Cadmium in PDB 2p5q: Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form

The structure of Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form, PDB code: 2p5q was solved by C.S.Koh, C.Didierjean, N.Navrot, S.Panjikar, G.Mulliert, N.Rouhier, J.-P.Jacquot, A.Aubry, O.Shawkataly, C.Corbier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	221.665, 221.665, 48.142, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 20

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form (pdb code 2p5q). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 32 binding sites of Cadmium where determined in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form, PDB code: 2p5q:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 32 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form


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 the Poplar Glutathione Peroxidase 5 in the Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd702 b:24.3 occ:1.00 OE1 A:GLU22 2.4 20.9 1.0 O A:HOH856 2.4 30.8 1.0 OD2 A:ASP103 2.5 15.1 1.0 OD1 A:ASP103 2.5 13.9 1.0 O A:HOH1018 2.5 34.6 1.0 O A:HOH1002 2.5 25.0 1.0 OE2 A:GLU22 2.7 22.3 1.0 CG A:ASP103 2.8 13.8 1.0 CD A:GLU22 2.9 20.7 1.0 O A:HOH979 3.3 57.7 1.0 O A:HOH1006 4.2 36.0 1.0 CB A:ASP103 4.3 14.8 1.0 ND2 A:ASN84 4.3 13.7 1.0 CG A:GLU22 4.4 19.6 1.0 O A:LYS104 4.4 16.2 1.0 O A:HOH876 4.5 25.6 1.0 O A:HOH891 4.7 26.5 1.0 N A:LYS104 5.0 15.7 1.0

Cadmium binding site 2 out of 32 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form


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 the Poplar Glutathione Peroxidase 5 in the Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd708 b:16.1 occ:1.00 OXT A:ACT803 2.5 17.4 1.0 OXT A:ACT801 2.6 20.2 1.0 O A:ACT801 2.6 17.4 1.0 SG A:CYS92 2.6 15.2 1.0 C A:ACT801 2.9 21.0 1.0 C A:ACT803 3.3 17.0 1.0 CB A:CYS92 3.4 12.8 1.0 CD A:CD731 3.7 15.6 1.0 O A:ACT803 3.9 18.4 1.0 CA A:CYS92 4.2 13.1 1.0 CH3 A:ACT803 4.3 17.8 1.0 O A:HOH869 4.4 22.5 1.0 CH3 A:ACT801 4.4 18.8 1.0 O A:HOH868 5.0 17.3 1.0

Cadmium binding site 3 out of 32 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form


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 the Poplar Glutathione Peroxidase 5 in the Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd713 b:36.4 occ:1.00 O A:HOH1009 2.2 21.9 1.0 OE1 A:GLU79 2.4 20.0 1.0 SG A:CYS44 2.6 19.5 1.0 O A:HOH930 2.7 27.8 1.0 O A:HOH971 2.7 24.9 1.0 NE1 A:TRP133 2.7 20.3 1.0 OE2 A:GLU79 3.0 31.3 1.0 CD A:GLU79 3.1 23.5 1.0 CB A:CYS44 3.5 18.5 1.0 CE2 A:TRP133 3.6 19.8 1.0 ND2 A:ASN134 3.7 14.2 1.0 CD1 A:TRP133 3.8 19.4 1.0 CA A:CYS44 3.9 19.4 1.0 N A:GLY45 3.9 19.4 1.0 CZ2 A:TRP133 3.9 22.6 1.0 C A:CYS44 4.4 19.6 1.0 CG A:GLU79 4.6 22.2 1.0 O A:HOH972 4.6 40.3 1.0 O B:HOH913 4.8 47.4 1.0 CG A:ASN134 4.9 14.4 1.0 CD2 A:TRP133 4.9 20.2 1.0 CE A:MET46 4.9 18.8 1.0 CG A:TRP133 4.9 17.7 1.0 CA A:GLY45 5.0 16.7 1.0

Cadmium binding site 4 out of 32 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form


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 the Poplar Glutathione Peroxidase 5 in the Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd716 b:39.0 occ:1.00 O B:THR153 2.4 12.3 1.0 OD1 A:ASP148 2.5 10.7 1.0 O A:HOH866 2.5 11.6 1.0 O A:HOH804 2.6 11.1 1.0 O B:HOH857 2.6 17.8 1.0 O A:HOH861 2.7 18.7 1.0 CG A:ASP148 3.3 13.5 1.0 OD2 A:ASP148 3.4 13.7 1.0 C B:THR153 3.5 14.7 1.0 O B:HOH872 3.8 24.9 1.0 O A:HOH900 3.9 22.1 1.0 O A:VAL147 4.1 15.4 1.0 CA B:THR154 4.2 13.1 1.0 N B:THR154 4.3 14.5 1.0 OD1 A:ASP162 4.3 12.6 1.0 O B:HOH875 4.3 26.3 1.0 N B:SER155 4.4 11.5 1.0 O A:HOH825 4.4 12.5 1.0 CB B:THR153 4.5 14.9 1.0 O A:HOH898 4.5 31.9 1.0 CA B:THR153 4.5 14.4 1.0 O A:HOH899 4.7 19.1 1.0 CB A:ASP148 4.7 12.2 1.0 C B:THR154 4.8 14.5 1.0 O B:HOH899 4.8 40.2 1.0 CG A:ASP162 4.9 12.3 1.0

Cadmium binding site 5 out of 32 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form


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 the Poplar Glutathione Peroxidase 5 in the Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd722 b:23.0 occ:1.00 OD1 A:ASP85 2.4 22.4 1.0 OD2 A:ASP89 2.4 18.1 1.0 OD1 A:ASP89 2.6 12.5 1.0 OD2 A:ASP85 2.7 23.0 1.0 CG A:ASP85 2.9 21.8 1.0 CG A:ASP89 2.9 15.2 1.0 O A:ASP85 4.3 17.5 1.0 CB A:ASP85 4.3 19.8 1.0 CB A:ASP89 4.4 15.6 1.0 O A:HOH869 4.4 22.5 1.0 C A:ASP85 4.8 16.8 1.0 CA A:ASP85 4.9 17.7 1.0 O A:HOH916 5.0 35.8 1.0

Cadmium binding site 6 out of 32 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form


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 the Poplar Glutathione Peroxidase 5 in the Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd727 b:48.5 occ:1.00 O A:HOH927 2.3 18.5 1.0 O A:HOH965 2.5 41.0 1.0 OE1 A:GLU78 2.5 26.8 1.0 OE2 A:GLU78 2.7 29.8 1.0 CD A:GLU78 2.9 26.8 1.0 CG A:GLU78 4.4 24.9 1.0 O A:HOH822 4.9 23.6 1.0

Cadmium binding site 7 out of 32 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form


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 the Poplar Glutathione Peroxidase 5 in the Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd731 b:15.6 occ:1.00 O A:CYS92 2.4 12.1 1.0 O A:ACT803 2.4 18.4 1.0 SG A:CYS92 2.6 15.2 1.0 O A:HOH1000 2.6 16.1 1.0 OXT A:ACT803 3.0 17.4 1.0 C A:ACT803 3.1 17.0 1.0 C A:CYS92 3.2 14.3 1.0 CA A:CYS92 3.6 13.1 1.0 CB A:CYS92 3.6 12.8 1.0 CD A:CD708 3.7 16.1 1.0 N A:THR93 4.3 12.1 1.0 NZ A:LYS96 4.3 10.8 1.0 CG A:LYS96 4.3 11.2 1.0 O A:HOH1001 4.5 19.1 1.0 CH3 A:ACT803 4.6 17.8 1.0 CA A:THR93 4.8 12.6 1.0 CA A:LYS96 4.8 12.0 1.0 CB A:LYS96 5.0 11.9 1.0 O A:ACT801 5.0 17.4 1.0

Cadmium binding site 8 out of 32 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form


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 the Poplar Glutathione Peroxidase 5 in the Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd701 b:35.8 occ:1.00 O B:HOH948 2.5 34.2 1.0 OD1 B:ASP85 3.2 38.4 1.0 OD2 B:ASP85 3.2 43.6 1.0 CG B:ASP85 3.4 38.9 1.0 CD B:CD706 3.5 32.3 1.0 O B:ACT808 3.6 53.9 1.0 CB B:ASP85 4.7 35.8 1.0 C B:ACT808 5.0 54.6 1.0

Cadmium binding site 9 out of 32 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form


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 the Poplar Glutathione Peroxidase 5 in the Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd706 b:32.3 occ:1.00 OD2 B:ASP89 2.5 26.2 1.0 OD1 B:ASP89 2.5 18.9 1.0 O B:ACT808 2.6 53.9 1.0 OD1 B:ASP85 2.7 38.4 1.0 CG B:ASP89 2.9 22.7 1.0 OD2 B:ASP85 3.1 43.6 1.0 CG B:ASP85 3.2 38.9 1.0 C B:ACT808 3.5 54.6 1.0 CD B:CD701 3.5 35.8 1.0 OXT B:ACT808 3.7 53.9 1.0 O B:HOH847 3.9 34.0 1.0 O B:HOH948 3.9 34.2 1.0 O B:ASP85 4.3 31.5 1.0 CB B:ASP89 4.4 25.4 1.0 CB B:ASP85 4.6 35.8 1.0 CH3 B:ACT808 4.7 54.6 1.0 C B:ASP85 4.8 31.5 1.0 O B:HOH891 5.0 36.4 1.0

Cadmium binding site 10 out of 32 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Reduced Form


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 the Poplar Glutathione Peroxidase 5 in the Reduced Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd712 b:42.2 occ:1.00 OE2 B:GLU79 2.5 33.0 1.0 OE1 B:GLU79 2.6 27.6 1.0 O B:HOH946 2.7 40.2 1.0 O B:HOH947 2.8 42.3 1.0 SG B:CYS44 2.8 29.0 1.0 CD B:GLU79 2.9 29.5 1.0 O B:HOH915 2.9 26.3 1.0 CB B:CYS44 3.5 26.3 1.0 NE1 B:TRP133 3.6 26.4 1.0 CA B:CYS44 3.6 26.4 1.0 N B:GLY45 3.8 26.0 1.0 C B:CYS44 4.2 26.0 1.0 CE2 B:TRP133 4.3 23.6 1.0 CZ2 B:TRP133 4.3 23.1 1.0 CG B:GLU79 4.4 29.9 1.0 ND2 B:ASN134 4.4 20.9 1.0 O B:LYS43 4.7 30.3 1.0 CD1 B:TRP133 4.7 24.6 1.0 O B:HOH933 4.8 52.3 1.0 O B:HOH919 4.9 37.3 1.0 N B:CYS44 4.9 27.8 1.0 CA B:GLY45 4.9 24.5 1.0

C.S.Koh, C.Didierjean, N.Navrot, S.Panjikar, G.Mulliert, N.Rouhier, J.P.Jacquot, A.Aubry, O.Shawkataly, C.Corbier. Crystal Structures of A Poplar Thioredoxin Peroxidase That Exhibits the Structure of Glutathione Peroxidases: Insights Into Redox-Driven Conformational Changes. J.Mol.Biol. V. 370 512 2007.
ISSN: ISSN 0022-2836
PubMed: 17531267
DOI: 10.1016/J.JMB.2007.04.031