Cobalt in PDB 4rdz: Crystal Structure of Vmolac in P64 Space Group

The structure of Crystal Structure of Vmolac in P64 Space Group, PDB code: 4rdz 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)	48.01 / 1.80
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	174.960, 174.960, 62.070, 90.00, 90.00, 120.00
R / Rfree (%)	13 / 16

The binding sites of Cobalt atom in the Crystal Structure of Vmolac in P64 Space Group (pdb code 4rdz). 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 in P64 Space Group, PDB code: 4rdz:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Vmolac in P64 Space Group


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 in P64 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:14.3 occ:1.00 O A:HOH985 1.9 17.7 1.0 OQ1 A:KCX138 2.0 14.5 1.0 OD1 A:ASP257 2.1 13.1 1.0 NE2 A:HIS25 2.1 13.6 1.0 O1 A:MYR404 2.2 25.5 1.0 NE2 A:HIS23 2.2 14.8 1.0 CE1 A:HIS25 3.0 12.7 1.0 CG A:ASP257 3.0 13.5 1.0 CX A:KCX138 3.1 14.5 1.0 CD2 A:HIS23 3.1 15.2 1.0 CD2 A:HIS25 3.2 12.3 1.0 CE1 A:HIS23 3.2 15.8 1.0 C1 A:MYR404 3.2 30.9 1.0 OD2 A:ASP257 3.3 14.4 1.0 OQ2 A:KCX138 3.4 13.1 1.0 CO A:CO402 3.4 16.0 1.0 O2 A:MYR404 3.6 25.6 1.0 ND1 A:HIS25 4.1 13.2 1.0 NZ A:KCX138 4.2 13.4 1.0 CG A:HIS25 4.2 12.6 1.0 ND1 A:HIS23 4.3 14.4 1.0 CG A:HIS23 4.3 13.2 1.0 CB A:LEU68 4.4 12.2 1.0 CB A:ASP257 4.4 12.8 1.0 C2 A:MYR404 4.5 32.5 1.0 CE1 A:HIS200 4.6 15.3 1.0 C3 A:MYR404 4.7 38.4 1.0 NE2 A:HIS200 4.7 14.8 1.0 CA A:ASP257 4.8 13.1 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Vmolac in P64 Space Group


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 in P64 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:16.0 occ:1.00 OQ2 A:KCX138 2.0 13.1 1.0 O A:HOH985 2.0 17.7 1.0 ND1 A:HIS171 2.1 12.9 1.0 NE2 A:HIS200 2.2 14.8 1.0 O2 A:MYR404 2.3 25.6 1.0 CE1 A:HIS171 3.0 13.4 1.0 CX A:KCX138 3.0 14.5 1.0 CE1 A:HIS200 3.1 15.3 1.0 CG A:HIS171 3.1 13.0 1.0 C1 A:MYR404 3.2 30.9 1.0 OQ1 A:KCX138 3.2 14.5 1.0 CD2 A:HIS200 3.3 14.0 1.0 CO A:CO401 3.4 14.3 1.0 CB A:HIS171 3.5 13.4 1.0 O1 A:MYR404 3.6 25.5 1.0 NH1 A:ARG224 3.6 15.5 1.0 CE1 A:HIS23 3.9 15.8 1.0 OH A:TYR98 4.1 16.0 1.0 NE2 A:HIS23 4.1 14.8 1.0 NE2 A:HIS171 4.2 14.3 1.0 OD2 A:ASP257 4.2 14.4 1.0 NZ A:KCX138 4.2 13.4 1.0 CD2 A:HIS171 4.2 14.1 1.0 ND1 A:HIS200 4.2 13.3 1.0 CE2 A:TYR98 4.2 14.2 1.0 CA A:HIS171 4.3 12.8 1.0 CG A:HIS200 4.4 12.9 1.0 CZ A:ARG224 4.4 16.1 1.0 C2 A:MYR404 4.5 32.5 1.0 CZ A:TYR98 4.6 15.5 1.0 OD1 A:ASP257 4.7 13.1 1.0 CE A:KCX138 4.8 13.0 1.0 NE A:ARG224 4.8 14.5 1.0 CG A:ASP257 4.8 13.5 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Vmolac in P64 Space Group


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 in P64 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:14.4 occ:1.00 O B:HOH1007 1.9 17.6 1.0 OQ1 B:KCX138 2.0 13.4 1.0 OD1 B:ASP257 2.1 12.9 1.0 NE2 B:HIS25 2.1 13.1 1.0 NE2 B:HIS23 2.2 14.8 1.0 O2 B:MYR404 2.2 29.5 1.0 CE1 B:HIS25 3.0 12.7 1.0 CG B:ASP257 3.0 16.2 1.0 CX B:KCX138 3.0 14.0 1.0 CD2 B:HIS25 3.1 12.8 1.0 CE1 B:HIS23 3.1 14.8 1.0 CD2 B:HIS23 3.2 15.9 1.0 C1 B:MYR404 3.2 33.1 1.0 OD2 B:ASP257 3.3 15.1 1.0 OQ2 B:KCX138 3.4 13.6 1.0 CO B:CO402 3.4 15.9 1.0 O1 B:MYR404 3.6 25.9 1.0 ND1 B:HIS25 4.2 13.9 1.0 NZ B:KCX138 4.2 13.6 1.0 CG B:HIS25 4.2 14.2 1.0 ND1 B:HIS23 4.3 15.8 1.0 CG B:HIS23 4.3 15.2 1.0 CB B:LEU68 4.4 13.3 1.0 CB B:ASP257 4.4 14.2 1.0 CE1 B:HIS200 4.5 15.0 1.0 C2 B:MYR404 4.5 34.0 1.0 NE2 B:HIS200 4.6 15.2 1.0 C4 B:MYR404 4.7 41.1 1.0 CA B:ASP257 4.8 13.1 1.0 C3 B:MYR404 4.8 41.1 1.0 O B:ASP257 5.0 13.4 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Vmolac in P64 Space Group


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 in P64 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Co402 b:15.9 occ:1.00 O B:HOH1007 1.9 17.6 1.0 OQ2 B:KCX138 2.0 13.6 1.0 ND1 B:HIS171 2.1 12.6 1.0 NE2 B:HIS200 2.1 15.2 1.0 O1 B:MYR404 2.3 25.9 1.0 CX B:KCX138 3.0 14.0 1.0 CE1 B:HIS171 3.0 16.1 1.0 CE1 B:HIS200 3.0 15.0 1.0 CG B:HIS171 3.1 13.2 1.0 C1 B:MYR404 3.2 33.1 1.0 CD2 B:HIS200 3.2 15.4 1.0 OQ1 B:KCX138 3.2 13.4 1.0 CO B:CO401 3.4 14.4 1.0 CB B:HIS171 3.5 12.9 1.0 O2 B:MYR404 3.6 29.5 1.0 NH1 B:ARG224 3.7 16.8 1.0 CE1 B:HIS23 3.9 14.8 1.0 OH B:TYR98 4.1 15.7 1.0 NE2 B:HIS171 4.1 14.6 1.0 NE2 B:HIS23 4.2 14.8 1.0 NZ B:KCX138 4.2 13.6 1.0 OD2 B:ASP257 4.2 15.1 1.0 ND1 B:HIS200 4.2 14.5 1.0 CD2 B:HIS171 4.2 13.7 1.0 CE2 B:TYR98 4.3 14.4 1.0 CA B:HIS171 4.3 12.8 1.0 CG B:HIS200 4.3 13.5 1.0 CZ B:ARG224 4.5 14.9 1.0 C2 B:MYR404 4.5 34.0 1.0 CZ B:TYR98 4.6 14.4 1.0 OD1 B:ASP257 4.7 12.9 1.0 CE B:KCX138 4.7 13.0 1.0 NE B:ARG224 4.8 14.8 1.0 CG B:ASP257 4.8 16.2 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