Sodium in PDB 4hmm: Crystal Structure of Mutant Rabbit Prp 121-230 (S174N)

The structure of Crystal Structure of Mutant Rabbit Prp 121-230 (S174N), PDB code: 4hmm 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)	61.28 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	29.590, 86.250, 87.080, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 19.3

The structure of Crystal Structure of Mutant Rabbit Prp 121-230 (S174N) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Mutant Rabbit Prp 121-230 (S174N) (pdb code 4hmm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Mutant Rabbit Prp 121-230 (S174N), PDB code: 4hmm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Mutant Rabbit Prp 121-230 (S174N)


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 Mutant Rabbit Prp 121-230 (S174N) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:8.4 occ:1.00 O A:HOH401 2.4 10.0 1.0 O A:GLU152 2.4 5.1 1.0 C A:GLU152 3.6 4.1 1.0 O A:HOH410 4.1 13.8 1.0 OD1 A:ASN153 4.1 7.7 1.0 OE2 A:GLU152 4.2 18.6 1.0 CA A:ASN153 4.3 4.5 1.0 N A:ASN153 4.4 4.7 1.0 CG A:GLU152 4.4 11.0 1.0 CD A:GLU152 4.7 16.6 1.0 CA A:GLU152 4.7 5.1 1.0 CG A:ASN153 4.9 6.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Mutant Rabbit Prp 121-230 (S174N)


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 Mutant Rabbit Prp 121-230 (S174N) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:16.5 occ:1.00 O B:HOH461 2.3 28.4 1.0 O B:HOH453 2.3 27.5 1.0 O B:GLY142 2.4 13.6 1.0 OD1 B:ASP144 2.5 12.6 1.0 CG B:ASP144 3.3 9.7 1.0 C B:GLY142 3.6 13.6 1.0 OD2 B:ASP144 3.8 10.0 1.0 N B:ASP144 3.8 9.0 1.0 O B:HOH422 4.1 17.4 1.0 CB B:ASP144 4.4 7.1 1.0 CA B:ASN143 4.4 11.0 1.0 N B:ASN143 4.5 12.1 1.0 C B:ASN143 4.5 8.7 1.0 CA B:ASP144 4.5 7.8 1.0 CA B:GLY142 4.6 14.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Mutant Rabbit Prp 121-230 (S174N)


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 Mutant Rabbit Prp 121-230 (S174N) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:15.0 occ:1.00 O B:ARG228 2.3 11.7 1.0 O B:HOH450 2.4 21.1 1.0 O B:HOH416 2.4 12.8 1.0 O B:HOH436 2.4 21.5 1.0 O B:HOH406 2.4 11.5 1.0 O B:HOH423 2.5 18.4 1.0 C B:ARG228 3.3 10.9 1.0 O B:HOH426 3.5 12.4 1.0 O B:HOH430 3.7 16.2 1.0 CA B:ARG228 3.9 10.1 1.0 O B:ALA230 4.0 9.8 1.0 O B:HOH447 4.2 25.6 1.0 N B:ALA229 4.4 9.5 1.0 O B:GLN227 4.5 10.7 1.0 O B:HOH492 4.6 29.9 1.0 O B:HOH414 4.6 18.9 1.0 O B:HOH444 4.6 19.3 1.0 C B:ALA229 4.7 8.2 1.0 O B:HOH455 4.7 23.2 1.0 CB B:ARG228 4.7 12.4 1.0 CA B:ALA229 4.7 10.1 1.0 N B:ALA230 4.8 8.0 1.0 O B:HOH405 4.8 13.2 1.0 O B:HOH496 5.0 35.5 1.0

B.Sweeting, E.Brown, M.Q.Khan, A.Chakrabartty, E.F.Pai. N-Terminal Helix-Cap in Alpha-Helix 2 Modulates Beta-State Misfolding in Rabbit and Hamster Prion Proteins. Plos One V. 8 63047 2013.
ISSN: ESSN 1932-6203
PubMed: 23675452
DOI: 10.1371/JOURNAL.PONE.0063047