Cobalt in PDB 1wn1: Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3

The structure of Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3, PDB code: 1wn1 was solved by J.Jeyakanthan, J.Taka, Y.Kitaguchi, Y.Shiro, S.Yokoyama, K.Yutani, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.966, 89.002, 147.159, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.8

The binding sites of Cobalt atom in the Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3 (pdb code 1wn1). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3, PDB code: 1wn1:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1001 b:65.8 occ:1.00 OD1 A:ASP226 2.7 34.4 1.0 OE2 A:GLU333 2.7 36.8 1.0 OE1 A:GLU319 2.8 43.0 1.0 OE2 A:GLU319 2.9 39.0 1.0 CG A:ASP226 3.2 29.4 1.0 OD2 A:ASP226 3.2 32.1 1.0 OE1 A:GLU333 3.2 39.5 1.0 CD A:GLU319 3.2 40.6 1.0 NE2 A:HIS290 3.3 33.0 1.0 CD A:GLU333 3.3 37.5 1.0 CO A:CO1003 3.4 82.8 1.0 CD2 A:HIS290 4.2 29.5 1.0 CE1 A:HIS290 4.2 29.9 1.0 CB A:ASP226 4.4 26.6 1.0 OD1 A:ASP215 4.5 34.0 1.0 OD2 A:ASP215 4.6 34.1 1.0 CG A:GLU319 4.7 40.1 1.0 CG A:GLU333 4.7 35.6 1.0 OG1 A:THR228 4.7 31.8 1.0 CG A:ASP215 4.9 29.1 1.0 OG1 A:THR317 4.9 29.5 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1003 b:82.8 occ:1.00 OD1 A:ASP215 2.1 34.0 1.0 OE1 A:GLU333 2.2 39.5 1.0 OD2 A:ASP226 2.3 32.1 1.0 O A:ILE227 2.5 26.0 1.0 OG1 A:THR228 2.6 31.8 1.0 CG A:ASP215 3.0 29.1 1.0 C A:ILE227 3.1 26.3 1.0 CG A:ASP226 3.4 29.4 1.0 CD A:GLU333 3.4 37.5 1.0 CO A:CO1001 3.4 65.8 1.0 N A:ILE227 3.5 25.4 1.0 OD2 A:ASP215 3.7 34.1 1.0 C A:ASP226 3.8 26.1 1.0 CA A:ILE227 3.8 26.0 1.0 N A:THR228 3.8 27.0 1.0 CB A:THR228 3.9 28.3 1.0 OE2 A:GLU333 4.0 36.8 1.0 CB A:ASP215 4.0 25.9 1.0 OD1 A:ASP226 4.1 34.4 1.0 O A:TYR216 4.1 20.9 1.0 CA A:ASP215 4.1 23.6 1.0 N A:TYR216 4.1 19.2 1.0 CA A:THR228 4.2 28.9 1.0 CZ A:PHE184 4.2 18.9 1.0 O A:ASP226 4.3 26.7 1.0 CA A:ASP226 4.3 24.9 1.0 C A:ASP215 4.4 21.0 1.0 CB A:ASP226 4.4 26.6 1.0 CG A:GLU333 4.6 35.6 1.0 OE1 A:GLU319 4.6 43.0 1.0 CB A:GLU333 4.8 31.6 1.0 NH1 A:ARG331 4.8 48.5 1.0 C A:TYR216 4.8 17.5 1.0 CG2 A:THR228 4.9 28.0 1.0 CE2 A:PHE184 4.9 21.4 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1002 b:51.9 occ:1.00 OD1 B:ASP226 2.1 22.3 1.0 NE2 B:HIS290 2.6 25.4 1.0 OE2 B:GLU333 2.7 24.7 1.0 CG B:ASP226 2.9 18.2 1.0 OE2 B:GLU319 3.0 29.4 1.0 OD2 B:ASP226 3.2 19.2 1.0 CO B:CO1004 3.4 65.5 1.0 CD2 B:HIS290 3.5 24.8 1.0 OE1 B:GLU319 3.5 28.7 1.0 CE1 B:HIS290 3.6 23.8 1.0 CD B:GLU333 3.6 26.0 1.0 CD B:GLU319 3.6 30.2 1.0 OE1 B:GLU333 3.7 25.8 1.0 CB B:ASP226 4.2 18.0 1.0 NE2 B:HIS297 4.4 41.6 1.0 OD2 B:ASP215 4.6 28.1 1.0 O B:HOH1009 4.6 38.7 1.0 ND1 B:HIS290 4.7 23.8 1.0 CG B:HIS290 4.7 23.7 1.0 OG1 B:THR317 4.8 19.2 1.0 CG1 B:VAL296 4.8 28.4 1.0 O B:HOH1008 4.9 54.0 1.0 CD2 B:HIS297 4.9 39.0 1.0 CG2 B:THR317 4.9 20.4 1.0 CG B:GLU333 5.0 22.2 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1004 b:65.5 occ:1.00 OD2 B:ASP226 2.3 19.2 1.0 OE1 B:GLU333 2.4 25.8 1.0 OD2 B:ASP215 2.4 28.1 1.0 OD1 B:ASP215 2.5 27.6 1.0 CG B:ASP215 2.5 23.7 1.0 OG1 B:THR228 2.6 17.2 1.0 O B:ILE227 3.1 21.1 1.0 CG B:ASP226 3.3 18.2 1.0 CD B:GLU333 3.4 26.0 1.0 CO B:CO1002 3.4 51.9 1.0 CB B:ASP215 3.7 22.8 1.0 OE2 B:GLU333 3.8 24.7 1.0 C B:ILE227 3.8 20.0 1.0 OD1 B:ASP226 3.8 22.3 1.0 CB B:THR228 4.0 17.5 1.0 OE1 B:GLU319 4.1 28.7 1.0 CZ B:PHE184 4.1 21.2 1.0 CA B:ASP215 4.1 20.8 1.0 N B:ILE227 4.1 16.5 1.0 N B:TYR216 4.3 16.2 1.0 NH1 B:ARG331 4.3 31.7 1.0 C B:ASP226 4.3 17.2 1.0 N B:THR228 4.4 18.5 1.0 C B:ASP215 4.4 18.4 1.0 CA B:ILE227 4.5 18.5 1.0 CA B:THR228 4.6 19.1 1.0 CB B:ASP226 4.6 18.0 1.0 O B:TYR216 4.7 20.1 1.0 CG B:GLU333 4.7 22.2 1.0 O B:ASP226 4.7 18.6 1.0 CA B:ASP226 4.8 17.1 1.0 CG2 B:THR228 4.8 18.0 1.0 CE1 B:PHE184 4.8 24.4 1.0 CE2 B:PHE184 4.9 23.1 1.0 CB B:GLU333 5.0 22.3 1.0

J.Jeyakanthan, J.Taka, Y.Kitaguchi, Y.Shiro, S.Yokoyama, K.Yutani. Crystal Structure of Dipeptiase From Pyrococcus Horikoshii OT3 To Be Published.