Cobalt in PDB 4rdy: Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl

The structure of Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl, PDB code: 4rdy was solved by J.Hiblot, J.Bzdrenga, C.Champion, G.Gotthard, D.Gonzalez, E.Chabriere, M.Elias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.75 / 2.00
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	174.740, 174.740, 61.550, 90.00, 90.00, 120.00
R / Rfree (%)	13.9 / 17.4

The binding sites of Cobalt atom in the Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl (pdb code 4rdy). 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 Vmolac Bound to 3-Oxo-C10 Ahl, PDB code: 4rdy:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl


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 Vmolac Bound to 3-Oxo-C10 Ahl within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:17.3 occ:1.00 O A:HOH830 1.8 17.8 1.0 OD1 A:ASP257 2.1 14.2 1.0 OQ2 A:KCX138 2.1 15.8 1.0 NE2 A:HIS25 2.1 13.9 1.0 NE2 A:HIS23 2.2 14.7 1.0 OAC A:3M5403 2.4 44.3 0.8 CAB A:3M5403 2.8 40.5 0.8 CX A:KCX138 3.0 14.8 1.0 CG A:ASP257 3.0 15.3 1.0 CD2 A:HIS23 3.0 13.5 1.0 CE1 A:HIS25 3.1 13.2 1.0 CD2 A:HIS25 3.1 13.3 1.0 CE1 A:HIS23 3.2 14.0 1.0 OD2 A:ASP257 3.3 19.2 1.0 OQ1 A:KCX138 3.3 15.3 1.0 CO A:CO402 3.5 18.5 1.0 C A:3M5403 3.6 41.0 0.8 NZ A:KCX138 4.1 14.4 1.0 O A:3M5403 4.1 30.3 0.8 ND1 A:HIS25 4.2 14.3 1.0 CB A:3M5403 4.2 49.9 0.8 CG A:HIS23 4.2 13.2 1.0 CG A:HIS25 4.3 13.9 1.0 ND1 A:HIS23 4.3 14.0 1.0 CB A:LEU68 4.3 14.5 1.0 CB A:ASP257 4.4 14.4 1.0 CE1 A:HIS200 4.5 13.5 1.0 CA A:3M5403 4.6 48.5 0.8 NE2 A:HIS200 4.7 14.1 1.0 CA A:ASP257 4.8 14.7 1.0 OAL A:3M5403 5.0 46.5 0.8

Cobalt binding site 2 out of 4 in the Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl


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 Vmolac Bound to 3-Oxo-C10 Ahl within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:18.5 occ:1.00 OQ1 A:KCX138 1.9 15.3 1.0 O A:HOH830 2.1 17.8 1.0 ND1 A:HIS171 2.1 13.2 1.0 NE2 A:HIS200 2.2 14.1 1.0 O A:3M5403 2.4 30.3 0.8 CX A:KCX138 3.0 14.8 1.0 CE1 A:HIS171 3.0 14.9 1.0 C A:3M5403 3.0 41.0 0.8 CE1 A:HIS200 3.1 13.5 1.0 CG A:HIS171 3.1 14.1 1.0 OAC A:3M5403 3.2 44.3 0.8 CD2 A:HIS200 3.2 14.1 1.0 OQ2 A:KCX138 3.4 15.8 1.0 CB A:HIS171 3.4 13.5 1.0 CO A:CO401 3.5 17.3 1.0 NH1 A:ARG224 3.6 26.9 1.0 CE1 A:HIS23 4.0 14.0 1.0 NE2 A:HIS23 4.1 14.7 1.0 NZ A:KCX138 4.1 14.4 1.0 NE2 A:HIS171 4.1 15.9 1.0 OH A:TYR98 4.2 16.4 1.0 CD2 A:HIS171 4.2 15.0 1.0 ND1 A:HIS200 4.2 13.9 1.0 OD2 A:ASP257 4.2 19.2 1.0 CG A:HIS200 4.3 14.0 1.0 CA A:3M5403 4.3 48.5 0.8 CA A:HIS171 4.3 14.6 1.0 CE2 A:TYR98 4.3 14.2 1.0 CAB A:3M5403 4.4 40.5 0.8 CZ A:ARG224 4.5 19.5 1.0 CE A:KCX138 4.7 13.9 1.0 CZ A:TYR98 4.7 16.4 1.0 OD1 A:ASP257 4.8 14.2 1.0 NE A:ARG224 4.9 20.9 1.0 N A:3M5403 4.9 43.5 0.8 CG A:ASP257 4.9 15.3 1.0 CB A:3M5403 5.0 49.9 0.8

Cobalt binding site 3 out of 4 in the Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl


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 Vmolac Bound to 3-Oxo-C10 Ahl within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:16.3 occ:1.00 O B:HOH829 1.9 17.8 1.0 OD1 B:ASP257 2.0 14.0 1.0 OQ1 B:KCX138 2.1 18.8 1.0 NE2 B:HIS23 2.1 14.9 1.0 NE2 B:HIS25 2.1 15.1 1.0 OAC B:3M5403 2.6 46.4 0.8 CAB B:3M5403 2.9 42.5 0.8 CG B:ASP257 3.0 15.0 1.0 CD2 B:HIS23 3.0 13.8 1.0 CX B:KCX138 3.0 17.2 1.0 CE1 B:HIS25 3.1 14.0 1.0 CE1 B:HIS23 3.1 14.7 1.0 CD2 B:HIS25 3.1 13.7 1.0 OD2 B:ASP257 3.3 18.4 1.0 OQ2 B:KCX138 3.4 14.2 1.0 CO B:CO402 3.5 17.8 1.0 C B:3M5403 3.7 41.8 0.8 O B:3M5403 4.0 34.1 0.8 ND1 B:HIS23 4.2 15.2 1.0 NZ B:KCX138 4.2 14.6 1.0 CG B:HIS23 4.2 14.1 1.0 ND1 B:HIS25 4.2 13.1 1.0 CG B:HIS25 4.3 13.0 1.0 CB B:3M5403 4.3 55.6 0.8 CB B:ASP257 4.3 14.2 1.0 CB B:LEU68 4.4 15.2 1.0 CE1 B:HIS200 4.6 14.6 1.0 NE2 B:HIS200 4.7 14.5 1.0 CA B:3M5403 4.7 53.8 0.8 CA B:ASP257 4.8 16.3 1.0 OAL B:3M5403 4.9 44.1 0.8 O B:ASP257 5.0 15.8 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl


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 Vmolac Bound to 3-Oxo-C10 Ahl within 5.0Å range: probe atom residue distance (Å) B Occ B:Co402 b:17.8 occ:1.00 OQ2 B:KCX138 1.9 14.2 1.0 O B:HOH829 2.0 17.8 1.0 ND1 B:HIS171 2.1 13.7 1.0 NE2 B:HIS200 2.2 14.5 1.0 O B:3M5403 2.3 34.1 0.8 CX B:KCX138 3.0 17.2 1.0 CE1 B:HIS171 3.0 13.4 1.0 CE1 B:HIS200 3.1 14.6 1.0 C B:3M5403 3.1 41.8 0.8 CG B:HIS171 3.2 12.9 1.0 CD2 B:HIS200 3.2 13.8 1.0 OQ1 B:KCX138 3.3 18.8 1.0 OAC B:3M5403 3.4 46.4 0.8 CO B:CO401 3.5 16.3 1.0 CB B:HIS171 3.5 14.1 1.0 NH1 B:ARG224 3.7 28.4 1.0 CE1 B:HIS23 3.9 14.7 1.0 NE2 B:HIS23 4.1 14.9 1.0 OH B:TYR98 4.2 16.0 1.0 NE2 B:HIS171 4.2 14.1 1.0 NZ B:KCX138 4.2 14.6 1.0 OD2 B:ASP257 4.2 18.4 1.0 ND1 B:HIS200 4.2 13.3 1.0 CD2 B:HIS171 4.3 15.5 1.0 CE2 B:TYR98 4.3 14.9 1.0 CG B:HIS200 4.3 13.9 1.0 CA B:HIS171 4.3 14.8 1.0 CA B:3M5403 4.3 53.8 0.8 CZ B:ARG224 4.4 21.8 1.0 CAB B:3M5403 4.4 42.5 0.8 CE B:KCX138 4.6 13.3 1.0 CZ B:TYR98 4.7 15.3 1.0 OD1 B:ASP257 4.8 14.0 1.0 NE B:ARG224 4.8 21.5 1.0 N B:3M5403 4.9 51.6 0.8 CG B:ASP257 4.9 15.0 1.0

J.Hiblot, J.Bzdrenga, C.Champion, E.Chabriere, M.Elias. Crystal Structure of Vmolac, A Tentative Quorum Quenching Lactonase From the Extremophilic Crenarchaeon Vulcanisaeta Moutnovskia. Sci Rep V. 5 8372 2015.
ISSN: ESSN 2045-2322
PubMed: 25670483
DOI: 10.1038/SREP08372