Cobalt in PDB 5ds0: Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09

The structure of Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09, PDB code: 5ds0 was solved by K.Michalska, G.Chhor, J.Mootz, M.Endres, R.Jedrzejczak, G.Babnigg, A.Steen, K.Lloyd, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	114.638, 165.372, 125.789, 90.00, 90.87, 90.00
R / Rfree (%)	19.3 / 20.6

Pages:

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

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 (pdb code 5ds0). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 24 binding sites of Cobalt where determined in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09, PDB code: 5ds0:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 24 in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09


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 Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:28.1 occ:1.00 OD2 A:ASP180 1.8 27.9 1.0 NE2 A:HIS325 2.1 31.3 1.0 OE1 A:GLU215 2.3 33.9 1.0 OE2 A:GLU215 2.3 33.8 1.0 CD A:GLU215 2.6 33.6 1.0 CG A:ASP180 2.8 28.7 1.0 CO A:CO402 3.0 23.9 1.0 CD2 A:HIS325 3.1 31.1 1.0 CE1 A:HIS325 3.1 33.2 1.0 OD1 A:ASP180 3.2 28.4 1.0 OE1 A:GLU214 3.8 47.7 1.0 CG A:GLU215 4.1 34.2 1.0 CB A:ASP180 4.1 29.5 1.0 ND1 A:HIS325 4.2 33.4 1.0 CG A:HIS325 4.2 32.4 1.0 NE2 A:HIS66 4.3 34.7 1.0 CE1 A:HIS66 4.4 34.9 1.0 CD A:GLU214 4.9 44.8 1.0 OE1 A:GLU237 4.9 38.6 1.0 CD1 A:ILE324 5.0 33.4 1.0

Cobalt binding site 2 out of 24 in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09


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 Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:23.9 occ:1.00 NE2 A:HIS66 2.0 34.7 1.0 OD1 A:ASP180 2.0 28.4 1.0 OE2 A:GLU237 2.2 42.7 1.0 OE1 A:GLU237 2.5 38.6 1.0 CD A:GLU237 2.6 40.1 1.0 OE1 A:GLU214 2.9 47.7 1.0 CG A:ASP180 3.0 28.7 1.0 CE1 A:HIS66 3.0 34.9 1.0 CD2 A:HIS66 3.0 34.9 1.0 CO A:CO401 3.0 28.1 1.0 OD2 A:ASP180 3.2 27.9 1.0 CD A:GLU214 3.6 44.8 1.0 OE1 A:GLU215 3.9 33.9 1.0 CB A:ASP181 4.0 35.4 1.0 ND1 A:HIS66 4.1 34.8 1.0 OE2 A:GLU214 4.1 47.6 1.0 CG A:HIS66 4.1 34.5 1.0 OE2 A:GLU215 4.2 33.8 1.0 CG A:GLU237 4.2 39.9 1.0 CD A:GLU215 4.2 33.6 1.0 CB A:ASP180 4.4 29.5 1.0 CG A:GLU214 4.5 42.7 1.0 CG A:ASP181 4.7 36.7 1.0 C A:ASP180 4.8 31.2 1.0 CA A:ASP180 4.8 30.5 1.0 OD2 A:ASP181 4.8 38.6 1.0 N A:ASP181 4.8 32.7 1.0 CG2 A:VAL238 4.9 38.3 1.0 CA A:ASP181 4.9 33.6 1.0

Cobalt binding site 3 out of 24 in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09


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 Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:35.5 occ:1.00 OD2 B:ASP180 1.9 36.1 1.0 NE2 B:HIS325 2.2 35.3 1.0 OE1 B:GLU215 2.2 34.5 1.0 OE2 B:GLU215 2.2 35.0 1.0 CD B:GLU215 2.5 34.7 1.0 CG B:ASP180 2.9 35.4 1.0 CO B:CO402 3.0 27.1 1.0 CE1 B:HIS325 3.1 36.0 1.0 CD2 B:HIS325 3.2 35.7 1.0 OD1 B:ASP180 3.2 34.2 1.0 OE2 B:GLU214 3.7 45.9 1.0 CG B:GLU215 4.0 34.9 1.0 NE2 B:HIS66 4.2 36.1 1.0 CB B:ASP180 4.2 35.6 1.0 ND1 B:HIS325 4.3 36.1 1.0 CE1 B:HIS66 4.3 36.1 1.0 CG B:HIS325 4.3 35.8 1.0 CD B:GLU214 4.7 43.3 1.0 OE1 B:GLU214 4.8 42.2 1.0 OE1 B:GLU237 4.9 34.2 1.0 OE2 B:GLU237 4.9 35.6 1.0 CB B:GLU215 5.0 35.5 1.0

Cobalt binding site 4 out of 24 in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09


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 Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co402 b:27.1 occ:1.00 NE2 B:HIS66 2.0 36.1 1.0 OD1 B:ASP180 2.0 34.2 1.0 OE2 B:GLU237 2.1 35.6 1.0 OE1 B:GLU237 2.5 34.2 1.0 CD B:GLU237 2.6 36.0 1.0 OE2 B:GLU214 2.9 45.9 1.0 CE1 B:HIS66 3.0 36.1 1.0 CG B:ASP180 3.0 35.4 1.0 CD2 B:HIS66 3.0 36.4 1.0 CO B:CO401 3.0 35.5 1.0 OD2 B:ASP180 3.2 36.1 1.0 CD B:GLU214 3.6 43.3 1.0 OE1 B:GLU214 3.9 42.2 1.0 OE1 B:GLU215 3.9 34.5 1.0 CB B:ASP181 4.0 40.9 1.0 ND1 B:HIS66 4.1 36.6 1.0 CG B:HIS66 4.1 36.8 1.0 CG B:GLU237 4.2 37.8 1.0 OE2 B:GLU215 4.2 35.0 1.0 CD B:GLU215 4.2 34.7 1.0 CB B:ASP180 4.4 35.6 1.0 CG B:GLU214 4.5 43.1 1.0 CG B:ASP181 4.7 43.0 1.0 C B:ASP180 4.7 37.2 1.0 CA B:ASP180 4.8 36.0 1.0 OD2 B:ASP181 4.8 45.4 1.0 N B:ASP181 4.8 38.5 1.0 CG2 B:VAL238 4.9 42.4 1.0 CA B:ASP181 4.9 39.1 1.0

Cobalt binding site 5 out of 24 in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co401 b:22.8 occ:1.00 OD1 C:ASP180 2.0 28.4 1.0 NE2 C:HIS66 2.1 36.9 1.0 OE2 C:GLU237 2.2 35.3 1.0 OE1 C:GLU237 2.5 33.8 1.0 CD C:GLU237 2.7 35.2 1.0 CG C:ASP180 2.9 28.3 1.0 CO C:CO402 2.9 30.0 1.0 OE1 C:GLU214 3.0 42.0 1.0 CE1 C:HIS66 3.0 36.6 1.0 CD2 C:HIS66 3.1 37.2 1.0 OD2 C:ASP180 3.1 28.0 1.0 CD C:GLU214 3.7 39.4 1.0 OE2 C:GLU215 3.8 37.2 1.0 CB C:ASP181 4.1 30.4 1.0 OE2 C:GLU214 4.1 39.7 1.0 ND1 C:HIS66 4.2 36.8 1.0 CD C:GLU215 4.2 37.3 1.0 CG C:GLU237 4.2 36.0 1.0 CG C:HIS66 4.2 37.3 1.0 OE1 C:GLU215 4.3 37.2 1.0 CB C:ASP180 4.3 28.7 1.0 CG C:GLU214 4.6 38.2 1.0 C C:ASP180 4.7 29.9 1.0 CG C:ASP181 4.7 30.5 1.0 CA C:ASP180 4.8 29.2 1.0 CG2 C:VAL238 4.8 35.2 1.0 N C:ASP181 4.9 30.1 1.0 OD2 C:ASP181 4.9 30.7 1.0 CA C:ASP181 5.0 30.1 1.0

Cobalt binding site 6 out of 24 in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co402 b:30.0 occ:1.00 OD2 C:ASP180 1.9 28.0 1.0 NE2 C:HIS325 2.1 34.0 1.0 OE2 C:GLU215 2.2 37.2 1.0 OE1 C:GLU215 2.4 37.2 1.0 CD C:GLU215 2.6 37.3 1.0 CG C:ASP180 2.8 28.3 1.0 CO C:CO401 2.9 22.8 1.0 CD2 C:HIS325 3.1 33.6 1.0 CE1 C:HIS325 3.1 35.8 1.0 OD1 C:ASP180 3.2 28.4 1.0 OE1 C:GLU214 3.7 42.0 1.0 CG C:GLU215 4.1 37.0 1.0 CB C:ASP180 4.2 28.7 1.0 NE2 C:HIS66 4.2 36.9 1.0 ND1 C:HIS325 4.2 36.2 1.0 CG C:HIS325 4.3 35.0 1.0 CE1 C:HIS66 4.4 36.6 1.0 CD C:GLU214 4.8 39.4 1.0 OE1 C:GLU237 4.9 33.8 1.0 OE2 C:GLU237 5.0 35.3 1.0

Cobalt binding site 7 out of 24 in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 within 5.0Å range: probe atom residue distance (Å) B Occ D:Co401 b:24.0 occ:1.00 OD1 D:ASP180 1.9 31.2 1.0 NE2 D:HIS66 2.0 32.3 1.0 OE2 D:GLU237 2.2 34.2 1.0 OE1 D:GLU237 2.5 33.1 1.0 CD D:GLU237 2.7 34.7 1.0 CG D:ASP180 2.9 31.5 1.0 CO D:CO402 2.9 30.6 1.0 CE1 D:HIS66 3.0 32.6 1.0 OE1 D:GLU214 3.0 41.5 1.0 CD2 D:HIS66 3.0 32.4 1.0 OD2 D:ASP180 3.1 31.8 1.0 CD D:GLU214 3.7 40.1 1.0 OE2 D:GLU215 3.7 39.0 1.0 CB D:ASP181 4.0 33.6 1.0 ND1 D:HIS66 4.1 32.9 1.0 CG D:HIS66 4.1 32.8 1.0 OE2 D:GLU214 4.2 40.2 1.0 CD D:GLU215 4.2 37.7 1.0 CG D:GLU237 4.2 35.9 1.0 CB D:ASP180 4.3 31.7 1.0 OE1 D:GLU215 4.3 37.6 1.0 CG D:GLU214 4.6 38.8 1.0 C D:ASP180 4.7 32.5 1.0 CG D:ASP181 4.7 34.4 1.0 CA D:ASP180 4.7 32.0 1.0 N D:ASP181 4.8 33.0 1.0 OD2 D:ASP181 4.8 35.8 1.0 CG2 D:VAL238 4.8 35.1 1.0 CA D:ASP181 4.9 33.3 1.0

Cobalt binding site 8 out of 24 in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 within 5.0Å range: probe atom residue distance (Å) B Occ D:Co402 b:30.6 occ:1.00 OD2 D:ASP180 1.9 31.8 1.0 OE2 D:GLU215 2.1 39.0 1.0 NE2 D:HIS325 2.2 31.5 1.0 OE1 D:GLU215 2.4 37.6 1.0 CD D:GLU215 2.6 37.7 1.0 CG D:ASP180 2.8 31.5 1.0 CO D:CO401 2.9 24.0 1.0 CE1 D:HIS325 3.1 33.3 1.0 CD2 D:HIS325 3.1 31.4 1.0 OD1 D:ASP180 3.2 31.2 1.0 OE1 D:GLU214 3.7 41.5 1.0 CG D:GLU215 4.1 37.5 1.0 NE2 D:HIS66 4.2 32.3 1.0 CB D:ASP180 4.2 31.7 1.0 ND1 D:HIS325 4.3 34.0 1.0 CE1 D:HIS66 4.3 32.6 1.0 CG D:HIS325 4.3 33.0 1.0 CD D:GLU214 4.8 40.1 1.0 OE1 D:GLU237 4.9 33.1 1.0 OE2 D:GLU237 4.9 34.2 1.0

Cobalt binding site 9 out of 24 in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 within 5.0Å range: probe atom residue distance (Å) B Occ E:Co401 b:27.4 occ:1.00 NE2 E:HIS66 1.9 31.7 1.0 OD1 E:ASP180 1.9 37.9 1.0 OE2 E:GLU237 2.2 38.8 1.0 OE1 E:GLU237 2.5 35.1 1.0 CD E:GLU237 2.7 37.1 1.0 CE1 E:HIS66 2.9 32.6 1.0 CG E:ASP180 2.9 37.5 1.0 CD2 E:HIS66 2.9 32.0 1.0 OE1 E:GLU214 3.0 45.5 1.0 CO E:CO402 3.1 30.8 1.0 OD2 E:ASP180 3.2 38.5 1.0 CD E:GLU214 3.7 44.7 1.0 OE2 E:GLU215 3.7 37.6 1.0 CB E:ASP181 3.9 36.0 1.0 ND1 E:HIS66 4.0 32.7 1.0 CG E:HIS66 4.1 32.9 1.0 CD E:GLU215 4.1 37.3 1.0 OE2 E:GLU214 4.2 46.1 1.0 CG E:GLU237 4.2 37.4 1.0 CB E:ASP180 4.3 36.6 1.0 OE1 E:GLU215 4.3 37.4 1.0 CG E:GLU214 4.6 43.9 1.0 C E:ASP180 4.6 36.1 1.0 CG E:ASP181 4.6 36.6 1.0 CA E:ASP180 4.7 36.4 1.0 N E:ASP181 4.7 35.8 1.0 OD2 E:ASP181 4.8 37.7 1.0 CA E:ASP181 4.8 35.7 1.0 CG2 E:VAL238 4.9 38.0 1.0

Cobalt binding site 10 out of 24 in the Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 within 5.0Å range: probe atom residue distance (Å) B Occ E:Co402 b:30.8 occ:1.00 OD2 E:ASP180 1.9 38.5 1.0 NE2 E:HIS325 2.0 33.8 1.0 OE2 E:GLU215 2.2 37.6 1.0 OE1 E:GLU215 2.4 37.4 1.0 CD E:GLU215 2.6 37.3 1.0 CG E:ASP180 2.9 37.5 1.0 CD2 E:HIS325 3.0 33.7 1.0 CE1 E:HIS325 3.0 35.7 1.0 CO E:CO401 3.1 27.4 1.0 OD1 E:ASP180 3.3 37.9 1.0 OE1 E:GLU214 3.8 45.5 1.0 CG E:GLU215 4.1 37.5 1.0 ND1 E:HIS325 4.1 36.1 1.0 CG E:HIS325 4.2 34.9 1.0 CB E:ASP180 4.2 36.6 1.0 NE2 E:HIS66 4.3 31.7 1.0 CE1 E:HIS66 4.4 32.6 1.0 CD E:GLU214 4.9 44.7 1.0 OE1 E:GLU237 5.0 35.1 1.0 CD1 E:ILE324 5.0 32.4 1.0

K.Michalska, G.Chhor, J.Mootz, M.Endres, R.Jedrzejczak, G.Babnigg, A.Steen, K.Lloyd, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). Crystal Structure of Tet Aminopeptidase From Marine Sediment Archaeon Thaumarchaeota Archaeon Scgc Ab-539-E09 To Be Published.