Sodium in PDB 6x5w: Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain

The structure of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain, PDB code: 6x5w was solved by S.Guo, P.L.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.54 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.163, 58.922, 63.249, 62.51, 85.81, 65.93
R / Rfree (%)	19 / 22.8

The structure of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain also contains other interesting chemical elements:

Calcium

(Ca)

18 atoms

The binding sites of Sodium atom in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain (pdb code 6x5w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain, PDB code: 6x5w:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na6634 b:60.0 occ:1.00 OG1 A:THR9 2.3 38.6 1.0 HB2 A:LYS33 3.1 47.5 0.3 HD2 A:LYS33 3.1 53.9 0.3 HB2 A:LYS33 3.2 47.3 0.7 HB A:THR9 3.3 45.9 1.0 CB A:THR9 3.4 38.3 1.0 HG3 A:LYS33 3.4 49.3 0.7 OD1 A:ASN11 3.6 42.4 1.0 HD2 A:LYS33 3.6 54.4 0.7 HG3 A:LYS33 3.6 49.8 0.3 H A:LYS33 3.6 41.0 0.7 H A:LYS33 3.7 42.0 0.3 HA2 A:GLY32 3.7 27.4 1.0 CD A:LYS33 3.8 44.9 0.3 CB A:LYS33 3.9 39.6 0.3 HD3 A:LYS33 3.9 53.9 0.3 CB A:LYS33 3.9 39.4 0.7 N A:LYS33 4.0 34.2 0.7 CG A:LYS33 4.0 41.5 0.3 N A:LYS33 4.0 35.0 0.3 CG A:LYS33 4.0 41.1 0.7 O A:THR9 4.1 29.9 1.0 HG21 A:THR9 4.2 52.4 1.0 O A:HOH4683 4.2 50.0 1.0 C A:THR9 4.2 31.6 1.0 CD A:LYS33 4.3 45.3 0.7 CG2 A:THR9 4.4 43.7 1.0 C A:GLY32 4.4 34.9 1.0 CA A:THR9 4.4 35.1 1.0 CA A:GLY32 4.4 22.8 1.0 CG A:ASN11 4.5 39.2 1.0 HD21 A:ASN11 4.5 47.0 1.0 CA A:LYS33 4.6 36.7 0.3 CA A:LYS33 4.6 36.9 0.7 HB3 A:LYS33 4.6 47.5 0.3 HE3 A:LYS33 4.6 55.5 0.7 HA3 A:GLY32 4.6 27.4 1.0 HB3 A:LYS33 4.7 47.3 0.7 N A:VAL10 4.7 31.8 1.0 HG23 A:THR9 4.8 52.4 1.0 ND2 A:ASN11 4.9 39.2 1.0 H A:THR9 4.9 44.1 1.0 HG2 A:LYS33 4.9 49.3 0.7 HG2 A:LYS33 4.9 49.8 0.3

Sodium binding site 2 out of 3 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na6635 b:49.6 occ:1.00 OE1 A:GLU127 2.6 38.3 1.0 CD A:GLU127 3.6 32.8 1.0 OE2 A:GLU127 3.8 35.2 1.0 CG A:GLU127 4.9 24.6 1.0 HA A:ASN124 5.0 36.0 1.0

Sodium binding site 3 out of 3 in the Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Peptide-Bound Structure of Marinomonas Primoryensis Peptide-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na6636 b:38.5 occ:1.00 OE2 A:GLU127 2.1 35.2 1.0 O A:HOH4284 2.6 30.9 1.0 HB3 A:GLU127 2.8 22.7 1.0 HA A:GLU127 3.1 20.4 1.0 CD A:GLU127 3.3 32.8 1.0 H A:GLY128 3.3 20.7 1.0 CB A:GLU127 3.5 18.9 1.0 CA A:GLU127 3.7 17.0 1.0 CG A:GLU127 3.9 24.6 1.0 N A:GLY128 4.0 17.2 1.0 HG3 A:GLU127 4.1 29.6 1.0 O A:HOH4277 4.3 33.1 1.0 OE1 A:GLU127 4.3 38.3 1.0 C A:GLU127 4.4 16.3 1.0 HB2 A:GLU127 4.4 22.7 1.0 HG2 A:GLU127 4.7 29.6 1.0 N A:GLU127 5.0 19.0 1.0 HA2 A:GLY128 5.0 22.6 1.0

P.L.Davies, S.Guo. Molecular Basis For A Bacterial Adhesins Peptide-Binding Module To Be Published.