Sodium in PDB 4dxz: Crystal Structure of A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli

The structure of Crystal Structure of A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli, PDB code: 4dxz was solved by S.Leysen, S.Vanheuverzwijn, K.Van Asten, L.Vanderkelen, 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)	40.16 / 1.25
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	80.316, 80.316, 31.098, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 17.1

The binding sites of Sodium atom in the Crystal Structure of A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli (pdb code 4dxz). 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 A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli, PDB code: 4dxz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli


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 A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:29.4 occ:1.00 HD2 A:HIS63 2.6 20.6 0.7 HG3 A:GLN131 2.7 20.2 0.3 CD2 A:HIS63 3.0 17.2 0.7 HB3 A:ASP129 3.1 20.8 1.0 O A:HIS63 3.1 12.3 1.0 O A:ASP129 3.2 12.5 1.0 H A:SER65 3.2 16.8 0.4 H A:SER65 3.2 16.8 0.3 H A:SER65 3.2 16.8 0.3 HB2 A:GLN131 3.3 14.0 0.7 CD A:GLN131 3.4 18.0 0.3 CG A:GLN131 3.4 16.9 0.3 HB2 A:GLN131 3.4 17.1 0.3 OG A:SER65 3.4 19.8 0.3 HB2 A:SER65 3.5 19.4 0.3 HB2 A:SER65 3.5 22.1 0.3 HB3 A:GLN131 3.5 14.0 0.7 HB3 A:SER65 3.5 19.4 0.3 HG A:SER65 3.5 23.8 0.3 OG A:SER65 3.6 19.2 0.4 HA A:VAL64 3.6 14.5 1.0 HB3 A:SER65 3.6 21.9 0.4 N A:SER65 3.6 13.9 1.0 NE2 A:HIS63 3.7 19.2 0.7 NE2 A:GLN131 3.7 20.3 0.3 HG A:SER65 3.7 23.0 0.4 OE1 A:GLN131 3.7 18.4 0.3 HE2 A:HIS63 3.8 23.0 0.7 HB3 A:HIS63 3.8 17.3 0.3 C A:HIS63 3.8 10.2 1.0 CG A:ASP129 3.8 23.6 1.0 C A:ASP129 3.8 13.8 1.0 H A:GLN131 3.8 13.9 0.3 H A:GLN131 3.8 13.9 0.7 CB A:ASP129 3.8 17.3 1.0 HE22 A:GLN131 3.8 24.4 0.3 CG A:HIS63 3.8 15.6 0.7 CB A:GLN131 3.9 11.7 0.7 CB A:SER65 3.9 16.2 0.3 CB A:GLN131 3.9 14.2 0.3 CB A:SER65 3.9 18.4 0.3 OD1 A:ASP129 4.0 25.9 1.0 HB3 A:HIS63 4.0 16.6 0.7 CB A:SER65 4.0 18.2 0.4 HE21 A:GLN131 4.1 24.4 0.3 CG A:HIS63 4.1 16.4 0.3 C A:VAL64 4.1 13.9 1.0 N A:GLN131 4.1 11.6 1.0 CA A:VAL64 4.1 12.1 1.0 OD2 A:ASP129 4.2 29.1 1.0 CD2 A:HIS63 4.2 17.5 0.3 N A:VAL64 4.2 11.2 1.0 HG2 A:GLN131 4.2 20.2 0.3 HA A:ILE130 4.3 12.3 1.0 HD2 A:HIS63 4.3 21.0 0.3 CB A:HIS63 4.3 14.4 0.3 CB A:HIS63 4.4 13.8 0.7 CA A:SER65 4.4 14.6 0.3 CA A:SER65 4.4 15.3 0.3 CA A:ASP129 4.4 13.9 1.0 N A:ILE130 4.4 11.4 1.0 CA A:SER65 4.5 15.3 0.4 ND1 A:HIS63 4.6 18.3 0.3 HB2 A:ASP129 4.6 20.8 1.0 CE1 A:HIS63 4.6 19.6 0.7 C A:ILE130 4.6 11.2 1.0 NE2 A:HIS63 4.7 19.1 0.3 CA A:GLN131 4.7 10.7 0.7 ND1 A:HIS63 4.7 17.5 0.7 CA A:ILE130 4.7 10.3 1.0 CA A:GLN131 4.7 11.7 0.3 HB3 A:GLN131 4.7 17.1 0.3 CA A:HIS63 4.7 11.8 0.3 CA A:HIS63 4.7 11.6 0.7 HB3 A:SER65 4.8 22.1 0.3 CE1 A:HIS63 4.9 18.6 0.3 HD1 A:HIS63 4.9 22.0 0.3 H A:VAL64 4.9 13.4 1.0 CD A:GLN131 4.9 15.9 0.7 OE1 A:GLN131 4.9 18.9 0.7 HB2 A:SER65 4.9 21.9 0.4 O A:VAL64 5.0 15.9 1.0 CG A:GLN131 5.0 14.4 0.7

Sodium binding site 2 out of 3 in the Crystal Structure of A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli


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 A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:32.7 occ:1.00 HE1 A:TYR49 3.0 23.3 1.0 OH A:TYR49 3.1 26.0 1.0 HG21 A:THR51 3.3 13.6 0.5 O A:HOH498 3.3 47.0 1.0 OE1 A:GLU108 3.4 26.9 1.0 CE1 A:TYR49 3.7 19.4 1.0 O A:HOH477 3.7 45.3 1.0 CZ A:TYR49 3.8 22.2 1.0 HH21 A:ARG110 3.9 38.9 1.0 NH2 A:ARG110 4.1 32.4 1.0 CG2 A:THR51 4.2 11.3 0.5 OG1 A:THR51 4.2 13.5 0.5 CD A:GLU108 4.3 24.8 1.0 HE A:ARG110 4.3 28.9 1.0 CZ A:ARG110 4.3 26.9 1.0 NE A:ARG110 4.4 24.1 1.0 HH22 A:ARG110 4.4 38.9 1.0 OE2 A:GLU108 4.4 28.3 1.0 HG22 A:THR51 4.4 13.6 0.5 HG1 A:THR51 4.5 16.2 0.5 HG23 A:THR51 4.5 13.6 0.5 HG21 A:THR51 4.6 16.0 0.5 HD3 A:ARG110 4.9 25.4 1.0 O A:HOH319 4.9 17.9 1.0 CD1 A:TYR49 5.0 16.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli


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 A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:27.0 occ:1.00 ND2 A:ASN116 2.4 23.8 1.0 H A:ASN116 2.5 24.6 1.0 HD21 A:ASN116 2.8 28.6 1.0 O A:HOH488 2.9 24.6 1.0 HB A:THR114 2.9 19.0 1.0 HB2 A:ARG115 3.0 27.6 1.0 HB2 A:ASN116 3.2 25.6 1.0 H A:ARG115 3.2 21.6 1.0 N A:ASN116 3.2 20.5 1.0 CG A:ASN116 3.4 23.6 1.0 N A:ARG115 3.6 18.0 1.0 CB A:ASN116 3.7 21.4 1.0 CB A:THR114 3.8 15.9 1.0 CB A:ARG115 3.9 23.0 1.0 CA A:ASN116 4.0 20.2 1.0 CA A:ARG115 4.1 20.2 1.0 HG1 A:THR114 4.1 20.1 1.0 C A:ARG115 4.1 20.6 1.0 OG1 A:THR114 4.2 16.8 1.0 HB3 A:ARG115 4.3 27.6 1.0 C A:THR114 4.4 16.7 1.0 HA A:ASN116 4.4 24.3 1.0 OD1 A:ASN116 4.4 25.8 1.0 O A:HOH366 4.6 22.9 1.0 HB3 A:ASN116 4.6 25.6 1.0 CA A:THR114 4.6 15.8 1.0 HA A:THR114 4.6 19.0 1.0 HG21 A:THR114 4.8 19.4 1.0 HG3 A:ARG115 4.8 36.4 1.0 CG2 A:THR114 4.8 16.1 1.0 CG A:ARG115 4.9 30.3 1.0 H A:ASP117 4.9 21.9 1.0 HG22 A:THR114 5.0 19.4 1.0

S.Leysen, L.Vandekelen, C.W.Michiels, S.V.Strelkov. Crystal Structure of A Plig-Ec Mutant, A Periplasmic Lysozyme Inhibitor of G-Type Lysozyme From Escherichia Coli To Be Published.