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

Protein crystallography data

The structure of Crystal Structure of Mutant Rabbit Prp 121-230 (S170N), PDB code: 4hls 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) 43.51 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 29.520, 86.080, 86.950, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 18

Other elements in 4hls:

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

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N) (pdb code 4hls). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N), PDB code: 4hls:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4hls

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Sodium binding site 1 out of 6 in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:10.5
occ:1.00
 O A:GLY142 2.3 10.0 1.0
O A:HOH420 2.4 18.2 1.0
O A:HOH418 2.4 24.6 1.0
OD1 A:ASP144 2.4 8.4 1.0
CG A:ASP144 3.3 6.8 1.0
C A:GLY142 3.5 8.7 1.0
OD2 A:ASP144 3.7 7.8 1.0
N A:ASP144 3.8 7.0 1.0
O A:HOH403 4.1 13.3 1.0
CA A:ASN143 4.3 7.7 1.0
N A:ASN143 4.3 8.0 1.0
CB A:ASP144 4.4 6.8 1.0
C A:ASN143 4.5 7.8 1.0
CA A:GLY142 4.5 9.9 1.0
CA A:ASP144 4.5 6.4 1.0

Sodium binding site 2 out of 6 in 4hls

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Sodium binding site 2 out of 6 in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:19.5
occ:1.00
 OG1 B:THR192 2.7 12.1 1.0
OG1 A:THR192 2.7 12.3 1.0
O B:GLU196 2.7 14.3 1.0
O A:GLU196 2.8 13.4 1.0
OD1 A:ASN197 3.2 24.0 1.0
OD1 B:ASN197 3.2 23.6 1.0
CB B:THR192 3.4 11.4 1.0
CB A:THR192 3.4 10.6 1.0
CG B:ASN197 3.6 21.3 1.0
CA B:THR192 3.6 11.5 1.0
CG A:ASN197 3.6 19.8 1.0
CA A:THR192 3.7 10.8 1.0
CA B:ASN197 3.8 14.7 1.0
C B:GLU196 3.8 13.0 1.0
C A:GLU196 3.9 12.4 1.0
CA A:ASN197 3.9 13.2 1.0
ND2 B:ASN197 4.2 22.2 1.0
CB B:ASN197 4.2 19.9 1.0
ND2 A:ASN197 4.2 21.0 1.0
CB A:ASN197 4.2 17.5 1.0
N B:ASN197 4.3 13.6 1.0
N A:ASN197 4.3 12.4 1.0
N B:THR192 4.6 12.6 1.0
N A:THR192 4.6 10.8 1.0
O B:THR192 4.6 14.4 1.0
O A:THR192 4.6 14.7 1.0
C B:THR192 4.6 12.6 1.0
C A:THR192 4.7 13.7 1.0
CG2 B:THR192 4.8 11.3 1.0
CG2 A:THR192 4.8 11.3 1.0
C B:ASN197 5.0 13.6 1.0
N B:PHE198 5.0 13.0 1.0

Sodium binding site 3 out of 6 in 4hls

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Sodium binding site 3 out of 6 in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N)


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 (S170N) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:17.2
occ:1.00
 O B:HOH495 2.2 28.2 1.0
O B:GLU152 2.4 11.2 1.0
O B:HOH412 2.5 21.1 1.0
C B:GLU152 3.6 10.3 1.0
OD1 B:ASN153 4.1 16.2 1.0
CA B:ASN153 4.3 11.1 1.0
O B:HOH442 4.4 26.7 1.0
N B:ASN153 4.4 10.2 1.0
CG B:GLU152 4.5 19.1 0.5
CA B:GLU152 4.6 9.7 0.5
CA B:GLU152 4.6 10.7 0.5
OE2 B:GLU152 4.8 25.6 0.5
CG B:ASN153 4.9 12.4 1.0

Sodium binding site 4 out of 6 in 4hls

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Sodium binding site 4 out of 6 in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N)


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 Mutant Rabbit Prp 121-230 (S170N) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:18.5
occ:1.00
 O B:SER132 2.8 13.7 1.0
OE1 B:GLN217 3.0 16.0 1.0
N B:VAL161 3.0 9.8 1.0
CA B:GLY131 3.4 12.1 1.0
C B:GLY131 3.4 12.8 1.0
CE B:MET134 3.4 16.2 1.0
CA B:GLN160 3.5 13.5 1.0
CG2 B:VAL161 3.6 11.4 1.0
O B:GLY131 3.7 13.2 1.0
C B:GLN160 3.7 11.4 1.0
N B:SER132 3.8 14.3 1.0
CD B:GLN217 3.8 13.4 1.0
C B:SER132 3.8 13.8 1.0
O B:VAL161 4.0 11.2 1.0
CA B:VAL161 4.1 9.0 1.0
N B:GLY131 4.1 11.4 1.0
CB B:GLN160 4.1 20.5 1.0
NE2 B:GLN217 4.3 12.8 1.0
CB B:VAL161 4.3 9.7 1.0
CA B:SER132 4.4 14.8 1.0
CG B:GLN160 4.5 28.8 1.0
C B:VAL161 4.5 9.6 1.0
N B:GLN160 4.7 11.3 1.0
O B:ASN159 4.7 12.8 1.0
CG1 B:VAL161 4.7 9.6 1.0
CG B:GLN217 4.7 11.2 1.0
N B:ALA133 4.8 15.2 1.0
O B:GLN160 4.9 12.9 1.0

Sodium binding site 5 out of 6 in 4hls

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Sodium binding site 5 out of 6 in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N)


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 Mutant Rabbit Prp 121-230 (S170N) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:20.3
occ:1.00
 O B:ARG228 2.3 16.1 1.0
O B:HOH431 2.3 21.7 1.0
O B:HOH448 2.4 26.0 1.0
O B:HOH409 2.4 15.6 1.0
O B:HOH446 2.4 28.3 1.0
C B:ARG228 3.3 13.2 1.0
O B:HOH436 3.5 19.0 1.0
O B:HOH501 3.7 30.5 1.0
O B:ALA230 3.9 11.5 1.0
CA B:ARG228 3.9 13.2 1.0
O B:HOH499 4.3 36.9 1.0
N B:ALA229 4.4 11.9 1.0
O B:HOH459 4.4 28.6 1.0
O B:GLN227 4.5 13.8 1.0
C B:ALA229 4.7 11.2 1.0
O B:HOH460 4.7 34.3 1.0
CA B:ALA229 4.7 11.2 1.0
CB B:ARG228 4.7 16.3 1.0
N B:ALA230 4.8 10.1 1.0

Sodium binding site 6 out of 6 in 4hls

Go back to Sodium Binding Sites List in 4hls
Sodium binding site 6 out of 6 in the Crystal Structure of Mutant Rabbit Prp 121-230 (S170N)


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 Mutant Rabbit Prp 121-230 (S170N) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:18.9
occ:1.00
 OXT B:ALA230 2.6 12.0 1.0
O2 B:GOL308 2.7 31.3 1.0
C B:ALA230 3.5 10.6 1.0
CA B:ALA230 3.5 10.7 1.0
C3 B:GOL308 3.7 28.8 1.0
C2 B:GOL308 3.7 34.4 1.0
CB B:ALA230 3.9 12.4 1.0
O B:HOH489 4.0 46.1 1.0
O B:HOH476 4.3 36.5 1.0
C1 B:GOL308 4.3 26.7 1.0
O B:ALA230 4.7 11.5 1.0
O1 B:GOL308 4.9 16.8 1.0
N B:ALA230 4.9 10.1 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: Mon Oct 7 15:50:25 2024

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