Sodium in PDB 3pqh: Crystal Structure of the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138

The structure of Crystal Structure of the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138, PDB code: 3pqh was solved by C.Browning, M.Shneider, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.52 / 1.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	48.080, 48.080, 553.203, 90.00, 90.00, 120.00
R / Rfree (%)	12.3 / 16

The structure of Crystal Structure of the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138 also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138 (pdb code 3pqh). 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 the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138, PDB code: 3pqh:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Crystal Structure of the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138


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 the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3 b:19.4 occ:1.00 O A:HOH267 3.1 30.9 0.8 OG A:SER215 4.5 13.9 1.0 O A:HOH112 4.7 47.2 0.7

Sodium binding site 2 out of 7 in the Crystal Structure of the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138


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 the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4 b:30.2 occ:1.00 OG1 A:THR205 2.7 16.0 0.9 O A:HOH279 2.8 15.1 0.7 O A:HOH282 2.9 36.4 1.0 O A:HOH265 2.9 39.1 0.8 CG2 A:THR205 3.3 10.8 0.1 CB A:THR205 3.5 9.3 0.1 CB A:THR205 3.6 14.3 0.9 CG2 A:THR207 3.7 15.3 1.0 OG1 A:THR213 3.9 15.1 1.0 CB A:THR213 4.0 12.6 1.0 O A:HOH307 4.1 44.6 0.8 O A:THR205 4.2 13.0 1.0 C A:THR205 4.4 10.8 1.0 O A:HOH284 4.5 20.5 0.7 OG1 A:THR205 4.5 15.0 0.1 CA A:THR205 4.6 8.8 0.1 CA A:THR205 4.6 10.9 0.9 O A:HOH97 4.6 40.8 0.7 O A:HOH53 4.6 22.2 0.8 N A:THR213 4.7 10.1 1.0 CG2 A:THR205 4.7 16.3 0.9 O A:HOH67 4.7 21.2 0.8 O A:ARG211 4.9 13.5 1.0 N A:THR207 4.9 10.9 1.0 CG2 A:THR213 4.9 15.5 1.0 O A:HOH89 4.9 33.8 0.7 CA A:THR213 4.9 10.6 1.0 O A:HOH83 5.0 23.7 0.6

Sodium binding site 3 out of 7 in the Crystal Structure of the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138


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 the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na5 b:15.6 occ:1.00 O A:HOH294 3.1 35.6 0.8 OG1 A:THR222 3.1 17.9 1.0 O A:HOH275 3.2 16.7 1.0 N A:GLY219 3.2 11.8 1.0 O A:HOH305 3.3 50.2 1.0 CA A:HIS223 3.4 10.0 1.0 O A:GLY217 3.6 17.5 1.0 N A:HIS223 3.6 10.3 1.0 CA A:ILE218 3.8 12.0 0.5 CB A:HIS223 3.8 10.3 1.0 CA A:ILE218 3.9 11.3 0.5 C A:THR222 3.9 10.5 1.0 O A:HOH438 4.0 50.5 0.7 C A:ILE218 4.0 12.4 1.0 O A:HOH326 4.1 37.7 0.8 CB A:THR222 4.1 15.4 1.0 O A:THR222 4.1 12.8 1.0 CA A:GLY219 4.2 11.8 1.0 O A:HOH335 4.2 40.1 0.8 O A:GLY219 4.3 11.2 1.0 O A:HOH253 4.4 29.9 0.9 CG2 A:ILE218 4.5 11.7 0.5 C A:GLY217 4.5 14.9 1.0 CA A:THR222 4.6 11.1 1.0 CB A:ILE218 4.7 12.2 0.5 N A:ILE218 4.7 11.8 1.0 C A:GLY219 4.8 11.6 1.0 C A:HIS223 4.8 9.8 1.0 CG2 A:ILE218 4.8 14.9 0.5 CD1 A:ILE218 4.9 16.9 0.5 CB A:ILE218 4.9 12.9 0.5 O A:HOH268 5.0 42.8 0.8

Sodium binding site 4 out of 7 in the Crystal Structure of the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138


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 the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na6 b:16.4 occ:1.00 O A:HOH259 4.5 49.3 1.0

Sodium binding site 5 out of 7 in the Crystal Structure of the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138


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 the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na11 b:37.9 occ:1.00 O A:HOH294 2.7 35.6 0.8 O A:GLY216 2.9 21.2 1.0 C A:GLY217 3.7 14.9 1.0 O A:GLY217 3.7 17.5 1.0 CA A:GLY217 3.8 14.8 1.0 C A:GLY216 4.0 14.6 1.0 O A:HOH268 4.0 42.8 0.8 CD1 A:ILE218 4.2 16.9 0.5 N A:ILE218 4.3 11.8 1.0 N A:GLY217 4.4 13.7 1.0 O A:HOH102 4.4 48.8 0.8 O A:HOH626 4.7 53.4 1.0 CG1 A:ILE218 4.7 13.2 0.5 CA A:ILE218 4.9 12.0 0.5 CA A:ILE218 5.0 11.3 0.5

Sodium binding site 6 out of 7 in the Crystal Structure of the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138


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 the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:27.1 occ:1.00 N B:MET212 2.9 19.7 0.5 N B:MET212 2.9 20.6 0.5 ND1 B:HIS221 3.0 21.1 1.0 CB B:LEU220 3.4 19.4 1.0 CA B:ARG211 3.5 21.8 1.0 CG B:HIS221 3.6 21.6 1.0 O B:MET212 3.6 15.1 0.5 C B:ARG211 3.7 21.0 1.0 N B:HIS221 3.7 16.7 1.0 O B:MET212 3.7 15.9 0.5 CB B:HIS221 3.8 16.8 1.0 CE1 B:HIS221 3.8 19.8 1.0 CA B:MET212 3.8 19.8 0.5 CA B:MET212 3.8 20.9 0.5 CB B:ARG211 3.9 22.1 1.0 CD B:ARG211 4.0 24.1 1.0 CB B:MET212 4.0 20.3 0.5 CG B:LEU220 4.0 19.6 1.0 CD2 B:LEU220 4.0 24.0 1.0 CB B:MET212 4.1 27.0 0.5 CG B:MET212 4.1 26.7 0.5 CA B:LEU220 4.1 16.4 1.0 C B:MET212 4.2 15.8 0.5 C B:MET212 4.2 16.9 0.5 N B:LEU220 4.2 17.1 1.0 C B:LEU220 4.2 16.8 1.0 CA B:HIS221 4.3 16.2 1.0 CG B:ARG211 4.5 25.1 1.0 CD2 B:HIS221 4.6 22.3 1.0 NE2 B:HIS221 4.6 23.0 1.0 O B:GLY210 4.7 19.0 1.0 N B:ARG211 4.8 23.1 1.0 NH1 B:ARG211 4.8 25.2 1.0 O B:ARG211 4.9 26.0 1.0

Sodium binding site 7 out of 7 in the Crystal Structure of the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138


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 the C-Terminal Fragment of the Bacteriophage PHI92 Membrane-Piercing Protein GP138 within 5.0Å range:

C.Browning, M.M.Shneider, V.D.Bowman, D.Schwarzer, P.G.Leiman. Phage Pierces the Host Cell Membrane with the Iron-Loaded Spike. Structure V. 20 326 2012.
ISSN: ISSN 0969-2126
PubMed: 22325780
DOI: 10.1016/J.STR.2011.12.009