Sodium in PDB 3gq9: Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in An Apo Form

The structure of Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in An Apo Form, PDB code: 3gq9 was solved by Y.Xiang, M.G.Rossmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.69 / 2.00
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.633, 89.633, 585.719, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 20.4

The binding sites of Sodium atom in the Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in An Apo Form (pdb code 3gq9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in An Apo Form, PDB code: 3gq9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in An Apo Form


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 Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in An Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:24.9 occ:1.00 O A:ASN305 2.3 21.6 1.0 O A:HOH935 2.4 27.0 1.0 OD1 A:ASP280 2.5 24.0 1.0 OD2 A:ASP280 2.5 24.6 1.0 OE1 A:GLU310 2.5 26.7 1.0 OD2 A:ASP279 2.6 25.7 1.0 CG A:ASP280 2.8 24.0 1.0 CG A:ASP279 3.5 24.8 1.0 ND2 A:ASN305 3.5 25.1 1.0 C A:ASN305 3.5 21.4 1.0 ND2 A:ASN307 3.6 20.5 1.0 CD A:GLU310 3.7 27.4 1.0 NA A:NA692 3.7 37.4 1.0 OD1 A:ASP279 3.8 26.1 1.0 CG A:ASN305 3.9 24.2 1.0 O A:HOH826 4.1 35.6 1.0 O A:HOH777 4.1 25.5 1.0 CB A:ASN305 4.1 22.2 1.0 CB A:ASP280 4.3 22.0 1.0 CG A:GLU310 4.4 22.5 1.0 N A:CYS306 4.4 21.0 1.0 O A:HOH80 4.5 17.1 1.0 N A:ASN307 4.5 19.7 1.0 C A:ASP279 4.5 22.6 1.0 CA A:ASN305 4.5 22.0 1.0 CA A:CYS306 4.5 21.1 1.0 CG A:ASN307 4.5 20.3 1.0 OD1 A:ASN305 4.6 24.4 1.0 N A:ASP280 4.6 21.7 1.0 O A:ASP279 4.6 22.4 1.0 OE2 A:GLU310 4.7 29.2 1.0 CB A:ASP279 4.7 23.0 1.0 CA A:ASP280 4.9 22.0 1.0 CB A:GLU310 4.9 20.2 1.0 CA A:ASP279 4.9 22.6 1.0 CB A:ASN307 4.9 19.4 1.0 OE1 A:GLU333 4.9 29.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in An Apo Form


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 Bacteriophage PHI29 Gene Product 12 N- Terminal Fragment in An Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na692 b:37.4 occ:1.00 O A:HOH80 2.2 17.1 1.0 OD2 A:ASP312 2.3 30.4 1.0 O A:HOH64 2.3 31.9 1.0 O A:HOH935 2.5 27.0 1.0 OD2 A:ASP280 3.2 24.6 1.0 OE1 A:GLU310 3.3 26.7 1.0 CG A:ASP312 3.5 24.0 1.0 NE2 A:HIS285 3.7 21.2 1.0 NA A:NA1 3.7 24.9 1.0 CG A:GLU310 3.7 22.5 1.0 CD A:GLU310 3.8 27.4 1.0 O A:HOH63 3.9 26.4 1.0 OD1 A:ASP279 4.0 26.1 1.0 NZ A:LYS335 4.1 27.8 1.0 CE1 A:HIS337 4.2 27.8 1.0 CB A:ASP312 4.2 20.5 1.0 O A:HOH826 4.3 35.6 1.0 OD1 A:ASP312 4.4 24.4 1.0 CG A:ASP280 4.4 24.0 1.0 CE1 A:HIS285 4.5 22.1 1.0 O A:HOH728 4.5 31.5 1.0 CE1 A:HIS240 4.5 22.3 1.0 OG1 A:THR283 4.6 20.8 1.0 CD2 A:HIS285 4.6 20.8 1.0 NE2 A:HIS337 4.7 27.5 1.0 CG A:ASP279 4.7 24.8 1.0 OD2 A:ASP279 4.8 25.7 1.0 OE2 A:GLU310 4.8 29.2 1.0 NE2 A:HIS240 5.0 20.1 1.0 CB A:GLU310 5.0 20.2 1.0

Y.Xiang, P.G.Leiman, L.Li, S.Grimes, D.L.Anderson, M.G.Rossmann. Crystallographic Insights Into the Autocatalytic Assembly Mechanism of A Bacteriophage Tail Spike. Mol.Cell V. 34 375 2009.
ISSN: ISSN 1097-2765
PubMed: 19450535
DOI: 10.1016/J.MOLCEL.2009.04.009