


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 Wild-Type Rabbit Prp 126-230 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2 b:23.6 occ:1.00 O A:ASN197 2.7 15.9 1.0 OD1 A:ASP202 2.7 9.4 1.0 O A:HOH55 2.8 17.8 1.0 CZ A:ARG156 3.3 10.3 1.0 NH1 A:ARG156 3.4 9.1 1.0 NE A:ARG156 3.5 12.7 1.0 C A:ASN197 3.7 14.2 1.0 CD A:ARG156 3.8 9.0 1.0 CG A:ASP202 3.8 10.4 1.0 CA A:PHE198 3.9 11.9 1.0 NH2 A:ARG156 3.9 9.4 1.0 N A:THR199 4.1 9.4 1.0 CG2 A:THR199 4.2 12.7 1.0 N A:PHE198 4.3 13.5 1.0 OD2 A:ASP202 4.3 11.0 1.0 C A:PHE198 4.4 11.8 1.0 CD2 A:PHE198 4.4 12.6 1.0 O A:HOH50 4.4 26.4 1.0 O A:HOH23 4.5 24.9 1.0 O A:HOH61 4.9 31.2 1.0 CA A:ASN197 4.9 15.0 0.7 CG A:ARG156 4.9 10.2 1.0 CB A:PHE198 4.9 11.7 1.0 CA A:ASN197 5.0 15.2 0.3

Sodium binding site 2 out of 4 in the Crystal Structure of Wild-Type Rabbit Prp 126-230


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 Wild-Type Rabbit Prp 126-230 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3 b:12.4 occ:1.00 O A:GLY142 2.3 11.0 1.0 O A:HOH36 2.4 20.6 1.0 OD1 A:ASP144 2.4 9.3 1.0 O A:HOH90 2.5 30.1 1.0 CG A:ASP144 3.2 8.8 1.0 C A:GLY142 3.5 10.5 1.0 OD2 A:ASP144 3.7 9.5 1.0 N A:ASP144 3.8 8.2 1.0 O A:HOH4 4.1 14.2 1.0 O A:HOH239 4.1 47.2 1.0 O A:HOH111 4.2 44.8 1.0 CA A:ASN143 4.3 9.9 1.0 N A:ASN143 4.3 9.7 1.0 CB A:ASP144 4.3 7.6 1.0 C A:ASN143 4.4 9.5 1.0 CA A:ASP144 4.5 7.5 1.0 CA A:GLY142 4.6 12.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Wild-Type Rabbit Prp 126-230


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 Wild-Type Rabbit Prp 126-230 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:21.6 occ:1.00 O B:HOH275 2.2 29.7 1.0 O B:GLY142 2.3 18.8 1.0 O B:HOH94 2.4 33.8 1.0 OD1 B:ASP144 2.6 14.4 1.0 CG B:ASP144 3.3 11.2 1.0 C B:GLY142 3.6 17.8 1.0 OD2 B:ASP144 3.8 14.4 1.0 N B:ASP144 3.8 12.0 1.0 O B:HOH27 4.0 22.7 1.0 O B:HOH25 4.1 21.8 1.0 CA B:ASN143 4.3 13.8 1.0 CB B:ASP144 4.3 11.0 1.0 N B:ASN143 4.4 15.8 1.0 C B:ASN143 4.5 12.8 1.0 CA B:ASP144 4.5 11.1 1.0 O B:HOH266 4.6 44.7 1.0 CA B:GLY142 4.6 17.4 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Wild-Type Rabbit Prp 126-230


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 Wild-Type Rabbit Prp 126-230 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na4 b:23.3 occ:1.00 O B:ARG228 2.3 16.9 1.0 O B:HOH31 2.4 16.2 1.0 O B:HOH96 2.5 33.1 1.0 O B:HOH19 2.5 15.4 1.0 C B:ARG228 3.3 15.5 1.0 O B:HOH240 3.5 47.3 1.0 CA B:ARG228 3.9 15.2 1.0 O B:ALA230 4.0 14.9 1.0 O B:HOH125 4.3 98.3 1.0 N B:ALA229 4.4 13.3 1.0 O B:GLN227 4.5 15.2 1.0 C B:ALA229 4.7 12.2 1.0 O B:HOH248 4.7 51.0 1.0 CA B:ALA229 4.7 13.5 1.0 CB B:ARG228 4.7 16.3 1.0 N B:ALA230 4.7 13.3 1.0

M.Q.Khan, B.Sweeting, V.K.Mulligan, P.E.Arslan, N.R.Cashman, E.F.Pai, A.Chakrabartty. Prion Disease Susceptibility Is Affected By Beta-Structure Folding Propensity and Local Side-Chain Interactions in Prp. Proc.Natl.Acad.Sci.Usa V. 107 19808 2010.
ISSN: ISSN 0027-8424
PubMed: 21041683
DOI: 10.1073/PNAS.1005267107