Cadmium in PDB 4hmp: Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4

The structure of Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4, PDB code: 4hmp was solved by W.Cheng, Q.Li, Y.-L.Jiang, Y.Chen, C.-Z.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.12 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.037, 86.299, 93.532, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 29.7

Pages:

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

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4 (pdb code 4hmp). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 31 binding sites of Cadmium where determined in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4, PDB code: 4hmp:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 31 in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4


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 Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd401 b:71.4 occ:1.00 O A:HOH514 2.5 20.1 1.0 O A:HOH515 3.1 16.4 1.0 O A:HOH513 3.4 16.3 1.0 OH A:TYR225 4.2 22.1 1.0 CE A:MSE213 4.3 20.0 1.0 NH1 A:ARG231 4.3 21.6 1.0 CH2 A:TRP63 4.3 23.4 1.0 NH2 A:ARG231 4.5 21.8 1.0 CE1 A:PHE255 4.5 29.7 1.0 CZ A:ARG231 4.8 21.9 1.0 CE1 A:TYR225 4.9 22.5 1.0 CZ3 A:TRP63 4.9 23.4 1.0 CZ A:PHE255 5.0 29.4 1.0

Cadmium binding site 2 out of 31 in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4


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 Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:19.8 occ:1.00 OD1 A:ASP127 2.2 20.1 1.0 O A:HOH501 2.4 2.0 1.0 OE1 A:GLU56 2.5 24.7 1.0 OD2 A:ASP127 2.7 19.6 1.0 CG A:ASP127 2.8 20.0 1.0 CD A:GLU56 3.3 24.4 1.0 CG A:GLU56 3.6 24.0 1.0 CB A:ASP127 4.2 20.0 1.0 OE2 A:GLU56 4.4 24.3 1.0 CD A:ARG57 4.5 19.9 1.0 CG A:ARG57 4.7 20.4 1.0 CB A:ARG57 4.8 20.8 1.0 CA A:ASP127 4.9 19.9 1.0

Cadmium binding site 3 out of 31 in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4


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 Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:43.4 occ:1.00 O A:HOH504 2.5 10.1 1.0 O A:HOH505 2.5 22.0 1.0 OD2 A:ASP164 2.5 20.2 1.0 OD1 A:ASP164 2.7 21.1 1.0 CG A:ASP164 2.9 20.1 1.0 CD1 A:LEU161 4.3 18.5 1.0 CB A:ASP164 4.4 19.2 1.0 N A:ASP164 4.8 18.7 1.0 CG A:LEU161 4.9 18.6 1.0 CB A:LEU161 4.9 18.7 1.0

Cadmium binding site 4 out of 31 in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4


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 Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:37.6 occ:1.00 OE1 A:GLU187 2.3 22.4 1.0 O A:HOH510 2.4 12.0 1.0 OE2 A:GLU187 2.4 23.1 1.0 O A:HOH508 2.4 11.6 1.0 O A:HOH509 2.5 16.1 1.0 CD A:GLU187 2.7 22.9 1.0 CG A:GLU187 4.2 22.7 1.0 CG2 A:ILE183 4.4 20.6 1.0 NE A:ARG163 4.5 18.7 1.0 CB A:GLU187 5.0 22.4 1.0

Cadmium binding site 5 out of 31 in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4


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 Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd405 b:42.7 occ:1.00 OE2 A:GLU327 2.3 28.1 1.0 O A:HOH530 2.4 21.4 1.0 OE1 A:GLU193 2.5 31.9 1.0 NZ A:LYS196 2.7 34.4 1.0 OE2 A:GLU193 3.0 31.9 1.0 CD A:GLU193 3.1 31.4 1.0 CD A:GLU327 3.2 27.7 1.0 CG A:GLU327 3.5 27.4 1.0 CE A:LYS196 3.9 34.3 1.0 CD A:LYS196 4.1 33.9 1.0 NH1 A:ARG189 4.3 24.2 1.0 NE2 A:HIS197 4.3 29.8 1.0 OE1 A:GLU327 4.4 27.7 1.0 CG A:GLU193 4.5 30.7 1.0 CB A:GLU327 5.0 27.2 1.0

Cadmium binding site 6 out of 31 in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4


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 Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd406 b:68.5 occ:1.00 OE2 A:GLU102 2.6 28.6 1.0 OE1 A:GLU102 2.9 29.5 1.0 OE1 A:GLU98 3.0 31.9 1.0 CD A:GLU102 3.1 28.7 1.0 OE2 A:GLU98 3.5 31.6 1.0 CD A:GLU98 3.6 30.8 1.0 O A:HOH503 3.8 26.4 1.0 NZ A:LYS99 4.1 26.2 1.0 CE A:LYS99 4.5 25.6 1.0 CG A:GLU102 4.6 27.1 1.0

Cadmium binding site 7 out of 31 in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4


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 Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd407 b:34.0 occ:1.00 OE2 A:GLU199 2.4 27.9 1.0 O A:HOH511 2.5 11.5 1.0 O A:HOH512 2.5 10.0 1.0 OE1 A:GLU199 2.6 28.7 1.0 CD A:GLU199 2.8 28.3 1.0 CG A:GLU199 4.3 28.3 1.0

Cadmium binding site 8 out of 31 in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4


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 Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd408 b:63.1 occ:1.00 O A:HOH521 2.4 16.7 1.0 O A:HOH534 2.5 21.8 1.0 OE1 A:GLU328 2.6 32.5 1.0 OE2 A:GLU328 3.1 33.0 1.0 CD A:GLU328 3.2 32.3 1.0 O A:HOH518 4.1 33.4 1.0 N A:LEU311 4.4 28.9 1.0 CB A:LEU311 4.5 28.6 1.0 CB A:PRO310 4.5 29.4 1.0 CG A:GLU328 4.7 30.6 1.0 CA A:LEU311 4.8 28.6 1.0 CG A:PRO310 4.9 29.6 1.0

Cadmium binding site 9 out of 31 in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4


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 Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd409 b:34.0 occ:1.00 OD1 A:ASP52 2.2 30.9 1.0 O A:LYS54 2.4 27.9 1.0 OE2 A:GLU56 2.4 24.3 1.0 O A:HOH502 2.6 16.4 1.0 CG A:ASP52 2.9 30.4 1.0 OD2 A:ASP52 2.9 30.9 1.0 CD A:GLU56 3.4 24.4 1.0 C A:LYS54 3.4 27.5 1.0 OE1 A:GLU56 3.7 24.7 1.0 CA A:LYS54 4.2 28.3 1.0 CB A:LYS54 4.2 28.8 1.0 N A:PRO55 4.2 26.7 1.0 N A:GLU56 4.3 24.5 1.0 CA A:PRO55 4.3 26.0 1.0 CB A:ASP52 4.4 30.1 1.0 N A:LYS54 4.5 28.5 1.0 CG A:GLU56 4.7 24.0 1.0 C A:PRO55 4.8 25.4 1.0

Cadmium binding site 10 out of 31 in the Crystal Structure of Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4


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 Iron Uptake Abc Transporter Substrate-Binding Protein Piaa From Streptococcus Pneumoniae TIGR4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd410 b:85.7 occ:1.00 O A:HOH525 2.9 17.9 1.0 OD1 A:ASP111 3.2 37.7 1.0 CG A:ASP111 4.1 37.5 1.0 OD2 A:ASP111 4.2 38.2 1.0 O A:LEU109 4.4 29.9 1.0

W.Cheng, Q.Li, Y.-L.Jiang, C.-Z.Zhou, Y.Chen. Structures of Streptococcus Pneumoniae Piaa and Its Complex with Ferrichrome Reveal Insights Into the Substrate Binding and Release of High Affinity Iron Transporters Plos One V. 8 71451 2013.
ISSN: ESSN 1932-6203
PubMed: 23951167
DOI: 10.1371/JOURNAL.PONE.0071451