Sodium in PDB 3oe3: Crystal Structure of Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium

The structure of Crystal Structure of Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium, PDB code: 3oe3 was solved by S.Leysen, J.M.Van Herreweghe, L.Callewaert, M.Heirbaut, P.Buntinx, C.W.Michiels, S.V.Strelkov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.77 / 1.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.383, 34.685, 74.910, 90.00, 98.41, 90.00
R / Rfree (%)	20.8 / 24.2

The binding sites of Sodium atom in the Crystal Structure of Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium (pdb code 3oe3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium, PDB code: 3oe3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium


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 Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na6 b:47.5 occ:1.00 N A:THR86 3.6 28.7 1.0 OG1 A:THR86 3.6 37.5 1.0 CE2 A:TYR87 3.9 27.3 1.0 CZ A:TYR87 4.0 28.3 1.0 CA A:TYR85 4.1 29.6 1.0 O A:HOH265 4.1 42.7 1.0 CD2 A:TYR87 4.2 23.7 1.0 OE1 A:GLU100 4.3 46.8 1.0 C A:TYR85 4.4 28.8 1.0 OH A:TYR87 4.4 35.1 1.0 CD1 A:TYR85 4.4 32.9 1.0 CA A:THR86 4.5 27.4 1.0 CB A:TYR85 4.5 29.4 1.0 CE1 A:TYR87 4.5 30.1 1.0 CB A:THR86 4.6 35.5 1.0 N A:TYR87 4.6 25.7 1.0 CG A:TYR87 4.7 24.3 1.0 O A:ASN84 4.8 40.1 1.0 C A:THR86 4.8 26.8 1.0 CD1 A:TYR87 4.8 27.7 1.0 CB A:GLU100 4.9 38.4 1.0 CG A:TYR85 4.9 33.5 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium


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 Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ C:Na4 b:38.3 occ:1.00 O C:HOH123 3.0 20.0 1.0 O C:HOH125 3.0 36.7 1.0 CG C:ASN37 3.3 21.8 1.0 OD1 C:ASN37 3.5 20.9 1.0 ND2 C:ASN37 3.5 22.8 1.0 CB C:ASN37 3.6 17.0 1.0 OD1 C:ASP38 4.0 47.5 1.0 CA C:ASN37 4.5 15.2 1.0 O C:HOH148 4.6 33.7 1.0 N C:ASP38 4.6 18.1 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium


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 Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ C:Na5 b:49.5 occ:1.00 O C:ASN48 3.1 18.6 1.0 O C:GLN27 3.2 30.1 1.0 O C:THR49 3.8 23.3 1.0 C C:THR49 3.9 19.5 1.0 N C:GLU50 3.9 20.9 1.0 CA C:GLU50 3.9 27.2 1.0 O C:HOH310 4.0 34.9 1.0 C C:GLN27 4.0 25.1 1.0 CG C:GLU28 4.1 21.0 1.0 C C:ASN48 4.2 18.7 1.0 CA C:GLU28 4.3 19.4 1.0 CG C:GLU50 4.5 33.2 1.0 N C:GLU28 4.6 19.0 1.0 CB C:GLN27 4.6 27.7 1.0 CA C:THR49 4.6 16.6 1.0 CB C:GLU28 4.7 20.4 1.0 CB C:GLU50 4.8 29.4 1.0 O C:HOH353 4.8 47.2 1.0 N C:THR49 4.8 17.6 1.0 O C:HOH438 4.8 33.0 1.0 CB C:ASN48 4.9 22.9 1.0 CA C:GLN27 4.9 26.8 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium


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 Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ D:Na2 b:30.5 occ:1.00 CG2 D:THR35 3.9 29.7 1.0 CB D:ALA113 4.0 19.1 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium


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 Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium within 5.0Å range:

Sodium binding site 6 out of 6 in the Crystal Structure of Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium


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 Plic-St, Periplasmic Lysozyme Inhibitor of C-Type Lysozyme From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ F:Na1 b:28.9 occ:1.00 O F:HOH142 3.2 57.9 1.0 O F:HOH276 3.5 44.2 1.0 CG1 F:VAL99 4.2 20.7 1.0 CE2 F:TYR90 4.4 35.0 1.0 CB F:ASP103 4.4 27.3 1.0 CD2 F:TYR90 4.6 35.8 1.0 O F:ASP103 4.7 25.4 1.0 CG F:ASP103 4.8 29.3 1.0 OD1 F:ASP103 5.0 36.6 1.0

S.Leysen, J.M.Van Herreweghe, L.Callewaert, M.Heirbaut, P.Buntinx, C.W.Michiels, S.V.Strelkov. Molecular Basis of Bacterial Defense Against Host Lysozymes: X-Ray Structures of Periplasmic Lysozyme Inhibitors Plii and Plic. J.Mol.Biol. V. 405 1233 2011.
ISSN: ISSN 0022-2836
PubMed: 21146533
DOI: 10.1016/J.JMB.2010.12.007