Cadmium in PDB 5swb: Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC

The structure of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC, PDB code: 5swb was solved by M.Robb, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.76 / 1.73
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.180, 110.600, 105.840, 90.00, 109.52, 90.00
R / Rfree (%)	18 / 22

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 34;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC (pdb code 5swb). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 34 binding sites of Cadmium where determined in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC, PDB code: 5swb:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 34 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd507 b:28.1 occ:1.00 OD1 A:ASP454 2.2 28.5 1.0 OD2 A:ASP456 2.3 28.4 1.0 OD2 A:ASP454 2.4 29.2 1.0 CD A:CD515 2.5 31.4 0.3 CG A:ASP454 2.7 29.8 1.0 CG A:ASP456 3.2 25.7 1.0 CB A:ASP456 3.5 24.2 1.0 NZ A:LYS249 4.0 35.7 1.0 O A:HOH821 4.0 34.9 1.0 CB A:ASP454 4.2 24.8 1.0 N A:ASP456 4.3 27.6 1.0 OD1 A:ASP456 4.3 29.0 1.0 CD A:PRO455 4.4 22.1 1.0 CA A:ASP456 4.5 26.1 1.0 CD A:CD512 4.7 40.2 0.5 CD2 A:HIS252 4.8 29.3 1.0 NZ A:LYS253 4.8 45.6 1.0 CG A:PRO455 4.9 24.1 1.0 CA A:ASP454 4.9 24.1 1.0 N A:PRO455 4.9 24.4 1.0 CG A:LYS249 5.0 24.4 1.0

Cadmium binding site 2 out of 34 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd508 b:49.9 occ:0.35 OD1 A:ASP53 2.4 41.3 1.0 CG A:ASP53 3.2 43.3 1.0 OD2 A:ASP53 3.4 48.0 1.0 ND2 A:ASN380 4.5 38.0 1.0 CB A:ASP53 4.6 34.6 1.0

Cadmium binding site 3 out of 34 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd509 b:23.1 occ:0.79 OE1 A:GLU333 2.3 25.8 1.0 O A:HOH900 2.4 34.0 1.0 CD A:CD516 2.6 34.6 0.3 OE2 A:GLU333 2.7 36.7 1.0 CD A:GLU333 2.8 34.2 1.0 O A:HOH935 4.3 25.9 1.0 CG A:GLU333 4.3 24.7 1.0 O A:HOH823 4.4 32.2 1.0 O A:LYS330 4.5 28.8 1.0 N A:LYS332 4.7 25.0 1.0 N A:GLU333 4.7 23.7 1.0 CB A:GLU333 4.9 25.8 1.0

Cadmium binding site 4 out of 34 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd510 b:29.1 occ:0.60 O D:HOH1045 2.3 30.8 1.0 O A:HOH869 2.4 27.4 1.0 OD1 A:ASP268 2.4 36.2 1.0 OD2 A:ASP268 2.6 34.8 1.0 CG A:ASP268 2.9 42.2 1.0 O A:HOH683 3.3 37.1 1.0 O D:HOH707 3.3 19.2 1.0 O D:HOH775 3.7 63.0 1.0 O A:HOH636 3.8 45.2 1.0 O A:HOH1034 4.1 55.1 1.0 CB A:ASP268 4.4 36.2 1.0 OD1 A:ASP50 4.5 30.2 1.0 N A:TRP81 4.5 29.5 1.0 O A:HOH738 4.5 45.1 1.0 CA A:GLY80 4.6 22.7 1.0 CG D:GLU96 4.7 30.3 1.0 CD D:GLU96 4.8 36.2 1.0 OE1 D:GLU96 4.8 31.2 1.0 N D:ASN97 4.9 27.1 1.0 N A:GLY82 4.9 31.6 1.0 CB D:GLU96 4.9 29.1 1.0 O A:ASP268 5.0 44.4 1.0

Cadmium binding site 5 out of 34 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd511 b:43.1 occ:0.71 O A:HOH682 2.1 39.6 1.0 OE2 A:GLU485 2.7 57.7 1.0 CD A:GLU485 3.7 52.5 1.0 OE1 A:GLU485 4.5 60.3 1.0 CG A:GLU485 4.5 38.1 1.0 O A:HOH836 4.9 43.7 1.0 CB A:GLU485 5.0 28.9 1.0

Cadmium binding site 6 out of 34 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd512 b:40.2 occ:0.46 O A:HOH790 1.9 39.7 1.0 O A:HOH821 2.0 34.9 1.0 NE2 A:HIS252 2.4 24.9 1.0 OD2 A:ASP454 2.5 29.2 1.0 CD2 A:HIS252 3.2 29.3 1.0 CG A:ASP454 3.4 29.8 1.0 CE1 A:HIS252 3.6 28.5 1.0 CB A:ASP454 3.6 24.8 1.0 CG A:HIS252 4.4 24.3 1.0 OE2 A:GLU256 4.5 41.5 1.0 OD1 A:ASP454 4.5 28.5 1.0 ND1 A:HIS252 4.6 23.7 1.0 CA A:ASP454 4.6 24.1 1.0 CD A:CD507 4.7 28.1 1.0 O A:HOH1036 4.7 64.9 1.0 CG A:GLU256 4.7 31.6 1.0 CD A:GLU256 4.8 36.3 1.0

Cadmium binding site 7 out of 34 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd513 b:32.4 occ:0.38 O A:HOH1041 2.5 36.9 1.0 O D:HOH808 2.5 41.2 1.0 O D:HOH1106 2.5 58.0 1.0 O D:HOH977 2.5 46.4 1.0 O D:HOH613 2.8 48.4 1.0 O D:HOH874 2.8 36.9 1.0 CD D:CD501 2.9 24.7 0.5 O D:HOH1014 3.4 27.0 1.0 CG A:GLU96 4.1 27.6 0.6 O D:HOH617 4.1 51.4 1.0 CG A:GLU96 4.3 25.9 0.4 CG D:ASP268 4.5 46.5 1.0 N D:TRP81 4.5 24.8 1.0 OD1 D:ASP268 4.6 48.8 1.0 CD A:GLU96 4.6 23.3 0.4 OD2 D:ASP268 4.6 40.8 1.0 CD A:GLU96 4.7 25.6 0.6 OE1 A:GLU96 4.7 29.2 0.4 OE1 A:GLU96 4.7 26.6 0.6 CA D:GLY80 4.7 25.9 1.0 N D:GLY82 4.7 26.0 1.0 O A:HOH998 4.7 49.9 1.0 CB D:ASP268 4.8 45.5 1.0 CB A:GLU96 4.9 27.4 0.4 CB A:GLU96 5.0 28.1 0.6

Cadmium binding site 8 out of 34 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd514 b:75.8 occ:0.51 O D:HOH681 2.4 42.8 1.0 OD2 A:ASP56 2.6 34.7 1.0 OD1 D:ASP56 2.7 37.0 1.0 CD A:CD517 2.7 47.2 0.4 O A:HOH831 2.8 60.9 1.0 O D:HOH1006 2.9 43.9 1.0 O A:HOH1018 2.9 48.7 1.0 OD1 A:ASP56 3.0 53.5 1.0 CG A:ASP56 3.1 41.9 1.0 CG D:ASP56 3.5 39.6 1.0 NZ A:LYS51 3.9 55.2 1.0 OD2 D:ASP56 4.0 39.4 1.0 OD1 D:ASP75 4.5 42.8 1.0 O A:HOH970 4.5 30.8 1.0 CB A:ASP56 4.6 31.1 1.0 CB D:ASP56 4.6 29.7 1.0 O D:HOH988 4.6 47.0 1.0 CE A:LYS51 4.6 56.0 1.0 CA D:ASP56 4.7 28.2 1.0 NZ D:LYS51 4.9 37.7 1.0 O D:HOH861 4.9 47.7 1.0

Cadmium binding site 9 out of 34 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd515 b:31.4 occ:0.33 CD A:CD507 2.5 28.1 1.0 NZ A:LYS253 3.1 45.6 1.0 OD2 A:ASP454 3.6 29.2 1.0 OD2 A:ASP456 3.7 28.4 1.0 CD2 A:HIS252 3.8 29.3 1.0 OD1 A:ASP454 3.8 28.5 1.0 CG A:LYS249 3.8 24.4 1.0 CB A:LYS249 3.8 23.0 1.0 CE A:LYS253 3.8 36.5 1.0 CA A:LYS249 3.9 23.8 1.0 CG A:ASP454 3.9 29.8 1.0 O A:HOH821 4.0 34.9 1.0 O A:LYS249 4.0 24.2 1.0 CD A:PRO455 4.0 22.1 1.0 NZ A:LYS249 4.0 35.7 1.0 CD A:LYS253 4.3 39.4 1.0 CG A:PRO455 4.3 24.1 1.0 CB A:HIS252 4.4 21.9 1.0 CG A:HIS252 4.4 24.3 1.0 C A:LYS249 4.4 23.3 1.0 CE A:LYS249 4.5 30.2 1.0 CG A:LYS253 4.7 33.4 1.0 CG A:ASP456 4.8 25.7 1.0 CD A:LYS249 4.8 26.2 1.0 NE2 A:HIS252 4.9 24.9 1.0

Cadmium binding site 10 out of 34 in the Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of N-Glycan Transport Solute Binding Protein (Ngts) From Streptococcus Pneumoniae in Complex with MAN5GLCNAC within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd516 b:34.6 occ:0.31 CD A:CD509 2.6 23.1 0.8 N A:LYS332 3.3 25.0 1.0 OE1 A:GLU333 3.5 25.8 1.0 O A:HOH900 3.5 34.0 1.0 O A:LYS330 3.6 28.8 1.0 C A:LYS330 3.7 29.6 1.0 CG A:LYS332 3.7 24.5 1.0 CB A:LYS332 3.7 21.1 1.0 O A:SER329 3.9 24.7 1.0 N A:ASN331 3.9 23.7 1.0 CA A:LYS332 4.1 24.4 1.0 CA A:ASN331 4.2 24.8 1.0 CD A:GLU333 4.2 34.2 1.0 C A:ASN331 4.2 24.7 1.0 CA A:LYS330 4.2 28.4 1.0 OE2 A:GLU333 4.3 36.7 1.0 CD A:LYS332 4.3 27.1 1.0 N A:GLU333 4.7 23.7 1.0 NZ A:LYS332 4.7 36.4 1.0 C A:SER329 4.7 24.7 1.0 N A:LYS330 4.9 27.2 1.0 C A:LYS332 4.9 27.4 1.0 O A:HOH935 5.0 25.9 1.0

M.Robb, J.K.Hobbs, S.A.Woodiga, S.Shapiro-Ward, M.D.Suits, N.Mcgregor, H.Brumer, H.Yesilkaya, S.J.King, A.B.Boraston. Molecular Characterization of N-Glycan Degradation and Transport in Streptococcus Pneumoniae and Its Contribution to Virulence. Plos Pathog. V. 13 06090 2017.
ISSN: ESSN 1553-7374
PubMed: 28056108
DOI: 10.1371/JOURNAL.PPAT.1006090