Sodium in PDB 7ook: Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz

The structure of Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz, PDB code: 7ook was solved by H.M.E.Duyvesteyn, F.Peccati, A.Martinez-Castillo, G.Jimenez-Oses, H.M.Oksanen, D.I.Stuart, N.G.A.Abrescia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.83 / 2.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	116.75, 122.75, 126.32, 90, 90, 90
R / Rfree (%)	17.6 / 21.6

The structure of Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz (pdb code 7ook). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz, PDB code: 7ook:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:72.2 occ:1.00 O C:HOH614 2.4 52.7 1.0 O C:ASN51 2.5 47.9 1.0 O C:HOH623 3.2 74.0 1.0 C C:ASN51 3.7 43.6 1.0 HA C:ASN51 3.9 47.3 1.0 CA C:ASN51 4.3 39.4 1.0 HB2 C:ARG52 4.4 50.5 1.0 HA C:ARG52 4.5 49.9 1.0 HB3 C:ASN51 4.6 33.4 1.0 N C:ARG52 4.7 41.8 1.0 CA C:ARG52 5.0 41.6 1.0

Sodium binding site 2 out of 5 in the Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:68.2 occ:1.00 O B:HOH532 2.3 45.2 1.0 O B:HOH626 2.3 60.2 1.0 O B:HOH592 2.4 50.7 1.0 O B:ASN199 2.5 42.1 1.0 O B:HOH601 2.7 50.2 1.0 HA B:ASN200 3.4 51.5 1.0 C B:ASN199 3.6 32.3 1.0 HD2 B:PHE203 3.7 47.0 1.0 HB2 B:PHE203 3.9 43.0 1.0 HB3 B:ASN199 3.9 53.3 1.0 HA B:ALA221 4.2 49.4 1.0 CA B:ASN200 4.3 43.0 1.0 N B:ASN200 4.4 35.9 1.0 OD1 B:ASN200 4.4 44.5 1.0 O B:ALA221 4.4 39.2 1.0 O B:HOH639 4.6 67.4 1.0 O B:CYS223 4.6 35.4 1.0 O B:ALA220 4.6 37.0 1.0 CD2 B:PHE203 4.6 39.2 1.0 CA B:ASN199 4.6 38.3 1.0 CB B:ASN199 4.7 44.5 1.0 HA B:ASN199 4.7 45.9 1.0 CB B:PHE203 4.8 35.9 1.0 O B:PHE203 4.9 45.7 1.0 HB2 B:ASN199 4.9 53.3 1.0 O B:ASN200 5.0 57.9 1.0

Sodium binding site 3 out of 5 in the Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:60.1 occ:1.00 OD2 B:ASP143 2.3 41.2 1.0 OD1 B:ASP149 2.3 68.9 1.0 O B:HOH602 2.5 49.4 1.0 O C:HOH580 2.6 52.8 1.0 OD1 B:ASN146 2.7 47.4 1.0 O C:HOH504 2.7 47.7 1.0 HB2 B:ASP149 2.8 53.2 1.0 CG B:ASP149 3.1 57.4 1.0 O B:HOH531 3.2 47.8 1.0 CG B:ASP143 3.3 40.8 1.0 CB B:ASP149 3.4 44.4 1.0 HA B:ASP149 3.5 40.8 1.0 HA B:ASN146 3.5 53.6 1.0 OD1 B:ASP143 3.6 34.4 1.0 CG B:ASN146 3.8 39.6 1.0 O B:HOH516 3.9 45.3 1.0 HB3 B:ASN146 3.9 47.2 1.0 CA B:ASP149 4.0 34.0 1.0 OD2 C:ASP136 4.0 41.6 1.0 HB2 C:ASP136 4.1 32.8 1.0 O B:ILE148 4.2 33.2 1.0 O B:HOH523 4.2 59.1 1.0 CB B:ASN146 4.2 39.4 1.0 HB3 B:ASP149 4.2 53.2 1.0 OD2 B:ASP149 4.2 76.1 1.0 CA B:ASN146 4.3 44.7 1.0 H B:ALA150 4.6 34.9 1.0 O C:ASP136 4.6 38.0 1.0 CB B:ASP143 4.7 35.8 1.0 CG C:ASP136 4.8 43.5 1.0 HB2 B:ASP143 4.8 42.9 1.0 HD3 C:PRO138 4.8 42.6 1.0 HB3 B:ASP143 4.9 42.9 1.0 C B:ILE148 4.9 28.4 1.0 CB C:ASP136 4.9 27.4 1.0 ND2 B:ASN146 4.9 47.3 1.0 N B:ASP149 4.9 32.9 1.0

Sodium binding site 4 out of 5 in the Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz within 5.0Å range: probe atom residue distance (Å) B Occ A:Na805 b:61.8 occ:1.00 OD2 A:ASP143 2.2 44.5 1.0 OD1 A:ASP149 2.3 69.9 1.0 O B:HOH566 2.5 50.5 1.0 O B:HOH522 2.5 45.7 1.0 O A:HOH994 2.6 53.5 1.0 OD1 A:ASN146 2.7 44.4 1.0 HB2 A:ASP149 3.1 53.1 1.0 CG A:ASP143 3.2 37.0 1.0 CG A:ASP149 3.2 57.6 1.0 OD1 A:ASP143 3.5 35.5 1.0 O A:HOH943 3.5 41.8 1.0 HA A:ASN146 3.5 48.3 1.0 CB A:ASP149 3.6 44.4 1.0 HA A:ASP149 3.7 45.6 1.0 CG A:ASN146 3.8 35.7 1.0 O A:HOH927 3.9 45.3 1.0 HB3 A:ASN146 3.9 43.3 1.0 HB2 B:ASP136 4.0 32.8 1.0 OD2 B:ASP136 4.1 40.9 1.0 CB A:ASN146 4.2 36.2 1.0 CA A:ASP149 4.2 38.1 1.0 OD2 A:ASP149 4.2 71.0 1.0 CA A:ASN146 4.3 40.3 1.0 O A:ILE148 4.3 41.6 1.0 HB3 A:ASP149 4.4 53.1 1.0 O B:ASP136 4.5 36.6 1.0 CB A:ASP143 4.5 37.1 1.0 H A:ALA150 4.7 44.4 1.0 HB3 A:ASP143 4.8 44.4 1.0 HB2 A:ASP143 4.8 44.4 1.0 CG B:ASP136 4.8 39.3 1.0 CB B:ASP136 4.8 27.4 1.0 ND2 A:ASN146 4.9 47.5 1.0

Sodium binding site 5 out of 5 in the Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Bacteriophage PRD1 Major Capsid Protein P3 in Complex with Cpz within 5.0Å range: probe atom residue distance (Å) B Occ A:Na808 b:69.7 occ:1.00 O A:HOH944 2.5 55.2 1.0 O A:ASN199 2.6 41.8 1.0 O A:HOH977 2.6 54.8 1.0 HA A:ASN200 3.3 58.2 1.0 C A:ASN199 3.7 37.7 1.0 HB3 A:ASN199 3.9 44.2 1.0 OD1 A:ASN200 3.9 60.8 1.0 CA A:ASN200 4.2 48.5 1.0 N A:ASN200 4.3 38.8 1.0 HD2 A:PHE203 4.3 50.8 1.0 HB2 A:PHE203 4.6 42.0 1.0 CB A:ASN199 4.7 36.9 1.0 HA A:ALA221 4.7 58.3 1.0 CA A:ASN199 4.7 37.7 1.0 O A:ALA221 4.8 46.7 1.0 CG A:ASN200 4.9 57.4 1.0 HB2 A:ASN199 4.9 44.2 1.0 HA A:ASN199 4.9 45.1 1.0

H.M.E.Duyvesteyn, I.Santos-Perez, F.Peccati, A.Martinez-Castillo, T.S.Walter, D.Reguera, F.M.Goni, G.Jimenez-Oses, H.M.Oksanen, D.I.Stuart, N.G.A.Abrescia. Bacteriophage PRD1 As A Nanoscaffold For Drug Loading Nanoscale V. 13 19875 2021.
ISSN: ISSN 2040-3364
DOI: 10.1039/D1NR04153C