Sodium in PDB 6e1r: Crystal Structure of the Acinetobacter Phage VB_APIP_P1 Tailspike Protein

The structure of Crystal Structure of the Acinetobacter Phage VB_APIP_P1 Tailspike Protein, PDB code: 6e1r was solved by M.Plattner, M.M.Shneider, H.Oliveira, J.Azeredo, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.12 / 2.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.123, 90.015, 508.604, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.8

The structure of Crystal Structure of the Acinetobacter Phage VB_APIP_P1 Tailspike Protein also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of the Acinetobacter Phage VB_APIP_P1 Tailspike Protein (pdb code 6e1r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Acinetobacter Phage VB_APIP_P1 Tailspike Protein, PDB code: 6e1r:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Acinetobacter Phage VB_APIP_P1 Tailspike Protein


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 Acinetobacter Phage VB_APIP_P1 Tailspike Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na801 b:55.1 occ:1.00 OE2 B:GLU739 2.8 48.4 1.0 O B:HOH975 2.8 31.1 1.0 NE2 C:HIS651 2.9 38.2 1.0 O C:HOH910 2.9 38.8 1.0 ND2 C:ASN745 3.3 29.4 1.0 CB B:ALA673 3.5 37.7 1.0 O B:HOH923 3.5 50.7 1.0 CD2 C:HIS651 3.6 38.8 1.0 CD B:GLU739 3.7 45.6 1.0 CG C:ASN745 3.7 31.5 1.0 OE1 B:GLU739 3.9 47.1 1.0 CE1 C:HIS651 3.9 37.3 1.0 OD1 C:ASN745 4.2 39.3 1.0 CB C:ASN745 4.3 25.6 1.0 OD1 B:ASN666 4.4 44.5 1.0 N B:ALA673 4.6 37.9 1.0 CA B:ALA673 4.7 38.5 1.0 O C:SER658 4.7 33.3 1.0 CD1 C:ILE654 4.7 33.8 1.0 CG C:HIS651 4.9 38.4 1.0 ND1 C:HIS651 5.0 36.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Acinetobacter Phage VB_APIP_P1 Tailspike Protein


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 Acinetobacter Phage VB_APIP_P1 Tailspike Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Na801 b:32.2 occ:1.00 OE1 C:GLU479 3.6 51.1 1.0 CZ C:TYR502 4.1 37.4 1.0 CE2 C:TYR502 4.1 38.2 1.0 OE2 C:GLU504 4.3 69.3 1.0 CE1 C:TYR502 4.4 34.0 1.0 CD2 C:TYR502 4.4 37.4 1.0 CB A:ASN444 4.4 30.9 1.0 OD2 C:ASP477 4.5 45.5 1.0 OH C:TYR502 4.5 28.7 1.0 ND2 A:ASN444 4.5 33.4 1.0 CD1 C:TYR502 4.6 31.3 1.0 CG C:TYR502 4.6 33.0 1.0 CD C:GLU479 4.7 49.9 1.0 CD1 A:ILE408 4.7 32.9 1.0 CB A:ALA445 4.8 48.8 1.0 CG A:LEU409 4.9 36.8 1.0 CD1 A:LEU409 4.9 37.6 1.0 OE2 C:GLU479 4.9 54.9 1.0 CD2 A:LEU409 5.0 35.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Acinetobacter Phage VB_APIP_P1 Tailspike Protein


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 Acinetobacter Phage VB_APIP_P1 Tailspike Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Na801 b:50.6 occ:1.00 OE2 F:GLU683 2.4 66.8 1.0 O E:HOH806 2.4 0.2 1.0 OE2 D:GLU683 2.5 49.0 1.0 OE2 E:GLU683 2.6 54.4 1.0 NE F:ARG662 3.2 67.8 1.0 CD F:ARG662 3.2 60.6 1.0 CD E:ARG662 3.4 53.7 1.0 NE E:ARG662 3.5 57.0 1.0 CD D:ARG662 3.5 58.9 1.0 NE D:ARG662 3.5 65.0 1.0 CZ E:ARG662 3.6 55.2 1.0 CD F:GLU683 3.6 63.1 1.0 NH1 E:ARG662 3.6 58.1 1.0 CD D:GLU683 3.7 49.7 1.0 CZ F:ARG662 3.7 66.5 1.0 CD E:GLU683 3.8 54.5 1.0 CZ D:ARG662 3.8 65.6 1.0 NH2 D:ARG662 4.1 70.5 1.0 NH2 F:ARG662 4.2 63.9 1.0 NH1 F:ARG662 4.3 64.7 1.0 NH2 E:ARG662 4.4 50.8 1.0 OE1 F:GLU683 4.4 64.8 1.0 CG D:GLU683 4.5 47.2 1.0 NH1 D:ARG662 4.5 61.9 1.0 CG F:GLU683 4.5 53.5 1.0 OE1 D:GLU683 4.6 46.4 1.0 CG E:ARG662 4.6 45.4 1.0 CG E:GLU683 4.6 49.6 1.0 CG F:ARG662 4.6 51.4 1.0 OE1 E:GLU683 4.7 53.0 1.0 CG D:ARG662 5.0 50.8 1.0

M.Plattner, M.M.Shneider, H.Oliveira, J.Azeredo, P.G.Leiman. Crystal Structure of the Acinetobacter Phage VB_APIP_P1 Tailspike Protein To Be Published.