Cobalt in PDB 1w8q: Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39

All present enzymatic activity of Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39:
3.4.16.4;

The structure of Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39, PDB code: 1w8q was solved by E.Sauvage, R.Herman, S.Petrella, C.Duez, J.M.Frere, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 2.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.560, 94.370, 106.960, 90.00, 94.05, 90.00
R / Rfree (%)	19.7 / 24.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 (pdb code 1w8q). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 18 binding sites of Cobalt where determined in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39, PDB code: 1w8q:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 18 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co510 b:54.1 occ:1.00 O A:GLU188 2.0 34.1 1.0 OE1 A:GLU251 2.0 43.7 1.0 NE2 A:HIS247 2.2 37.6 1.0 CD A:GLU251 2.8 43.3 1.0 OE2 A:GLU251 3.0 44.8 1.0 CD2 A:HIS247 3.1 35.5 1.0 C A:GLU188 3.2 35.8 1.0 CE1 A:HIS247 3.3 37.4 1.0 O A:ALA186 3.9 34.7 1.0 CB A:GLU188 3.9 40.6 1.0 CA A:GLU188 4.0 36.8 1.0 N A:GLY189 4.1 36.9 1.0 CA A:GLY189 4.2 37.9 1.0 CG A:GLU251 4.2 42.1 1.0 N A:GLU188 4.3 37.2 1.0 CG A:HIS247 4.3 35.3 1.0 ND1 A:HIS247 4.3 36.8 1.0 C A:GLY189 4.7 38.4 1.0 N A:TYR190 4.8 39.1 1.0 C A:ALA187 4.9 35.8 1.0 C A:ALA186 5.0 33.4 1.0

Cobalt binding site 2 out of 18 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co511 b:46.8 occ:1.00 ND1 A:HIS462 2.0 28.8 1.0 CE1 A:HIS462 2.8 27.8 1.0 CG A:HIS462 3.1 29.9 1.0 CG2 A:VAL406 3.6 39.0 1.0 CB A:HIS462 3.6 31.4 1.0 NE2 A:HIS462 4.0 27.5 1.0 CD2 A:HIS462 4.2 29.1 1.0 CA A:HIS462 4.2 34.4 1.0 O A:ALA402 4.5 40.1 1.0 N A:GLN463 4.7 37.2 1.0 O A:GLN463 4.7 41.1 1.0 C A:HIS462 4.9 35.7 1.0 CB A:VAL406 5.0 39.4 1.0

Cobalt binding site 3 out of 18 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co512 b:93.6 occ:1.00 O A:LEU63 2.2 35.1 1.0 ND1 A:HIS67 2.7 35.3 1.0 OD1 A:ASP66 3.1 45.5 1.0 CB A:HIS67 3.2 33.1 1.0 C A:LEU63 3.3 33.4 1.0 CG A:HIS67 3.4 33.6 1.0 CA A:HIS67 3.6 33.7 1.0 CA A:LEU63 3.8 33.7 1.0 N A:HIS67 3.9 34.3 1.0 CE1 A:HIS67 3.9 34.9 1.0 CG A:ASP66 4.3 46.7 1.0 N A:GLY64 4.4 33.0 1.0 CB A:LEU63 4.5 34.2 1.0 O A:GLY64 4.6 35.1 1.0 CD2 A:HIS67 4.7 35.3 1.0 CA A:GLY64 4.8 34.4 1.0 O A:VAL62 4.9 35.4 1.0 NE2 A:HIS67 4.9 36.4 1.0 C A:ASP66 5.0 35.8 1.0

Cobalt binding site 4 out of 18 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co513 b:0.4 occ:1.00 NE2 A:HIS158 2.4 35.0 1.0 OE2 A:GLU168 2.8 50.1 1.0 O3 A:SO4504 2.9 73.4 1.0 CE1 A:HIS158 3.3 34.1 1.0 OE1 A:GLU168 3.4 50.0 1.0 CD2 A:HIS158 3.4 34.5 1.0 CD A:GLU168 3.5 46.9 1.0 S A:SO4504 4.2 74.6 1.0 O2 A:SO4504 4.4 71.0 1.0 ND1 A:HIS158 4.4 34.2 1.0 CG A:HIS158 4.5 34.6 1.0 CG A:GLU168 4.9 42.7 1.0 O4 A:SO4504 4.9 72.4 1.0

Cobalt binding site 5 out of 18 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co514 b:83.8 occ:1.00 NE2 A:HIS282 2.3 36.2 1.0 OD1 A:ASP102 2.5 42.9 1.0 CE1 A:HIS282 3.1 35.3 1.0 CG A:ASP102 3.4 42.4 1.0 CD2 A:HIS282 3.4 36.4 1.0 OD2 A:ASP102 3.6 40.9 1.0 O A:HOH2005 3.6 30.4 1.0 O A:THR97 3.8 36.5 1.0 OG1 A:THR97 4.0 37.2 1.0 OD2 A:ASP95 4.2 44.9 1.0 CA A:SER284 4.2 32.1 1.0 ND1 A:HIS282 4.2 35.7 1.0 CB A:SER284 4.4 31.7 1.0 CG A:HIS282 4.4 36.3 1.0 C A:THR97 4.4 34.9 1.0 O A:THR283 4.6 29.3 1.0 CB A:ASP102 4.6 41.3 1.0 CB A:THR97 4.8 35.3 1.0 CA A:LEU98 4.8 32.2 1.0 N A:SER284 4.9 30.8 1.0 N A:LEU98 4.9 33.1 1.0

Cobalt binding site 6 out of 18 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co510 b:88.6 occ:1.00 O B:GLU188 2.2 35.4 1.0 OE2 B:GLU251 2.4 58.0 1.0 NE2 B:HIS247 2.4 47.2 1.0 CD B:GLU251 3.0 55.4 1.0 OE1 B:GLU251 3.2 56.0 1.0 CE1 B:HIS247 3.3 48.1 1.0 C B:GLU188 3.4 33.8 1.0 CD2 B:HIS247 3.4 46.4 1.0 CA B:GLY189 4.2 33.0 1.0 N B:GLY189 4.2 33.3 1.0 CB B:GLU188 4.4 36.3 1.0 CA B:GLU188 4.4 34.2 1.0 CG B:GLU251 4.4 52.9 1.0 ND1 B:HIS247 4.5 47.4 1.0 CG B:HIS247 4.5 46.1 1.0 C B:GLY189 4.7 34.7 1.0 N B:GLU188 4.7 34.3 1.0 O B:ALA186 4.7 33.0 1.0 N B:TYR190 5.0 36.5 1.0

Cobalt binding site 7 out of 18 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co512 b:0.7 occ:1.00 ND1 B:HIS67 2.4 49.9 1.0 O B:LEU63 2.7 55.0 1.0 CG B:HIS67 3.3 50.0 1.0 OE2 B:GLU313 3.3 65.9 1.0 CE1 B:HIS67 3.4 50.0 1.0 CB B:HIS67 3.4 51.5 1.0 C B:LEU63 3.5 53.2 1.0 CA B:LEU63 3.5 52.3 1.0 CB B:LEU63 4.1 51.6 1.0 CD2 B:LEU63 4.3 49.8 1.0 CA B:HIS67 4.3 52.5 1.0 CD2 B:HIS67 4.4 50.7 1.0 NE2 B:HIS67 4.4 50.8 1.0 O B:VAL62 4.5 53.2 1.0 CD B:GLU313 4.5 64.9 1.0 N B:GLY64 4.8 53.2 1.0 N B:LEU63 4.8 52.0 1.0 CG B:LEU63 4.8 50.9 1.0 N B:HIS67 5.0 54.6 1.0

Cobalt binding site 8 out of 18 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co513 b:0.2 occ:1.00 NE2 B:HIS158 2.2 46.7 1.0 OE2 B:GLU168 2.9 56.4 1.0 CE1 B:HIS158 3.2 45.3 1.0 CD2 B:HIS158 3.2 44.5 1.0 CD B:GLU168 3.6 54.5 1.0 O1 B:SO4504 3.9 81.2 1.0 OE1 B:GLU168 4.0 58.5 1.0 ND1 B:HIS158 4.3 46.5 1.0 CG B:HIS158 4.3 44.7 1.0 CG B:GLU168 4.5 48.5 1.0 CB B:GLU168 4.8 43.0 1.0 CD2 B:LEU235 4.9 16.4 1.0

Cobalt binding site 9 out of 18 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co514 b:84.7 occ:1.00 NE2 B:HIS282 1.9 51.6 1.0 OD2 B:ASP102 2.0 54.2 1.0 CE1 B:HIS282 2.7 50.7 1.0 CG B:ASP102 2.7 52.1 1.0 OD1 B:ASP102 3.0 52.9 1.0 CD2 B:HIS282 3.0 51.2 1.0 ND1 B:HIS282 3.8 51.9 1.0 CB B:ASP102 3.9 51.1 1.0 CG B:HIS282 4.0 50.7 1.0 O B:THR97 4.1 49.2 1.0 O B:THR283 4.6 49.2 1.0 OD2 B:ASP95 4.6 50.5 1.0 OG1 B:THR97 4.8 48.2 1.0 C B:THR97 4.9 48.5 1.0 OG B:SER99 4.9 43.0 1.0 CA B:SER284 4.9 51.5 1.0 N B:SER99 5.0 44.4 1.0 CA B:LEU98 5.0 45.1 1.0

Cobalt binding site 10 out of 18 in the Crystal Structure of the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39


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 the Dd-Transpeptidase-Carboxypeptidase From Actinomadura R39 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co510 b:85.7 occ:1.00 NE2 C:HIS247 2.2 44.5 1.0 O C:GLU188 2.4 43.0 1.0 OE1 C:GLU251 2.6 45.0 1.0 OE2 C:GLU251 2.9 47.9 1.0 CD C:GLU251 3.0 45.8 1.0 CE1 C:HIS247 3.1 44.6 1.0 CD2 C:HIS247 3.3 43.6 1.0 C C:GLU188 3.4 41.8 1.0 ND1 C:HIS247 4.2 44.3 1.0 CB C:GLU188 4.3 41.4 1.0 N C:GLY189 4.3 42.2 1.0 CA C:GLY189 4.3 42.2 1.0 CG C:GLU251 4.3 46.1 1.0 CA C:GLU188 4.3 40.9 1.0 CG C:HIS247 4.3 43.1 1.0 O C:ALA186 4.6 41.0 1.0 N C:GLU188 4.6 39.2 1.0 C C:GLY189 4.6 42.6 1.0 N C:TYR190 4.9 42.8 1.0

E.Sauvage, R.Herman, S.Petrella, C.Duez, F.Bouillenne, J.M.Frere, P.Charlier. Crystal Structure of the Actinomadura R39 Dd- Peptidase Reveals New Domains in Penicillin- Binding Proteins. J.Biol.Chem. V. 280 31249 2005.
ISSN: ISSN 0021-9258
PubMed: 15987687
DOI: 10.1074/JBC.M503271200