Sodium in PDB 2gju: Crystal Structure of Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3

The structure of Crystal Structure of Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3, PDB code: 2gju was solved by H.Yamamoto, N.Kunishima, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.43 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.742, 129.571, 113.557, 90.00, 104.46, 90.00
R / Rfree (%)	19.7 / 21.4

The binding sites of Sodium atom in the Crystal Structure of Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3 (pdb code 2gju). 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 Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3, PDB code: 2gju:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3


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 Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2001 b:29.9 occ:1.00 O A:TYR186 2.5 18.0 1.0 O A:HOH3065 2.5 25.4 1.0 O A:HOH3060 2.6 23.9 1.0 O A:LYS166 2.7 18.8 1.0 O A:HOH3073 2.7 23.6 1.0 O A:TYR168 2.7 18.3 1.0 C A:TYR186 3.3 19.3 1.0 C A:LYS166 3.6 17.9 1.0 C A:TYR168 3.6 19.1 1.0 CA A:GLY187 3.8 19.8 1.0 N A:GLY187 3.9 18.3 1.0 CA A:LYS166 4.0 17.6 1.0 CA A:GLU169 4.2 19.7 1.0 CA A:TYR186 4.2 17.8 1.0 N A:TYR168 4.2 18.8 1.0 N A:GLU169 4.2 19.2 1.0 O A:HOH3066 4.3 54.9 1.0 C A:GLU167 4.4 19.9 1.0 CA A:TYR168 4.5 18.9 1.0 CB A:LYS166 4.6 17.0 1.0 N A:GLU167 4.6 18.7 1.0 O A:HOH3124 4.6 37.0 1.0 OE1 A:GLU169 4.7 28.1 1.0 O A:GLU167 4.7 21.8 1.0 CD A:GLU169 4.7 29.4 1.0 CE A:MET162 4.7 16.1 1.0 CA A:GLU167 4.8 20.8 1.0 OE2 A:GLU169 4.8 33.8 1.0 C A:GLU169 4.8 19.6 1.0 CB A:TYR186 4.9 17.2 1.0 O A:GLU169 5.0 17.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3


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 Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2002 b:30.8 occ:1.00 O B:TYR186 2.4 18.6 1.0 O B:HOH3226 2.5 33.4 1.0 O B:TYR168 2.7 21.1 1.0 O B:HOH3033 2.7 25.4 1.0 O B:LYS166 2.7 19.9 1.0 O B:HOH3227 2.8 32.1 1.0 C B:TYR186 3.2 20.6 1.0 C B:LYS166 3.5 20.6 1.0 C B:TYR168 3.5 21.1 1.0 N B:GLY187 3.8 20.0 1.0 CA B:GLY187 3.8 20.2 1.0 CA B:LYS166 4.0 19.9 1.0 CA B:TYR186 4.1 20.9 1.0 N B:TYR168 4.2 21.8 1.0 CA B:GLU169 4.2 21.0 1.0 N B:GLU169 4.2 20.1 1.0 C B:GLU167 4.4 24.0 1.0 CA B:TYR168 4.5 21.2 1.0 CB B:LYS166 4.5 21.5 1.0 N B:GLU167 4.6 21.9 1.0 OE2 B:GLU169 4.6 31.5 1.0 CB B:TYR186 4.7 21.6 1.0 CD B:GLU169 4.7 27.0 1.0 CE B:MET162 4.8 16.2 1.0 OE1 B:GLU169 4.8 26.7 1.0 O B:GLU167 4.8 26.7 1.0 CA B:GLU167 4.9 24.0 1.0 C B:GLU169 4.9 21.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3


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 Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na2003 b:29.3 occ:1.00 O C:HOH3108 2.5 28.1 1.0 O C:TYR186 2.6 22.5 1.0 O C:LYS166 2.6 20.4 1.0 O C:HOH3109 2.6 28.2 1.0 O C:HOH3057 2.6 26.6 1.0 O C:TYR168 2.7 19.2 1.0 C C:TYR186 3.3 20.7 1.0 C C:LYS166 3.5 20.1 1.0 C C:TYR168 3.5 21.4 1.0 N C:GLY187 3.9 19.7 1.0 CA C:GLY187 3.9 20.1 1.0 CA C:LYS166 3.9 18.9 1.0 N C:TYR168 4.1 21.2 1.0 CA C:GLU169 4.1 21.6 1.0 N C:GLU169 4.1 20.2 1.0 CA C:TYR186 4.2 20.1 1.0 OE2 C:GLU169 4.3 35.1 1.0 C C:GLU167 4.3 23.1 1.0 CA C:TYR168 4.4 21.1 1.0 O C:HOH3071 4.4 41.1 1.0 N C:GLU167 4.5 20.3 1.0 CB C:LYS166 4.5 17.8 1.0 CD C:GLU169 4.6 31.3 1.0 O C:HOH3110 4.6 38.9 1.0 CA C:GLU167 4.7 22.9 1.0 CE C:MET162 4.7 17.5 1.0 OE1 C:GLU169 4.8 30.1 1.0 O C:GLU167 4.8 24.6 1.0 C C:GLU169 4.8 20.9 1.0 CB C:TYR186 4.8 18.5 1.0 O C:VAL165 4.9 13.9 1.0 O C:GLU169 4.9 20.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3


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 Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na2004 b:27.9 occ:1.00 O D:HOH3037 2.5 28.5 1.0 O D:TYR186 2.6 18.7 1.0 O D:HOH3020 2.6 19.5 1.0 O D:TYR168 2.6 21.6 1.0 O D:HOH3064 2.7 28.5 1.0 O D:LYS166 2.7 19.4 1.0 C D:TYR186 3.4 19.9 1.0 C D:TYR168 3.4 21.7 1.0 C D:LYS166 3.6 18.5 1.0 CA D:GLY187 3.9 19.7 1.0 N D:GLY187 4.0 18.6 1.0 CA D:GLU169 4.0 20.6 1.0 N D:GLU169 4.0 20.7 1.0 CA D:LYS166 4.1 17.6 1.0 N D:TYR168 4.1 21.4 1.0 OE2 D:GLU169 4.2 38.1 1.0 CA D:TYR186 4.3 18.1 1.0 CA D:TYR168 4.3 21.0 1.0 C D:GLU167 4.4 24.3 1.0 CD D:GLU169 4.4 31.5 1.0 OE1 D:GLU169 4.6 34.0 1.0 N D:GLU167 4.6 20.7 1.0 O D:GLU167 4.7 24.0 1.0 CE D:MET162 4.7 15.5 1.0 CB D:LYS166 4.7 17.7 1.0 C D:GLU169 4.7 20.0 1.0 O D:GLU169 4.9 17.3 1.0 CA D:GLU167 4.9 23.2 1.0 O D:VAL165 5.0 15.7 1.0

H.Yamamoto, N.Kunishima. Crystal Structure of Hypothetical Protein PH1004 From Pyrococcus Horikoshii OT3 To Be Published.