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Sodium in PDB 4xhs: Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction

Protein crystallography data

The structure of Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction, PDB code: 4xhs was solved by T.Jin, M.Huang, J.Jiang, T.Xiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.99 / 1.70
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.720, 103.620, 186.740, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 19

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction (pdb code 4xhs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction, PDB code: 4xhs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4xhs

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Sodium binding site 1 out of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction


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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:37.1
occ:1.00
 O A:ASP237 2.3 20.8 1.0
O A:SER239 2.4 22.4 1.0
O A:HOH1059 2.4 44.4 1.0
O A:HOH618 2.4 20.4 1.0
O A:HOH974 2.4 42.3 1.0
C A:ASP237 3.4 18.4 1.0
C A:SER239 3.6 19.0 1.0
O A:HOH701 3.9 29.9 1.0
O A:ILE236 4.0 17.6 1.0
C A:THR238 4.2 17.7 1.0
CA A:ASP237 4.2 18.9 1.0
O A:THR238 4.2 20.5 1.0
N A:SER239 4.3 15.8 1.0
CA A:ALA240 4.4 25.8 1.0
N A:THR238 4.4 16.0 1.0
N A:ALA240 4.5 18.2 1.0
O A:VAL241 4.5 22.5 1.0
C A:ALA240 4.6 28.0 1.0
CA A:SER239 4.6 18.3 1.0
CA A:THR238 4.7 17.5 1.0
N A:VAL241 4.8 20.6 1.0
O A:ALA240 5.0 25.3 1.0
C A:ILE236 5.0 16.9 1.0

Sodium binding site 2 out of 7 in 4xhs

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Sodium binding site 2 out of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction


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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:43.0
occ:1.00
 CZ A:TYR342 2.6 23.7 0.4
CE2 A:TYR342 2.7 24.0 0.4
CE1 A:TYR342 2.7 24.8 0.4
CD2 A:TYR342 2.8 21.6 0.4
CD1 A:TYR342 2.8 21.7 0.4
CG A:TYR342 2.9 19.6 0.4
NH2 A:ARG67 2.9 19.6 0.5
O A:SER338 3.0 19.2 1.0
NH1 A:ARG67 3.4 26.8 0.5
OH A:TYR342 3.5 28.1 0.4
CZ A:ARG67 3.6 22.5 0.5
N A:TYR342 3.7 17.9 1.0
OG A:SER338 3.7 38.7 1.0
O A:HOH628 3.8 36.3 1.0
C A:SER338 3.9 22.5 1.0
CB A:TRP341 3.9 17.6 1.0
CB A:TYR342 3.9 22.0 0.6
CB A:TYR342 4.0 22.0 0.4
CA A:TYR342 4.1 19.6 0.6
CA A:TYR342 4.1 19.6 0.4
CA A:SER338 4.1 20.2 1.0
O A:HOH982 4.1 37.1 1.0
NH1 A:ARG67 4.2 26.2 0.5
C A:TRP341 4.3 18.2 1.0
O A:HOH872 4.3 39.5 1.0
CB A:SER338 4.5 21.9 1.0
O4 A:MAL501 4.6 15.1 1.0
CA A:TRP341 4.6 13.8 1.0
CD2 A:TYR342 4.8 28.8 0.6
NE A:ARG67 4.9 16.8 0.5
CG A:TYR342 4.9 23.0 0.6

Sodium binding site 3 out of 7 in 4xhs

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Sodium binding site 3 out of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction


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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:20.5
occ:1.00
 O B:HOH943 2.3 25.1 1.0
OG B:SER234 2.4 22.7 1.0
O B:ASP297 2.4 15.6 1.0
O B:HOH779 2.5 23.4 1.0
O B:LYS296 2.5 18.9 1.0
O B:HOH992 2.6 32.0 1.0
C B:ASP297 3.2 17.2 1.0
CB B:SER234 3.3 15.5 1.0
O B:HOH624 3.4 32.8 1.0
C B:LYS296 3.4 19.6 1.0
CA B:ASP297 3.8 14.8 1.0
O B:HOH741 3.9 29.5 1.0
O B:HOH881 3.9 28.0 1.0
N B:ASP297 4.0 14.8 1.0
O B:HOH1056 4.1 26.1 1.0
O B:HOH829 4.2 26.0 1.0
N B:LYS298 4.2 13.6 1.0
O B:HOH664 4.3 30.2 1.0
CA B:SER234 4.4 15.2 1.0
CA B:LYS296 4.5 17.9 1.0
CA B:LYS298 4.6 14.4 0.5
CA B:LYS298 4.6 14.3 0.5
O B:ASN295 4.7 17.4 1.0
O B:HOH1035 4.8 40.9 1.0

Sodium binding site 4 out of 7 in 4xhs

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Sodium binding site 4 out of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction


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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:38.0
occ:1.00
 O B:HOH978 2.4 40.1 1.0
O B:GLY328 2.4 22.6 1.0
O B:GLN326 2.5 20.7 1.0
O B:HOH871 2.5 43.0 1.0
O B:HOH806 2.6 32.8 1.0
O B:HOH614 2.7 41.4 1.0
C B:GLN326 3.5 21.4 1.0
C B:GLY328 3.6 21.4 1.0
O B:HOH970 4.0 39.3 1.0
O B:ALA325 4.1 17.1 1.0
CA B:GLN326 4.2 17.9 1.0
C B:LYS327 4.2 21.5 1.0
N B:GLY328 4.2 16.2 1.0
OE1 B:GLU329 4.3 39.7 1.0
CD B:GLU329 4.4 43.2 1.0
O B:LYS327 4.4 20.7 1.0
N B:LYS327 4.4 17.6 1.0
N B:GLU329 4.5 17.6 1.0
CA B:GLU329 4.5 22.2 1.0
CA B:GLY328 4.6 17.0 1.0
OE2 B:GLU329 4.6 49.0 1.0
CA B:LYS327 4.6 18.9 1.0
O B:HOH997 4.7 50.8 1.0
O B:HOH1007 4.9 49.8 1.0

Sodium binding site 5 out of 7 in 4xhs

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Sodium binding site 5 out of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction


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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na506

b:18.4
occ:1.00
 O B:SER239 2.3 19.5 1.0
O B:ASP237 2.4 15.3 1.0
O B:HOH986 2.5 26.5 1.0
O B:HOH646 2.5 17.2 1.0
NA B:NA507 3.2 27.3 1.0
C B:ASP237 3.4 16.1 1.0
C B:SER239 3.5 15.0 1.0
N B:SER239 4.1 15.1 1.0
C B:THR238 4.1 17.4 1.0
O B:ILE236 4.1 15.4 1.0
O B:HOH1059 4.2 34.6 1.0
CA B:ASP237 4.3 14.4 1.0
N B:THR238 4.3 15.8 1.0
CA B:ALA240 4.3 17.7 1.0
O B:HOH1036 4.3 37.8 1.0
N B:ALA240 4.4 15.3 1.0
CA B:THR238 4.4 16.2 1.0
CA B:SER239 4.4 13.6 1.0
O B:THR238 4.5 17.1 1.0
C B:ALA240 4.7 21.9 1.0
O B:HOH710 4.7 16.9 1.0
O B:VAL241 4.7 18.6 1.0
N B:VAL241 4.8 16.6 1.0
O B:HOH1033 4.9 30.8 1.0
O B:HOH1003 4.9 22.9 1.0

Sodium binding site 6 out of 7 in 4xhs

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Sodium binding site 6 out of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction


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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na507

b:27.3
occ:1.00
 O B:HOH1003 2.4 22.9 1.0
O B:HOH986 2.4 26.5 1.0
O B:HOH1033 2.4 30.8 1.0
O B:ASP237 2.5 15.3 1.0
NA B:NA506 3.2 18.4 1.0
C B:ASP237 3.5 16.1 1.0
CA B:THR238 4.3 16.2 1.0
N B:THR238 4.3 15.8 1.0
CA B:ASP237 4.4 14.4 1.0
O B:HOH710 4.5 16.9 1.0
CB B:ASP237 4.5 13.3 1.0
C B:THR238 5.0 17.4 1.0
O B:HOH646 5.0 17.2 1.0

Sodium binding site 7 out of 7 in 4xhs

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Sodium binding site 7 out of 7 in the Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction


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 Human NLRP12 Pyd Domain and Implication in Homotypic Interaction within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na508

b:45.5
occ:1.00
 O B:SER338 2.7 21.2 1.0
CE2 B:TYR342 2.7 26.0 0.4
CZ B:TYR342 2.7 30.3 0.4
CD2 B:TYR342 2.7 26.6 0.4
CE1 B:TYR342 2.7 29.4 0.4
CD1 B:TYR342 2.8 26.7 0.4
CG B:TYR342 2.8 27.0 0.4
NH2 B:ARG67 3.0 17.7 0.5
C B:SER338 3.5 23.0 1.0
N B:TYR342 3.6 19.6 1.0
OH B:TYR342 3.6 34.3 0.4
NH1 B:ARG67 3.6 21.1 0.5
C B:FMT503 3.7 43.0 1.0
CZ B:ARG67 3.7 23.2 0.5
CA B:SER338 3.8 19.9 1.0
CB B:TYR342 3.8 24.1 0.6
CB B:TYR342 3.8 24.1 0.4
O2 B:FMT503 3.9 42.8 1.0
CB B:SER338 3.9 25.9 1.0
CB B:TRP341 3.9 17.0 1.0
CA B:TYR342 4.0 22.5 0.6
CA B:TYR342 4.0 22.5 0.4
NH1 B:ARG345 4.1 46.9 1.0
C B:TRP341 4.3 20.2 1.0
NH2 B:ARG67 4.3 22.7 0.5
NH2 B:ARG345 4.4 38.0 1.0
CD1 B:TYR342 4.5 34.0 0.6
CA B:TRP341 4.6 17.4 1.0
CZ B:ARG345 4.7 41.1 1.0
CG B:TYR342 4.7 28.8 0.6
O4 B:MAL501 4.7 18.6 1.0
N B:ALA339 4.8 21.9 1.0
O1 B:FMT503 4.8 39.5 1.0
OG B:SER338 4.8 30.6 1.0
N B:TRP341 5.0 17.5 1.0
NE B:ARG67 5.0 17.7 0.5

Reference:

T.Jin, M.Huang, J.Jiang, P.Smith, T.Xiao. Crystal Structure of Human NLRP12 Pyd Domain and Implication in Homotypic Interaction To Be Published.
Page generated: Mon Oct 7 19:06:26 2024

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