Sodium in PDB 4imm: The Crystal Structure of Bamb From Moraxella Catarrhalis

The structure of The Crystal Structure of Bamb From Moraxella Catarrhalis, PDB code: 4imm was solved by C.R.J.Agnew, R.L.Brady, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.54 / 2.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.300, 78.620, 70.990, 90.00, 92.11, 90.00
R / Rfree (%)	18.9 / 24.1

The structure of The Crystal Structure of Bamb From Moraxella Catarrhalis also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Calcium	(Ca)	3 atoms

The binding sites of Sodium atom in the The Crystal Structure of Bamb From Moraxella Catarrhalis (pdb code 4imm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Crystal Structure of Bamb From Moraxella Catarrhalis, PDB code: 4imm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the The Crystal Structure of Bamb From Moraxella Catarrhalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Bamb From Moraxella Catarrhalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:34.0 occ:1.00 OE1 A:GLN381 2.5 32.2 1.0 N A:ALA87 2.9 28.5 1.0 O A:GLN76 3.0 30.2 1.0 O A:ALA87 3.4 27.9 1.0 C A:GLN76 3.4 31.7 1.0 CD A:GLN381 3.4 32.6 1.0 CA A:ALA86 3.5 30.1 1.0 CG2 A:VAL115 3.5 20.8 1.0 NE2 A:GLN381 3.6 24.1 1.0 C A:ALA86 3.7 29.9 1.0 CA A:ALA87 3.9 28.7 1.0 N A:ILE77 3.9 26.8 1.0 CB A:LEU75 3.9 27.4 1.0 CB A:ALA86 3.9 28.3 1.0 N A:GLN76 4.0 31.5 1.0 C A:ALA87 4.1 30.7 1.0 CA A:ILE77 4.1 27.1 1.0 CB A:ALA87 4.1 22.1 1.0 C A:LEU75 4.2 33.4 1.0 CA A:GLN76 4.2 31.4 1.0 N A:VAL115 4.4 27.9 1.0 CB A:VAL115 4.5 22.3 1.0 O A:LEU75 4.5 32.2 1.0 O A:ILE85 4.6 29.6 1.0 CA A:LEU75 4.7 28.9 1.0 CG1 A:ILE77 4.7 32.3 1.0 N A:ALA86 4.7 27.9 1.0 O A:GLY114 4.8 26.0 1.0 CG A:GLN381 4.8 31.3 1.0 C A:GLY114 4.9 26.7 1.0 O A:ALA86 4.9 27.2 1.0 CD1 A:LEU75 4.9 25.3 1.0

Sodium binding site 2 out of 6 in the The Crystal Structure of Bamb From Moraxella Catarrhalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Bamb From Moraxella Catarrhalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:28.5 occ:1.00 O A:LYS291 2.7 21.2 1.0 N A:SER302 2.9 22.1 1.0 O A:LYS290 3.0 22.6 1.0 OG A:SER288 3.1 20.7 1.0 CA A:GLY301 3.3 21.7 1.0 CD A:PRO333 3.4 20.7 1.0 C A:LYS290 3.4 23.2 1.0 C A:LYS291 3.5 26.2 1.0 CB A:LYS290 3.5 22.0 1.0 C A:GLY301 3.6 26.1 1.0 O A:SER302 3.8 24.6 1.0 CD2 A:LEU292 3.8 21.3 1.0 CA A:SER302 3.9 23.6 1.0 CA A:LYS290 3.9 23.1 1.0 N A:LEU292 4.0 21.5 1.0 CB A:SER302 4.1 24.3 1.0 CA A:LEU292 4.1 22.4 1.0 N A:LYS291 4.2 25.4 1.0 CG A:PRO333 4.2 21.7 1.0 CB A:SER288 4.3 20.8 1.0 C A:SER302 4.3 22.6 1.0 OG A:SER302 4.3 27.8 1.0 N A:LYS290 4.3 25.5 1.0 CA A:LYS291 4.5 25.4 1.0 CA A:ASN332 4.6 20.7 1.0 CG A:LEU292 4.6 24.6 1.0 N A:PRO333 4.7 24.1 1.0 N A:GLY301 4.7 21.6 1.0 CG A:LYS290 4.7 23.4 1.0 O A:ILE300 4.7 24.1 1.0 O A:GLY301 4.8 23.6 1.0 O A:HOH561 4.9 24.0 1.0 CB A:LEU292 4.9 22.3 1.0 CB A:ASN332 4.9 22.9 1.0

Sodium binding site 3 out of 6 in the The Crystal Structure of Bamb From Moraxella Catarrhalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Bamb From Moraxella Catarrhalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:33.2 occ:1.00 O A:HOH505 2.6 23.2 1.0 NZ A:LYS201 2.8 31.1 1.0 O A:ALA157 2.8 22.6 1.0 N A:ILE117 3.1 23.8 1.0 O A:ILE117 3.1 21.8 1.0 CE A:LYS201 3.1 24.0 1.0 CA A:GLY116 3.6 23.6 1.0 C A:GLY116 3.8 23.9 1.0 C A:ILE117 3.9 23.3 1.0 C A:ALA157 4.0 21.8 1.0 CA A:LEU158 4.0 21.5 1.0 CA A:ILE117 4.1 26.0 1.0 O A:HOH547 4.2 32.5 1.0 N A:ILE159 4.3 22.4 1.0 N A:LEU158 4.5 20.8 1.0 CG2 A:ILE117 4.5 23.6 1.0 CD1 A:ILE159 4.5 28.3 1.0 CD A:LYS201 4.6 22.2 1.0 C A:LEU158 4.6 25.4 1.0 CB A:ILE117 4.9 27.8 1.0 N A:GLY116 4.9 23.1 1.0 CB A:PRO156 4.9 22.3 1.0 O A:VAL115 5.0 28.4 1.0 O A:GLY116 5.0 27.4 1.0

Sodium binding site 4 out of 6 in the The Crystal Structure of Bamb From Moraxella Catarrhalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of Bamb From Moraxella Catarrhalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:28.5 occ:1.00 N A:ILE167 2.9 19.8 1.0 O A:PRO156 3.0 22.1 1.0 OG A:SER153 3.1 26.3 1.0 O A:ALA155 3.2 25.5 1.0 CG2 A:ILE167 3.3 19.1 1.0 CA A:VAL166 3.5 21.6 1.0 C A:PRO156 3.6 21.9 1.0 C A:VAL166 3.7 22.6 1.0 O A:ILE167 3.7 20.8 1.0 CA A:ALA157 3.8 23.3 1.0 C A:ALA155 3.8 23.6 1.0 CG1 A:VAL166 3.9 21.1 1.0 N A:ALA157 3.9 20.1 1.0 CD A:PRO202 3.9 23.6 1.0 CA A:ILE167 3.9 19.6 1.0 O A:ILE165 4.0 20.1 1.0 CB A:ILE167 4.1 22.0 1.0 CB A:SER153 4.2 24.5 1.0 CB A:VAL166 4.2 23.8 1.0 O A:HOH544 4.2 22.4 1.0 CB A:ALA155 4.3 23.6 1.0 C A:ILE167 4.3 20.7 1.0 CG A:PRO202 4.3 23.9 1.0 CA A:ALA155 4.5 25.9 1.0 N A:PRO156 4.6 25.1 1.0 N A:VAL166 4.6 22.4 1.0 CB A:ALA157 4.6 19.3 1.0 CA A:PRO156 4.6 23.0 1.0 C A:ILE165 4.7 22.5 1.0 N A:ALA155 4.7 22.0 1.0 CG2 A:VAL166 4.8 23.8 1.0 C A:ALA157 4.8 21.8 1.0 O A:VAL166 4.9 23.0 1.0

Sodium binding site 5 out of 6 in the The Crystal Structure of Bamb From Moraxella Catarrhalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Crystal Structure of Bamb From Moraxella Catarrhalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:43.9 occ:1.00 OG A:SER94 2.5 35.1 1.0 O A:ILE92 2.7 32.2 1.0 CG2 A:ILE92 3.4 33.2 1.0 O A:ASP55 3.5 41.9 1.0 C A:ILE92 3.5 36.9 1.0 CB A:ILE92 3.7 32.8 1.0 CB A:SER94 3.7 31.6 1.0 N A:SER94 3.8 34.2 1.0 O A:ALA86 3.9 27.2 1.0 OG A:SER88 4.0 38.2 1.0 CB A:LEU54 4.0 42.6 1.0 N A:ASP55 4.0 43.2 1.0 N A:SER88 4.1 30.0 1.0 CB A:SER88 4.1 34.5 1.0 CA A:ILE92 4.3 32.0 1.0 C A:VAL93 4.3 33.6 1.0 CD2 A:LEU54 4.3 36.6 1.0 N A:VAL93 4.3 29.5 1.0 CA A:SER94 4.3 30.2 1.0 CA A:VAL93 4.4 28.2 1.0 C A:ASP55 4.4 47.9 1.0 C A:LEU54 4.5 43.7 1.0 CA A:LEU54 4.5 46.0 1.0 CG A:LEU54 4.5 38.4 1.0 CA A:ASP55 4.6 49.0 1.0 CD1 A:LEU54 4.6 36.8 1.0 C A:ALA87 4.6 30.7 1.0 CA A:ALA87 4.7 28.7 1.0 CA A:SER88 4.7 32.2 1.0 CB A:ASP55 4.7 50.9 1.0 C A:ALA86 4.8 29.9 1.0 CG1 A:ILE92 5.0 34.8 1.0

Sodium binding site 6 out of 6 in the The Crystal Structure of Bamb From Moraxella Catarrhalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Crystal Structure of Bamb From Moraxella Catarrhalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:39.5 occ:1.00 NE A:ARG233 2.3 27.0 1.0 OG1 A:THR280 2.7 27.1 1.0 O A:GLY278 2.8 32.4 1.0 CD A:ARG233 3.1 23.5 1.0 CZ A:ARG233 3.3 29.7 1.0 NH2 A:ARG233 3.5 25.6 1.0 N A:THR280 3.5 30.0 1.0 CD1 A:PHE273 3.8 24.8 1.0 CE1 A:PHE273 3.8 25.8 1.0 C A:ARG279 3.8 34.8 1.0 C A:GLY278 3.8 37.0 1.0 CB A:THR280 3.9 28.4 1.0 CA A:THR280 4.1 28.4 1.0 CA A:ARG279 4.1 35.8 1.0 CG A:ARG233 4.2 25.9 1.0 O A:ARG279 4.4 32.6 1.0 N A:ARG279 4.4 36.3 1.0 NH1 A:ARG233 4.5 30.9 1.0

C.R.J.Agnew, R.L.Brady. The Crystal Structure of Translocation Complex Component Bamb From Moraxella Catarrhalis To Be Published.