Calcium in PDB 7e4u: Crystal Structure of Peroxiredoxin-1

The structure of Crystal Structure of Peroxiredoxin-1, PDB code: 7e4u was solved by S.Ahmed, Y.K.Mok, C.Jobichen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.49 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	217.452, 60.606, 205.142, 90, 94.23, 90
R / Rfree (%)	20.6 / 25.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Peroxiredoxin-1 (pdb code 7e4u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Crystal Structure of Peroxiredoxin-1, PDB code: 7e4u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in the Crystal Structure of Peroxiredoxin-1


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 Peroxiredoxin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:81.4 occ:1.00 O A:HOH336 2.2 53.5 1.0 O A:HOH330 2.8 62.7 1.0 O A:GLY70 3.0 47.9 1.0 NE2 A:GLN164 3.5 47.6 1.0 C A:GLY70 3.9 55.3 1.0 CA A:GLY70 4.0 55.6 1.0 N A:TYR38 4.0 41.3 1.0 CD1 A:TYR38 4.1 36.0 1.0 O A:ILE69 4.2 56.6 1.0 CA A:LYS37 4.3 48.2 1.0 CD A:GLN164 4.5 44.3 1.0 O A:GLY36 4.6 44.6 1.0 C A:LYS37 4.6 45.2 1.0 CB A:TYR38 4.7 40.0 1.0 CB A:ASP135 4.7 48.4 1.0 CG A:TYR38 4.9 37.9 1.0 CG A:GLN164 4.9 40.9 1.0 CE1 A:TYR38 4.9 37.7 1.0 C A:ILE69 5.0 53.4 1.0

Calcium binding site 2 out of 11 in the Crystal Structure of Peroxiredoxin-1


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 Peroxiredoxin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:84.5 occ:1.00 OD1 A:ASP107 3.2 51.0 1.0 N A:ARG109 3.5 44.6 1.0 CB A:ARG109 3.6 52.0 1.0 CA A:ASP107 3.6 46.4 1.0 CG A:ARG109 3.6 62.1 1.0 C A:ASP107 3.8 43.6 1.0 N A:THR108 3.9 42.3 1.0 OG1 A:THR111 4.0 39.1 1.0 CA A:ARG109 4.1 46.1 1.0 O A:SER106 4.2 49.2 1.0 CG A:ASP107 4.2 48.7 1.0 CD A:ARG109 4.3 73.6 1.0 N A:ARG110 4.4 45.3 1.0 CB A:ASP107 4.4 47.4 1.0 O A:ASP107 4.5 45.9 1.0 CG1 A:ILE112 4.6 39.1 1.0 C A:THR108 4.6 43.0 1.0 C A:ARG109 4.6 44.6 1.0 CD1 A:ILE112 4.6 38.2 1.0 OG1 A:THR108 4.6 44.2 1.0 N A:ASP107 4.7 44.9 1.0 CA A:THR108 4.8 44.1 1.0 C A:SER106 4.8 42.7 1.0 N A:THR111 4.9 37.1 1.0 CB A:ALA17 4.9 41.3 1.0

Calcium binding site 3 out of 11 in the Crystal Structure of Peroxiredoxin-1


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 Peroxiredoxin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:85.5 occ:1.00 OE1 A:GLU171 2.7 51.7 1.0 NH2 B:ARG128 3.6 47.2 1.0 CD A:GLU171 3.7 55.6 1.0 CG A:GLU171 3.8 54.5 1.0 O A:VAL172 3.9 44.8 1.0 NH1 B:ARG128 4.0 45.4 1.0 CB B:CYS52 4.0 47.2 1.0 CZ B:ARG128 4.1 46.1 1.0 O B:HOH315 4.3 35.6 1.0 N B:GLY150 4.4 35.8 1.0 O B:PRO148 4.4 37.0 1.0 OG1 B:THR54 4.6 62.3 1.0 O B:CYS52 4.6 52.6 1.0 CA B:GLY150 4.7 37.9 1.0 OE2 A:GLU171 4.8 51.7 1.0 N B:CYS52 4.9 48.5 1.0 CA B:CYS52 5.0 50.3 1.0

Calcium binding site 4 out of 11 in the Crystal Structure of Peroxiredoxin-1


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 Peroxiredoxin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:90.5 occ:1.00 O A:HOH329 2.3 52.1 1.0 O A:HOH339 2.6 70.2 1.0 O A:GLY24 3.7 57.6 1.0 CZ D:PHE50 4.1 83.0 1.0 CE2 D:PHE50 4.1 83.0 1.0 CD2 A:PHE26 4.2 44.3 1.0 CE2 A:PHE26 4.2 47.1 1.0 N A:PHE26 4.4 52.5 1.0 CD2 A:LEU85 4.5 51.0 1.0 CA A:GLN25 4.5 48.9 1.0 CG A:PHE26 4.5 43.5 1.0 CZ A:PHE26 4.6 48.3 1.0 C A:GLY24 4.7 51.1 1.0 CD1 A:PHE26 4.8 45.1 1.0 C A:GLN25 4.9 51.4 1.0 CE1 A:PHE26 4.9 48.5 1.0

Calcium binding site 5 out of 11 in the Crystal Structure of Peroxiredoxin-1


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 Peroxiredoxin-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:121.2 occ:1.00 O B:GLY124 2.2 50.2 1.0 CD B:ARG110 3.0 57.2 1.0 C B:GLY124 3.2 47.6 1.0 NH1 B:ARG110 3.3 66.8 1.0 CA B:GLY124 3.6 50.0 1.0 CG B:ARG110 3.6 48.7 1.0 NE B:ARG110 3.8 66.8 1.0 CZ B:ARG110 3.9 65.4 1.0 CG2 B:VAL78 4.0 37.2 1.0 CB B:VAL78 4.2 38.8 1.0 CG1 B:VAL78 4.4 41.3 1.0 N B:ILE125 4.4 45.6 1.0 CD1 B:ILE125 4.9 50.6 1.0 O B:ASP123 4.9 53.5 1.0 N B:GLY124 4.9 47.9 1.0

Calcium binding site 6 out of 11 in the Crystal Structure of Peroxiredoxin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Peroxiredoxin-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:74.3 occ:1.00 O C:HOH420 2.7 45.6 1.0 N D:ILE8 3.4 41.6 1.0 CG1 D:ILE8 3.8 44.9 1.0 CA D:GLN7 3.8 50.0 1.0 CB D:ILE8 4.0 42.7 1.0 C D:GLN7 4.1 44.0 1.0 O C:GLY117 4.3 43.2 1.0 CB D:GLN7 4.3 55.9 1.0 CA D:ILE8 4.3 41.6 1.0 CD1 D:ILE142 4.5 33.8 1.0 CG D:GLN7 4.6 64.2 1.0 CE2 C:TYR127 4.6 38.4 1.0 CD2 C:TYR127 4.8 41.5 1.0 O D:ILE8 4.8 42.9 1.0 O D:ALA6 4.8 39.2 1.0 CD1 C:ILE144 4.8 31.4 1.0 CD1 D:ILE8 4.9 45.0 1.0

Calcium binding site 7 out of 11 in the Crystal Structure of Peroxiredoxin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Peroxiredoxin-1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca202 b:86.3 occ:1.00 O E:HOH305 2.2 40.3 1.0 O E:HOH323 3.2 47.5 1.0 CG E:ARG109 4.0 65.1 1.0 CD E:ARG109 4.1 67.5 1.0 CB E:ALA17 4.2 45.1 1.0 O E:SER106 4.2 54.2 1.0 O E:THR16 4.2 53.7 1.0 CB E:ARG109 4.3 56.5 1.0 OD1 E:ASP107 4.5 49.2 1.0 N E:ARG109 4.5 53.7 1.0 CA E:ALA17 4.5 45.4 1.0 CA E:ASP107 4.6 48.6 1.0 N E:THR108 4.6 53.3 1.0 OG1 E:THR111 4.7 52.9 1.0 OG1 E:THR108 4.7 55.7 1.0 CD1 E:ILE112 4.9 45.3 1.0 C E:ASP107 4.9 48.5 1.0

Calcium binding site 8 out of 11 in the Crystal Structure of Peroxiredoxin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Peroxiredoxin-1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca204 b:78.0 occ:1.00 N F:ILE8 3.5 42.4 1.0 CG1 F:ILE8 3.8 46.4 1.0 CA F:GLN7 3.8 47.2 1.0 CB F:ILE8 4.1 46.3 1.0 CD1 F:ILE142 4.1 36.2 1.0 CB F:GLN7 4.1 53.0 1.0 C F:GLN7 4.2 44.7 1.0 O E:GLY117 4.4 45.8 1.0 CA F:ILE8 4.4 46.1 1.0 CG F:GLN7 4.4 62.5 1.0 O F:ALA6 4.7 46.2 1.0 CD1 E:ILE144 4.7 40.7 1.0 CD2 E:TYR127 4.9 42.5 1.0 CE2 E:TYR127 4.9 41.3 1.0 CD1 F:ILE8 4.9 44.1 1.0 CG2 E:ILE144 5.0 35.8 1.0

Calcium binding site 9 out of 11 in the Crystal Structure of Peroxiredoxin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Peroxiredoxin-1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca205 b:81.3 occ:1.00 O F:HOH307 2.2 53.5 1.0 CB F:ASP135 4.5 62.5 1.0 CG F:ASP135 4.5 70.5 1.0 NE2 F:GLN164 4.5 36.3 1.0 O F:GLY36 4.6 69.0 1.0 CD1 F:TYR38 4.6 40.7 1.0 OD1 F:ASP135 4.6 70.1 1.0 O F:GLY70 4.8 45.9 1.0 OD2 F:ASP135 4.8 72.9 1.0

Calcium binding site 10 out of 11 in the Crystal Structure of Peroxiredoxin-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Peroxiredoxin-1 within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca201 b:88.6 occ:1.00 O I:HOH313 2.4 62.4 1.0 N I:PHE26 3.9 57.5 1.0 CD2 I:PHE26 4.1 50.2 1.0 CG I:PHE26 4.2 53.2 1.0 NE2 I:GLN25 4.2 73.4 1.0 CA I:GLN25 4.3 59.6 1.0 CB I:PHE26 4.4 55.5 1.0 CE2 I:PHE26 4.6 51.5 1.0 O I:GLY24 4.6 60.7 1.0 C I:GLN25 4.6 54.0 1.0 CD1 I:PHE26 4.7 51.8 1.0 CG I:GLN25 4.7 67.6 1.0 CB I:GLN25 4.8 68.5 1.0 CA I:PHE26 4.8 57.0 1.0 CD I:GLN25 5.0 74.1 1.0

S.Ahmed, Y.K.Mok, C.Jobichen. Crystal Structure of Peroxiredoxin-1 To Be Published.