Sodium in PDB 6wsh: Crystal Structure of Eutv From Enterococcus Faecalis

The structure of Crystal Structure of Eutv From Enterococcus Faecalis, PDB code: 6wsh was solved by S.F.Ataide, J.L.Walshe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.84 / 2.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.539, 85.688, 97.456, 90, 90, 90
R / Rfree (%)	23.9 / 24.1

The structure of Crystal Structure of Eutv From Enterococcus Faecalis also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Eutv From Enterococcus Faecalis (pdb code 6wsh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Crystal Structure of Eutv From Enterococcus Faecalis, PDB code: 6wsh:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the Crystal Structure of Eutv From Enterococcus Faecalis


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 Eutv From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:48.9 occ:1.00 NH1 A:ARG177 2.4 49.5 1.0 HH12 A:ARG177 2.4 59.4 1.0 CZ A:ARG177 2.5 52.9 1.0 NH2 A:ARG177 2.6 50.5 1.0 HH22 A:ARG177 2.6 60.6 1.0 HH11 A:ARG177 2.9 59.4 1.0 HH21 A:ARG177 3.1 60.6 1.0 NE A:ARG177 3.3 54.6 1.0 HE A:ARG177 3.6 65.5 1.0 HD3 A:ARG177 3.7 52.4 1.0 CD A:ARG177 4.1 43.7 1.0 HD2 A:ARG177 4.6 52.4 1.0

Sodium binding site 2 out of 11 in the Crystal Structure of Eutv From Enterococcus Faecalis


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 Eutv From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:33.9 occ:1.00 HG2 A:LYS104 2.7 39.1 1.0 HA A:PRO105 3.0 38.0 1.0 HB2 A:LEU106 3.0 22.6 1.0 N A:LEU106 3.1 23.2 1.0 HB3 A:LEU106 3.4 22.6 1.0 CB A:LEU106 3.5 18.8 1.0 HE2 A:LYS104 3.6 40.1 1.0 CG A:LYS104 3.6 32.6 1.0 HA A:LYS104 3.8 26.2 1.0 HB3 A:LYS104 3.8 34.1 1.0 CA A:PRO105 3.8 31.6 1.0 HG23 A:THR14 3.9 39.6 1.0 CA A:LEU106 3.9 25.3 1.0 C A:PRO105 4.0 28.5 1.0 HD3 A:LYS104 4.0 39.7 1.0 CB A:LYS104 4.1 28.4 1.0 HG21 A:THR14 4.2 39.6 1.0 CD A:LYS104 4.2 33.1 1.0 HG3 A:LYS104 4.3 39.1 1.0 CE A:LYS104 4.3 33.4 1.0 HA A:LEU106 4.4 30.4 1.0 CA A:LYS104 4.4 21.9 1.0 CG2 A:THR14 4.5 33.0 1.0 HB3 A:PRO105 4.5 18.4 1.0 CB A:PRO105 4.6 15.3 1.0 HB2 A:PRO105 4.6 18.4 1.0 HD22 A:LEU106 4.7 33.0 1.0 HE3 A:LYS104 4.8 40.1 1.0 HD11 A:ILE18 4.9 37.3 1.0 CG A:LEU106 4.9 29.9 1.0 HD23 A:LEU106 4.9 33.0 1.0 N A:PRO105 4.9 23.5 1.0

Sodium binding site 3 out of 11 in the Crystal Structure of Eutv From Enterococcus Faecalis


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 Eutv From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:55.0 occ:1.00 O A:HOH356 2.5 36.3 1.0 OD1 A:ASP133 2.7 39.2 1.0 H1 A:HOH356 2.9 36.3 1.0 HB2 A:SER136 3.1 19.5 1.0 H2 A:HOH356 3.2 36.3 1.0 HG A:LEU137 3.5 34.8 1.0 HA A:ASP133 3.6 27.1 1.0 HB3 A:SER136 3.6 19.5 1.0 CB A:SER136 3.8 16.3 1.0 HD21 A:LEU137 3.8 27.3 1.0 CG A:ASP133 3.9 44.3 1.0 HD22 A:LEU137 4.0 27.3 1.0 CD2 A:LEU137 4.2 22.8 1.0 O A:ASP133 4.2 27.7 1.0 CG A:LEU137 4.3 29.0 1.0 H A:LEU137 4.4 19.2 1.0 CA A:ASP133 4.5 22.6 1.0 N A:LEU137 4.6 16.0 1.0 OG A:SER136 4.6 34.7 1.0 OD2 A:ASP133 4.7 49.0 1.0 CB A:ASP133 4.8 21.1 1.0 HA A:LEU137 4.8 19.8 1.0 HD12 A:LEU137 4.8 26.7 1.0 HG A:SER136 4.8 41.6 1.0 C A:ASP133 4.9 21.3 1.0 C A:SER136 4.9 16.0 1.0 CA A:SER136 5.0 19.3 1.0

Sodium binding site 4 out of 11 in the Crystal Structure of Eutv From Enterococcus Faecalis


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 Eutv From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:62.7 occ:1.00 HB2 A:GLN124 2.7 31.6 1.0 HA A:GLN124 3.2 24.2 1.0 HD11 A:LEU127 3.4 30.0 1.0 CB A:GLN124 3.5 26.4 1.0 H1 A:HOH314 3.6 21.2 1.0 CA A:GLN124 3.7 20.1 1.0 OE2 A:GLU120 3.7 32.4 1.0 HG3 A:GLN124 3.7 40.4 1.0 O A:HOH314 3.8 21.2 1.0 H2 A:HOH314 4.0 21.2 1.0 H A:GLN124 4.0 14.2 1.0 N A:GLN124 4.0 11.8 1.0 CG A:GLN124 4.1 33.6 1.0 HD12 A:LEU127 4.2 30.0 1.0 CD1 A:LEU127 4.2 25.0 1.0 HB3 A:GLN124 4.2 31.6 1.0 OE1 A:GLN124 4.4 35.4 1.0 O A:GLU120 4.5 5.8 1.0 HG3 A:GLU120 4.6 15.9 1.0 CD A:GLU120 4.6 16.7 1.0 HD13 A:LEU127 4.6 30.0 1.0 HH21 A:ARG121 4.7 20.6 1.0 CD A:GLN124 4.8 35.9 1.0 C A:LYS123 4.8 12.8 1.0 HB2 A:LYS123 4.9 15.5 1.0 HG2 A:GLN124 5.0 40.4 1.0

Sodium binding site 5 out of 11 in the Crystal Structure of Eutv From Enterococcus Faecalis


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 Eutv From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:36.3 occ:1.00 H2 B:HOH312 2.1 40.9 1.0 O B:HOH312 2.3 40.9 1.0 O B:HOH359 2.4 45.9 1.0 H2 B:HOH359 2.5 45.9 1.0 H1 B:HOH312 2.7 40.9 1.0 HA B:ALA75 2.8 17.5 1.0 C B:ALA75 2.9 16.2 1.0 O B:GLN73 3.0 10.6 1.0 CA B:ALA75 3.1 14.6 1.0 H1 B:HOH359 3.1 45.9 1.0 N B:SER76 3.1 12.8 1.0 N B:ALA75 3.1 16.6 1.0 NE2 B:GLN126 3.1 28.4 1.0 H B:SER76 3.3 15.4 1.0 O B:ALA75 3.4 14.7 1.0 H B:ALA75 3.4 19.9 1.0 HG B:SER76 3.4 11.6 1.0 HE21 B:GLN126 3.4 34.0 1.0 C B:LEU74 3.5 14.8 1.0 HA B:SER76 3.5 15.7 1.0 C B:GLN73 3.7 10.6 1.0 OG B:SER76 3.7 9.7 1.0 CA B:SER76 3.8 13.1 1.0 O B:LEU74 3.8 17.8 1.0 O B:PRO48 3.9 15.0 1.0 OE1 B:GLN47 4.0 28.1 1.0 HB3 B:GLN73 4.0 12.7 1.0 CA B:LEU74 4.2 16.0 1.0 CD B:GLN126 4.2 32.9 1.0 N B:LEU74 4.2 13.4 1.0 HA B:LEU74 4.2 19.2 1.0 CB B:SER76 4.4 14.5 1.0 OE1 B:GLN126 4.5 36.4 1.0 HA B:GLN73 4.5 14.0 1.0 CB B:ALA75 4.6 13.3 1.0 CA B:GLN73 4.6 11.7 1.0 HB3 B:GLN47 4.6 19.8 1.0 HA B:GLN47 4.7 18.0 1.0 CB B:GLN73 4.8 10.6 1.0 HB2 B:ALA75 4.9 16.0 1.0 HB2 B:SER76 4.9 17.4 1.0 H B:LEU74 4.9 16.1 1.0

Sodium binding site 6 out of 11 in the Crystal Structure of Eutv From Enterococcus Faecalis


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 Eutv From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:41.2 occ:1.00 OE1 B:GLN124 2.6 36.4 1.0 H2 B:HOH324 2.9 38.0 1.0 HB3 B:GLN124 3.0 19.2 1.0 HD3 B:ARG121 3.0 13.4 1.0 H1 B:HOH324 3.0 38.0 1.0 HB3 B:ARG121 3.0 9.7 1.0 O B:HOH324 3.1 38.0 1.0 O B:ARG121 3.1 9.3 1.0 HA B:ARG121 3.1 8.1 1.0 OG1 B:THR125 3.2 18.3 1.0 CD B:GLN124 3.3 35.7 1.0 NE B:ARG121 3.4 7.5 1.0 HG1 B:THR125 3.4 22.0 1.0 CD B:ARG121 3.6 11.1 1.0 CA B:ARG121 3.6 6.7 1.0 CB B:ARG121 3.7 8.1 1.0 C B:ARG121 3.7 11.7 1.0 CB B:GLN124 3.8 16.0 1.0 H B:THR125 3.8 15.7 1.0 HG21 A:THR125 3.9 24.2 1.0 OG1 A:THR125 3.9 10.0 1.0 CG B:GLN124 3.9 40.9 1.0 HG2 B:GLN124 4.0 49.1 1.0 NE2 B:GLN124 4.1 35.1 1.0 HD21 A:LEU99 4.1 14.4 1.0 N B:THR125 4.1 13.1 1.0 HE22 B:GLN124 4.1 42.2 1.0 CG B:ARG121 4.3 5.6 1.0 HB2 B:GLN124 4.4 19.2 1.0 HG1 A:THR125 4.4 12.0 1.0 HH21 B:ARG121 4.4 13.6 1.0 HD2 B:ARG121 4.4 13.4 1.0 HG23 A:THR125 4.5 24.2 1.0 HA B:THR125 4.5 20.2 1.0 CB B:THR125 4.5 15.6 1.0 CG2 A:THR125 4.5 20.2 1.0 HB2 B:ARG121 4.5 9.7 1.0 CZ B:ARG121 4.5 11.9 1.0 CA B:THR125 4.6 16.8 1.0 C B:GLN124 4.7 14.3 1.0 HE21 B:GLN124 4.7 42.2 1.0 HD22 A:LEU99 4.8 14.4 1.0 CA B:GLN124 4.8 20.0 1.0 HD21 B:LEU99 4.8 15.1 1.0 HG3 B:GLN124 4.9 49.1 1.0 CB A:THR125 4.9 16.8 1.0 HG2 B:ARG121 4.9 6.7 1.0 NH2 B:ARG121 4.9 11.3 1.0 CD2 A:LEU99 4.9 12.0 1.0 HG3 B:ARG121 4.9 6.7 1.0 HD12 B:LEU128 4.9 22.4 1.0 O A:HOH330 4.9 33.1 1.0 HB B:THR125 5.0 18.7 1.0 N B:GLY122 5.0 8.9 1.0

Sodium binding site 7 out of 11 in the Crystal Structure of Eutv From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Eutv From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:32.4 occ:1.00 H2 B:HOH360 2.5 24.4 1.0 O B:HOH360 2.9 24.4 1.0 H2 B:HOH348 3.0 20.6 1.0 HD2 B:LYS95 3.2 33.3 1.0 HG2 B:LYS92 3.3 20.2 1.0 HA B:LYS92 3.3 13.1 1.0 O B:HOH348 3.5 20.6 1.0 H1 B:HOH360 3.5 24.4 1.0 HB2 B:LYS95 3.6 21.7 1.0 HD3 B:LYS95 3.7 33.3 1.0 H1 B:HOH348 3.8 20.6 1.0 CD B:LYS95 3.9 27.7 1.0 HB3 B:LYS95 4.1 21.7 1.0 CG B:LYS92 4.2 16.8 1.0 CB B:LYS95 4.2 18.1 1.0 CA B:LYS92 4.3 10.9 1.0 HG3 B:LYS92 4.5 20.2 1.0 HZ3 B:LYS95 4.5 57.1 1.0 HE3 B:LYS92 4.7 40.5 1.0 CG B:LYS95 4.7 18.7 1.0 CB B:LYS92 4.7 18.8 1.0 HB3 B:LYS92 4.8 22.6 1.0 O B:ASP91 4.8 15.7 1.0 HZ2 B:LYS95 4.9 57.1 1.0 N B:LYS92 5.0 11.8 1.0

Sodium binding site 8 out of 11 in the Crystal Structure of Eutv From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Eutv From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na206 b:49.4 occ:1.00 OE2 B:GLU28 2.5 41.6 1.0 H B:VAL29 3.2 20.1 1.0 HH22 B:ARG19 3.4 36.0 1.0 HH21 B:ARG19 3.4 36.0 1.0 HD13 B:ILE23 3.5 38.0 1.0 CD B:GLU28 3.6 48.7 1.0 NH2 B:ARG19 3.6 30.0 1.0 HD11 B:ILE23 3.6 38.0 1.0 HB B:VAL29 3.6 15.4 1.0 O B:VAL29 3.9 24.9 1.0 N B:VAL29 3.9 16.7 1.0 CD1 B:ILE23 4.0 31.6 1.0 HA B:GLU28 4.0 14.8 1.0 HG12 B:ILE23 4.0 31.1 1.0 OE1 B:GLU28 4.2 43.9 1.0 CB B:VAL29 4.4 12.9 1.0 HG3 B:GLU28 4.4 37.4 1.0 CA B:VAL29 4.5 16.0 1.0 C B:VAL29 4.5 16.6 1.0 CZ B:ARG19 4.5 43.8 1.0 CG1 B:ILE23 4.6 25.9 1.0 CG B:GLU28 4.6 31.2 1.0 HG22 B:VAL29 4.6 16.1 1.0 CA B:GLU28 4.8 12.3 1.0 C B:GLU28 4.8 15.6 1.0 HD12 B:ILE23 4.8 38.0 1.0

Sodium binding site 9 out of 11 in the Crystal Structure of Eutv From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Eutv From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na207 b:65.8 occ:1.00 H1 B:HOH325 2.6 27.9 1.0 O B:HOH325 2.6 27.9 1.0 O A:HOH342 2.7 35.2 1.0 OE1 B:GLU160 2.7 29.1 1.0 H1 A:HOH342 2.9 35.2 1.0 H2 A:HOH342 3.0 35.2 1.0 HZ1 A:LYS149 3.0 40.5 1.0 OE2 B:GLU160 3.0 43.0 1.0 CD B:GLU160 3.2 37.3 1.0 HZ3 A:LYS149 3.2 40.5 1.0 H1 B:HOH310 3.3 22.5 1.0 H2 B:HOH325 3.4 27.9 1.0 NZ A:LYS149 3.5 33.8 1.0 O B:HOH310 3.7 22.5 1.0 NA B:NA208 4.1 41.2 1.0 HZ2 A:LYS149 4.2 40.5 1.0 HE3 A:LYS149 4.2 28.9 1.0 HB2 A:TYR164 4.2 28.1 1.0 H2 B:HOH310 4.4 22.5 1.0 CE A:LYS149 4.5 24.1 1.0 HZ1 B:LYS149 4.5 24.3 1.0 CG B:GLU160 4.7 21.4 1.0 HB3 A:TYR164 4.7 28.1 1.0 HA A:GLU161 4.7 23.4 1.0 CB A:TYR164 4.8 23.4 1.0 CG A:TYR164 4.8 16.1 1.0 HE2 B:LYS149 4.8 33.9 1.0 H2 B:HOH336 4.8 23.3 1.0 HG3 B:GLU146 4.8 36.5 1.0 HZ3 B:LYS149 4.9 24.3 1.0 HG2 B:GLU160 4.9 25.6 1.0 HD2 A:LYS149 4.9 23.6 1.0 HB3 B:GLU160 5.0 24.9 1.0 CD1 A:TYR164 5.0 25.4 1.0 HG3 A:GLU161 5.0 44.0 1.0

Sodium binding site 10 out of 11 in the Crystal Structure of Eutv From Enterococcus Faecalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Eutv From Enterococcus Faecalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:41.2 occ:1.00 HG3 B:GLU146 3.1 36.5 1.0 O B:GLU146 3.2 13.8 1.0 HG2 B:GLU146 3.4 36.5 1.0 H B:GLY150 3.6 11.2 1.0 CG B:GLU146 3.7 30.5 1.0 HB2 B:LYS149 3.7 16.8 1.0 OE2 B:GLU160 3.9 43.0 1.0 N B:GLY150 3.9 9.4 1.0 HA B:GLU146 4.0 25.7 1.0 HA3 B:GLY150 4.0 19.1 1.0 HE2 B:LYS149 4.0 33.9 1.0 HA2 B:GLY150 4.0 19.1 1.0 HB3 B:LYS149 4.0 16.8 1.0 C B:GLU146 4.1 15.1 1.0 NA B:NA207 4.1 65.8 1.0 CA B:GLY150 4.2 15.9 1.0 CB B:LYS149 4.3 14.0 1.0 CA B:GLU146 4.4 21.4 1.0 HG2 B:GLU160 4.4 25.6 1.0 CD B:GLU160 4.4 37.3 1.0 CB B:GLU146 4.6 27.3 1.0 C B:LYS149 4.7 13.4 1.0 CD B:GLU146 4.8 42.6 1.0 H1 B:HOH325 4.8 27.9 1.0 H2 B:HOH336 4.9 23.3 1.0 CE B:LYS149 4.9 28.2 1.0 HD3 B:LYS149 5.0 32.1 1.0

S.F.Ataide, J.L.Walshe. Structural Characterisation of the E. Faecalis Anti-Terminator Protein Eutv Bound to Rna To Be Published.