Calcium in PDB 2p5r: Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form

The structure of Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form, PDB code: 2p5r 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)	50.00 / 2.45
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.580, 71.580, 117.820, 90.00, 90.00, 120.00
R / Rfree (%)	21.1 / 28

The binding sites of Calcium atom in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form (pdb code 2p5r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form, PDB code: 2p5r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:34.7 occ:1.00 O A:HIS13 2.6 26.6 1.0 OD2 A:ASP26 2.7 29.2 1.0 OD1 A:ASP26 2.7 28.2 1.0 O A:HOH374 2.7 44.1 1.0 OG A:SER28 2.8 27.2 1.0 O A:HOH375 2.8 28.6 1.0 CG A:ASP26 3.1 28.2 1.0 O A:HOH379 3.2 49.0 1.0 CB A:SER28 3.7 23.9 1.0 C A:HIS13 3.8 25.3 1.0 CA A:ASP14 4.1 26.1 1.0 N A:ASP14 4.4 25.5 1.0 N A:SER28 4.4 25.5 1.0 C A:ASP14 4.5 27.3 1.0 OD1 A:ASP14 4.5 28.5 1.0 CB A:ASP26 4.6 27.7 1.0 CA A:SER28 4.6 24.9 1.0 O A:HOH387 4.6 26.0 1.0 N A:PHE15 4.7 27.3 1.0 CA A:HIS13 4.9 25.3 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:76.3 occ:1.00 O A:HOH403 2.9 50.4 1.0 OE1 A:GLU78 2.9 89.7 1.0 O A:HOH442 3.2 45.7 1.0 CG A:GLU78 3.3 89.0 1.0 CD A:GLU78 3.5 89.5 1.0 O A:HOH336 3.8 49.6 1.0 O A:HOH413 3.9 45.8 1.0 O A:HOH381 4.3 47.5 1.0 OE2 A:GLU78 4.7 89.0 1.0 CB A:GLU78 4.7 88.9 1.0 CB A:GLU79 4.7 0.4 1.0 N A:GLU78 4.8 82.1 1.0 N A:GLU79 4.8 96.4 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:66.4 occ:1.00 O A:HOH376 2.7 24.5 1.0 O B:THR153 2.7 26.2 1.0 OD2 A:ASP148 2.8 25.1 1.0 O A:HOH420 3.0 49.0 1.0 CA A:CA305 3.2 63.5 1.0 CG A:ASP148 3.6 23.5 1.0 OD1 A:ASP148 3.7 19.5 1.0 C B:THR153 4.0 25.3 1.0 O A:HOH377 4.0 33.2 1.0 O A:VAL147 4.3 23.3 1.0 CA B:THR154 4.5 30.3 1.0 N B:SER155 4.5 31.9 1.0 OD1 A:ASP162 4.5 32.2 1.0 O A:HOH354 4.6 47.1 1.0 O A:HOH419 4.7 21.9 1.0 N B:THR154 4.7 26.2 1.0 CB B:THR153 4.9 23.3 1.0 CG A:ASP162 4.9 32.4 1.0 CA B:THR153 5.0 24.5 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:63.5 occ:1.00 O A:HOH420 2.8 49.0 1.0 OD1 A:ASP148 2.9 19.5 1.0 CA A:CA303 3.2 66.4 1.0 OD1 A:ASP162 3.7 32.2 1.0 CG A:ASP148 3.8 23.5 1.0 CB A:ASP162 3.9 30.1 1.0 OD2 A:ASP148 4.0 25.1 1.0 CG A:ASP162 4.0 32.4 1.0 O A:HOH376 4.1 24.5 1.0 NE2 A:GLN165 4.3 55.2 1.0 CG A:LEU166 4.3 45.9 1.0 CD2 A:LEU166 4.3 43.5 1.0 O A:ASP162 4.3 32.7 1.0 CA A:ASP162 4.3 32.1 1.0 CD A:GLN165 4.5 53.9 1.0 CD1 A:LEU166 4.6 46.5 1.0 OE1 A:GLN165 4.7 52.9 1.0 C A:ASP162 4.8 31.9 1.0 OD2 A:ASP162 4.8 36.0 1.0 CG2 A:VAL147 4.9 24.3 1.0 CB A:GLN165 4.9 47.8 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Poplar Glutathione Peroxidase 5 in the Oxidized Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:82.2 occ:1.00 O B:HOH363 3.1 46.0 1.0 OD1 B:ASP106 3.2 41.4 1.0 O B:HOH364 3.4 62.8 1.0 OD1 B:ASN74 3.4 44.0 1.0 OD2 B:ASP106 3.8 43.9 1.0 CG B:ASP106 3.9 42.0 1.0 CG B:GLN75 4.0 43.0 1.0 CG B:ASN74 4.4 42.5 1.0 ND2 B:ASN74 4.5 42.8 1.0 CD B:GLN75 4.7 45.8 1.0 NE2 B:GLN75 4.7 44.4 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