Sodium in PDB 3zmo: VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1)

The structure of VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1), PDB code: 3zmo was solved by I.Rissanen, J.M.Grimes, A.Pawlowski, S.Mantynen, K.Harlos, J.K.H.Bamford, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.56 / 1.80
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	61.850, 61.850, 251.220, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 21.5

The structure of VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1) (pdb code 3zmo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1), PDB code: 3zmo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1175 b:37.6 occ:0.50 O A:ARG35 2.7 24.5 1.0 O A:HOH2205 2.9 24.7 0.5 C A:ARG35 3.7 25.9 1.0 CB A:GLN34 3.9 24.1 1.0 CG2 A:VAL36 4.1 27.6 1.0 CA A:VAL36 4.2 21.9 1.0 O A:HOH2056 4.3 27.5 1.0 OE1 A:GLN34 4.3 26.3 1.0 N A:VAL36 4.3 21.1 1.0 N A:ARG35 4.5 24.7 1.0 O A:HOH2014 4.6 32.3 1.0 C A:GLN34 4.7 26.8 1.0 CG A:GLN34 4.7 26.1 1.0 CB A:VAL36 4.7 26.3 1.0 O A:HOH2055 4.7 25.8 1.0 CA A:ARG35 4.8 25.1 1.0 CD A:GLN34 4.9 24.4 1.0 CA A:GLN34 4.9 23.2 1.0

Sodium binding site 2 out of 2 in the VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of VP16, A Capsid Protein of Bacteriophage P23-77 (VP16-Type-1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1176 b:41.6 occ:0.50 OD2 A:ASP63 2.7 36.8 1.0 O A:HOH2100 2.9 28.9 1.0 CG A:ASP63 3.4 34.0 1.0 OD1 A:ASP63 4.0 32.7 1.0 CB A:ASP63 4.1 30.9 1.0 ND2 A:ASN67 4.2 38.0 1.0 CG2 A:VAL149 4.3 28.3 1.0 O A:HOH2098 4.5 30.1 1.0 CA A:VAL149 4.5 24.8 1.0 CG1 A:VAL149 4.6 27.8 1.0 CB A:VAL149 4.7 27.4 1.0 O A:GLY148 4.8 32.5 1.0 N A:GLY65 4.8 33.9 1.0

I.Rissanen, J.M.Grimes, A.Pawlowski, S.Mantynen, K.Harlos, J.K.H.Bamford, D.I.Stuart. Bacteriophage P23-77 Capsid Protein Structures Reveal the Archetype of An Ancient Branch From A Major Virus Lineage. Structure V. 21 718 2013.
ISSN: ISSN 0969-2126
PubMed: 23623731
DOI: 10.1016/J.STR.2013.02.026