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Sodium in PDB 3ngj: Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica

Protein crystallography data

The structure of Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica, PDB code: 3ngj was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.38 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.260, 70.780, 126.750, 90.00, 92.46, 90.00
R / Rfree (%) 14.6 / 17.5

Other elements in 3ngj:

The structure of Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica (pdb code 3ngj). 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 A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica, PDB code: 3ngj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3ngj

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Sodium binding site 1 out of 4 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


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 A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na249

b:12.2
occ:1.00
 O A:ALA122 2.3 9.7 1.0
OG A:SER119 2.4 9.1 1.0
O A:GLY120 2.4 12.0 1.0
O A:HOH276 2.4 22.8 1.0
O A:HOH263 2.5 12.4 1.0
O A:HOH306 2.6 14.8 1.0
C A:ALA122 3.5 10.8 1.0
CB A:SER119 3.5 9.1 1.0
C A:GLY120 3.5 11.9 1.0
N A:GLY120 3.9 10.2 1.0
C A:SER119 3.9 9.2 1.0
O A:HOH822 4.0 36.7 1.0
N A:ALA122 4.1 11.1 1.0
O A:VAL116 4.1 9.2 1.0
OG1 A:THR124 4.2 11.2 1.0
C A:LYS121 4.2 12.9 1.0
O A:SER119 4.2 9.8 1.0
CA A:GLY120 4.3 11.3 1.0
CA A:SER119 4.3 9.1 1.0
O A:HOH818 4.3 32.1 1.0
CA A:ALA122 4.4 10.3 1.0
O A:HOH821 4.4 38.7 1.0
N A:LEU123 4.4 10.5 1.0
N A:LYS121 4.4 13.0 1.0
O A:HOH593 4.5 26.9 1.0
OE2 A:GLU151 4.5 16.8 1.0
CA A:LEU123 4.5 10.7 1.0
OE1 A:GLU151 4.5 9.9 1.0
CA A:LYS121 4.6 13.8 1.0
O A:LYS121 4.7 13.5 1.0
C A:LEU123 4.8 10.2 1.0
N A:THR124 4.8 9.6 1.0
CD A:GLU151 5.0 13.1 1.0

Sodium binding site 2 out of 4 in 3ngj

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Sodium binding site 2 out of 4 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


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 A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na249

b:17.3
occ:1.00
 O B:ALA122 2.2 16.4 1.0
OG B:SER119 2.3 14.6 1.0
O B:HOH226 2.4 18.3 1.0
O B:GLY120 2.5 18.6 1.0
O B:HOH227 2.5 14.4 1.0
O B:HOH355 2.5 23.9 1.0
CB B:SER119 3.4 14.4 1.0
C B:ALA122 3.4 16.5 1.0
C B:GLY120 3.5 18.9 1.0
C B:SER119 4.0 15.3 1.0
O B:HOH780 4.0 41.9 1.0
N B:GLY120 4.0 17.0 1.0
N B:ALA122 4.0 18.0 1.0
O B:VAL116 4.1 13.5 1.0
O B:HOH847 4.2 25.5 1.0
OG1 B:THR124 4.2 14.2 1.0
C B:LYS121 4.2 20.4 1.0
O B:SER119 4.3 14.9 1.0
N B:LEU123 4.3 15.6 1.0
CA B:SER119 4.3 14.5 1.0
CA B:LEU123 4.3 15.6 1.0
CA B:GLY120 4.3 18.4 1.0
CA B:ALA122 4.3 16.9 1.0
OE2 B:GLU151 4.4 17.7 1.0
OE1 B:GLU151 4.5 14.5 1.0
N B:LYS121 4.5 20.5 1.0
N B:THR124 4.6 13.5 1.0
C B:LEU123 4.6 14.7 1.0
O B:LYS121 4.6 20.4 1.0
CA B:LYS121 4.7 21.3 1.0
CD B:GLU151 4.8 16.6 1.0

Sodium binding site 3 out of 4 in 3ngj

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Sodium binding site 3 out of 4 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


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 A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na249

b:15.3
occ:1.00
 O C:ALA122 2.2 14.0 1.0
O C:GLY120 2.3 16.4 1.0
OG C:SER119 2.4 14.3 1.0
O C:HOH318 2.4 18.4 1.0
O C:HOH220 2.6 29.8 1.0
O C:HOH240 2.7 14.4 1.0
C C:ALA122 3.4 14.0 1.0
CB C:SER119 3.4 14.1 1.0
C C:GLY120 3.5 16.9 1.0
C C:SER119 3.8 15.2 1.0
N C:GLY120 3.8 16.2 1.0
N C:ALA122 4.0 14.7 1.0
O C:SER119 4.1 14.2 1.0
O C:VAL116 4.2 14.9 1.0
CA C:GLY120 4.2 17.3 1.0
CA C:SER119 4.2 14.6 1.0
C C:LYS121 4.2 16.1 1.0
N C:LEU123 4.3 14.0 1.0
CA C:ALA122 4.3 14.2 1.0
OG1 C:THR124 4.4 14.8 1.0
CA C:LEU123 4.4 14.1 1.0
O C:HOH436 4.4 26.2 1.0
N C:LYS121 4.5 16.7 1.0
OE2 C:GLU151 4.5 18.5 1.0
O C:LYS121 4.6 17.4 1.0
OE1 C:GLU151 4.7 13.6 1.0
CA C:LYS121 4.7 17.4 1.0
C C:LEU123 4.7 13.3 1.0
N C:THR124 4.8 12.0 1.0

Sodium binding site 4 out of 4 in 3ngj

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Sodium binding site 4 out of 4 in the Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica


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 A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na249

b:9.9
occ:1.00
 O D:ALA122 2.2 9.6 1.0
OG D:SER119 2.3 6.6 1.0
O D:HOH433 2.4 16.1 1.0
O D:HOH462 2.4 17.2 1.0
O D:GLY120 2.4 12.2 1.0
O D:HOH220 2.5 10.3 1.0
C D:ALA122 3.4 9.2 1.0
CB D:SER119 3.5 8.6 1.0
C D:GLY120 3.5 10.2 1.0
N D:GLY120 3.9 7.7 1.0
C D:SER119 3.9 7.7 1.0
O D:HOH734 4.0 32.1 1.0
N D:ALA122 4.0 9.6 1.0
O D:VAL116 4.1 8.1 1.0
O D:SER119 4.2 6.3 1.0
C D:LYS121 4.2 11.9 1.0
OG1 D:THR124 4.3 9.2 1.0
CA D:GLY120 4.3 10.2 1.0
N D:LEU123 4.3 9.6 1.0
CA D:SER119 4.3 6.4 1.0
CA D:ALA122 4.3 9.7 1.0
O D:HOH733 4.4 21.8 1.0
CA D:LEU123 4.4 9.6 1.0
N D:LYS121 4.4 11.7 1.0
OE2 D:GLU151 4.5 14.2 1.0
OE1 D:GLU151 4.6 8.0 1.0
CA D:LYS121 4.6 12.4 1.0
O D:LYS121 4.7 13.0 1.0
N D:THR124 4.7 7.3 1.0
C D:LEU123 4.7 8.4 1.0
CD D:GLU151 5.0 8.2 1.0

Reference:

J.Abendroth, A.Gardberg, B.Staker. Crystal Structure of A Putative Deoxyribose-Phosphate Aldolase From Entamoeba Histolytica To Be Published.
Page generated: Mon Oct 7 11:52:10 2024

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