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Sodium in PDB 4hmr: Crystal Structure of Mutant Rabbit Prp 121-230 (S170N/S174N)

Protein crystallography data

The structure of Crystal Structure of Mutant Rabbit Prp 121-230 (S170N/S174N), PDB code: 4hmr 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) 61.35 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 29.530, 86.440, 87.090, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 20.7

Other elements in 4hmr:

The structure of Crystal Structure of Mutant Rabbit Prp 121-230 (S170N/S174N) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N/S174N) (pdb code 4hmr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N/S174N), PDB code: 4hmr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4hmr

Go back to Sodium Binding Sites List in 4hmr
Sodium binding site 1 out of 2 in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N/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 (S170N/S174N) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:12.7
occ:1.00
O A:GLY142 2.3 12.1 1.0
OD1 A:ASP144 2.4 10.4 1.0
O A:HOH402 2.4 14.3 1.0
O A:HOH418 2.4 26.1 1.0
CG A:ASP144 3.3 7.8 1.0
C A:GLY142 3.5 10.2 1.0
OD2 A:ASP144 3.8 10.2 1.0
N A:ASP144 3.8 9.0 1.0
O A:HOH401 4.1 15.2 1.0
CA A:ASN143 4.3 8.5 1.0
N A:ASN143 4.4 9.5 1.0
CB A:ASP144 4.4 7.9 1.0
C A:ASN143 4.5 8.1 1.0
CA A:GLY142 4.5 12.7 1.0
CA A:ASP144 4.5 7.3 1.0

Sodium binding site 2 out of 2 in 4hmr

Go back to Sodium Binding Sites List in 4hmr
Sodium binding site 2 out of 2 in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N/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 (S170N/S174N) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:19.3
occ:1.00
O B:HOH438 2.2 31.7 1.0
O B:HOH442 2.4 34.3 1.0
O B:GLU152 2.4 14.5 1.0
O B:HOH415 2.5 25.1 1.0
C B:GLU152 3.6 11.7 1.0
O B:HOH402 4.0 22.2 1.0
OD1 B:ASN153 4.1 18.1 1.0
O B:HOH447 4.3 28.8 1.0
CA B:ASN153 4.4 11.4 1.0
N B:ASN153 4.4 11.9 1.0
CA B:GLU152 4.6 12.0 1.0
CG B:ASN153 4.9 13.2 1.0
CB B:GLU152 5.0 16.7 1.0

Reference:

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
Page generated: Tue Dec 15 06:43:35 2020

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