Cadmium in PDB 4hmq: Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome

The structure of Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome, PDB code: 4hmq 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)	36.86 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.102, 84.272, 93.776, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 24.8

The structure of Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome (pdb code 4hmq). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 24 binding sites of Cadmium where determined in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome, PDB code: 4hmq:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 24 in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome


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 Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd402 b:9.8 occ:1.00 ND1 A:HIS197 2.2 13.0 1.0 O A:HOH501 2.3 8.1 1.0 O A:HOH623 2.4 5.5 1.0 CL A:CL413 2.6 18.2 1.0 CE1 A:HIS197 3.1 13.0 1.0 CG A:HIS197 3.3 12.6 1.0 CB A:HIS197 3.6 12.6 1.0 CA A:HIS197 4.0 12.5 1.0 NE2 A:HIS197 4.3 13.3 1.0 O A:LYS196 4.4 13.0 1.0 CD2 A:HIS197 4.4 12.8 1.0 O A:HOH516 4.7 25.9 1.0 C A:HIS197 5.0 12.4 1.0 N A:HIS197 5.0 12.7 1.0

Cadmium binding site 2 out of 24 in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome


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 Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd403 b:29.1 occ:0.50 O A:HOH656 2.2 16.6 1.0 OE1 A:GLU327 2.3 14.7 1.0 O A:HOH743 2.5 25.8 1.0 OE2 A:GLU327 2.6 13.7 1.0 CD A:GLU327 2.8 13.5 1.0 CD A:CD404 3.5 15.9 0.5 O A:HOH744 4.3 35.0 1.0 CG A:GLU327 4.3 11.9 1.0 O A:HOH745 4.4 29.4 1.0 O A:HOH590 4.5 25.6 1.0 NE2 A:HIS197 4.5 13.3 1.0 OE2 A:GLU193 4.7 13.8 1.0 CE1 A:HIS197 4.7 13.0 1.0 CE A:LYS196 4.8 18.5 1.0

Cadmium binding site 3 out of 24 in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome


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 Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd404 b:15.9 occ:0.50 O A:HOH632 2.2 16.9 1.0 O A:HOH656 2.4 16.6 1.0 OE2 A:GLU193 2.4 13.8 1.0 OE1 A:GLU193 2.5 13.7 1.0 O A:HOH590 2.7 25.6 1.0 OE1 A:GLU327 2.8 14.7 1.0 CD A:GLU193 2.8 13.6 1.0 CD A:CD403 3.5 29.1 0.5 CD A:GLU327 3.7 13.5 1.0 CD A:LYS196 4.2 17.1 1.0 CB A:GLU327 4.2 10.8 1.0 CE A:LYS196 4.2 18.5 1.0 CG A:GLU193 4.3 12.8 1.0 NH2 A:ARG189 4.4 12.3 1.0 OE2 A:GLU327 4.4 13.7 1.0 NE2 A:HIS197 4.4 13.3 1.0 CG A:GLU327 4.5 11.9 1.0 NH1 A:ARG189 4.5 12.2 1.0 CZ A:ARG189 4.9 12.1 1.0

Cadmium binding site 4 out of 24 in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome


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 Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd405 b:18.6 occ:0.50 O A:HOH525 2.4 17.4 1.0 O A:HOH624 2.5 20.3 1.0 O A:HOH502 2.6 2.0 1.0 OE1 A:GLU328 2.6 17.4 1.0 OE2 A:GLU328 2.8 18.8 1.0 CD A:GLU328 3.0 16.2 1.0 CB A:LEU311 4.3 8.8 1.0 CG A:GLU328 4.6 13.6 1.0 N A:LEU311 4.6 9.0 1.0 CB A:PRO310 4.9 9.4 1.0 CA A:LEU311 4.9 9.0 1.0

Cadmium binding site 5 out of 24 in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome


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 Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd406 b:16.9 occ:0.50 O A:HOH729 2.4 28.5 1.0 OE2 A:GLU252 2.5 24.3 1.0 O A:HOH611 2.7 33.1 1.0 OE1 A:GLU252 2.9 24.6 1.0 CD A:GLU252 3.0 24.4 1.0 O A:HOH703 3.5 28.6 1.0 O A:HOH536 4.0 28.5 1.0 N A:ASP253 4.1 22.8 1.0 CB A:ASP253 4.5 22.6 1.0 N A:SER254 4.5 20.7 1.0 CG A:GLU252 4.5 23.8 1.0 CA A:ASP253 4.8 22.4 1.0 CB A:SER254 4.8 19.9 1.0 CA A:GLU252 5.0 23.8 1.0

Cadmium binding site 6 out of 24 in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome


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 Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd407 b:8.7 occ:0.50 O A:HOH629 2.2 30.2 1.0 OD1 A:ASP111 2.3 16.1 1.0 O A:HOH542 2.4 17.3 1.0 O A:HOH508 2.5 7.3 1.0 OD2 A:ASP111 2.6 17.2 1.0 O A:HOH580 2.7 23.9 1.0 CG A:ASP111 2.8 15.4 1.0 O A:HOH673 3.7 33.4 1.0 NZ A:LYS81 3.9 16.6 1.0 CB A:ASP111 4.3 14.7 1.0 O A:HOH555 4.6 25.0 1.0 O A:LEU109 4.6 12.7 1.0 O A:HOH576 4.7 26.1 1.0 CE A:LYS81 4.9 15.4 1.0 O A:HOH642 4.9 29.8 1.0

Cadmium binding site 7 out of 24 in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome


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 Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd408 b:54.9 occ:1.00 OE2 A:GLU56 2.4 19.2 1.0 O A:HOH517 2.5 28.1 1.0 O A:HOH625 2.7 9.7 1.0 OE1 A:GLU56 2.8 18.7 1.0 CD A:GLU56 2.9 17.6 1.0 CG A:GLU56 4.4 15.4 1.0

Cadmium binding site 8 out of 24 in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome


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 Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd409 b:27.4 occ:0.50 OD2 A:ASP140 2.4 9.8 1.0 O A:HOH696 2.4 17.2 1.0 O A:HOH667 2.4 13.7 1.0 O A:HOH666 2.4 16.3 1.0 O A:HOH731 2.8 42.7 1.0 CG A:ASP140 3.2 9.6 1.0 OD1 A:ASP140 3.4 9.8 1.0 O A:HOH721 3.5 23.0 1.0 O A:HOH668 4.0 23.5 1.0 CG2 A:THR137 4.1 8.6 1.0 OG1 A:THR137 4.3 8.4 1.0 N A:THR137 4.3 7.7 1.0 O A:GLY135 4.3 7.0 1.0 CB A:ASP140 4.5 8.8 1.0 CA A:ILE136 4.5 7.2 1.0 CB A:THR137 4.8 8.3 1.0 CD1 A:LEU116 4.8 13.6 1.0 C A:ILE136 4.9 7.4 1.0 CG A:LEU116 4.9 14.6 1.0

Cadmium binding site 9 out of 24 in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome


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 Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd410 b:29.0 occ:0.50 O A:HOH552 2.3 17.0 1.0 OE2 A:GLU187 2.3 11.5 1.0 OE1 A:GLU187 2.3 11.3 1.0 O A:HOH522 2.6 15.8 1.0 CD A:GLU187 2.7 11.4 1.0 O A:HOH549 2.7 24.7 1.0 O A:HOH577 3.9 29.7 1.0 CG2 A:ILE183 4.2 8.0 1.0 CG A:GLU187 4.2 10.6 1.0 O A:HOH569 4.5 6.8 1.0 NE A:ARG163 4.7 5.6 1.0 CG A:LYS184 4.9 10.6 1.0 O A:HOH561 4.9 21.1 1.0 CB A:GLU187 5.0 10.0 1.0 C1 A:EDO414 5.0 23.9 1.0

Cadmium binding site 10 out of 24 in the Crystal Structure of Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome


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 Streptococcus Pneumoniae TIGR4 Piaa in Complex with Ferrichrome within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd411 b:25.8 occ:0.50 OE1 A:GLU176 2.5 16.1 1.0 O A:HOH710 2.6 33.7 1.0 O A:HOH732 2.6 29.9 1.0 O A:HOH534 2.7 22.7 1.0 OE2 A:GLU176 2.7 15.4 1.0 CD A:GLU176 3.0 15.4 1.0 O A:HOH709 3.1 33.0 1.0 NZ A:LYS171 4.4 11.5 1.0 CG A:GLU176 4.5 13.3 1.0 CE A:LYS171 4.6 11.2 1.0 CD A:LYS171 5.0 10.2 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