Cobalt in PDB 3h7y: Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form

The structure of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form, PDB code: 3h7y was solved by M.Rajavel, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.33 / 2.22
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.661, 68.661, 211.525, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 26

The structure of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Cobalt atom in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form (pdb code 3h7y). 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 Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form, PDB code: 3h7y:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form


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 Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co244 b:14.3 occ:1.00 O A:HOH328 2.1 13.7 1.0 NE2 A:HIS50 2.2 13.7 1.0 OE1 A:GLN56 2.2 7.8 1.0 O A:HOH327 2.2 12.7 1.0 NE2 A:HIS91 2.2 4.1 1.0 NE2 A:HIS52 2.2 8.0 1.0 CE1 A:HIS91 3.1 3.7 1.0 CD A:GLN56 3.1 7.1 1.0 CD2 A:HIS50 3.1 12.8 1.0 CE1 A:HIS50 3.2 13.9 1.0 CE1 A:HIS52 3.2 7.9 1.0 CD2 A:HIS52 3.2 7.5 1.0 CD2 A:HIS91 3.3 4.3 1.0 NE2 A:GLN56 3.5 5.8 1.0 CD A:LYS107 4.2 16.5 1.0 ND1 A:HIS91 4.3 3.3 1.0 ND1 A:HIS50 4.3 13.3 1.0 CG A:HIS50 4.3 12.5 1.0 ND1 A:HIS52 4.3 8.4 1.0 CG A:HIS91 4.4 3.9 1.0 CG A:HIS52 4.4 8.8 1.0 CG A:GLN56 4.5 6.6 1.0 O A:HOH266 4.6 32.5 1.0 CB A:GLN56 4.7 6.2 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form


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 Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co245 b:11.1 occ:1.00 O1 A:PPY246 2.1 8.9 1.0 O3 A:PPY246 2.1 10.2 1.0 NE2 A:HIS202 2.2 3.2 1.0 OE1 A:GLN168 2.2 7.0 1.0 NE2 A:HIS164 2.2 7.1 1.0 NE2 A:HIS162 2.3 9.9 1.0 C2 A:PPY246 2.8 9.8 1.0 C1 A:PPY246 2.8 10.1 1.0 CE1 A:HIS162 3.1 11.2 1.0 CE1 A:HIS202 3.1 2.3 1.0 CD A:GLN168 3.1 6.8 1.0 CD2 A:HIS202 3.1 2.9 1.0 CE1 A:HIS164 3.2 7.0 1.0 CD2 A:HIS164 3.2 7.4 1.0 CD2 A:HIS162 3.3 10.8 1.0 NE2 A:GLN168 3.4 6.7 1.0 O2 A:PPY246 4.0 9.4 1.0 ND1 A:HIS202 4.2 3.6 1.0 ND1 A:HIS162 4.2 11.7 1.0 C3 A:PPY246 4.3 11.4 1.0 CG A:HIS202 4.3 3.9 1.0 ND1 A:HIS164 4.3 7.0 1.0 CG A:HIS164 4.3 7.8 1.0 CE1 A:PHE218 4.4 5.4 1.0 CG A:HIS162 4.4 10.5 1.0 CG A:GLN168 4.5 7.3 1.0 C6' A:PPY246 4.7 12.8 1.0 CZ A:PHE218 4.7 5.8 1.0 CB A:GLN168 4.9 8.3 1.0 C1' A:PPY246 5.0 13.0 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form


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 Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Co244 b:19.2 occ:1.00 O B:HOH282 2.0 19.7 1.0 OE1 B:GLN56 2.1 9.3 1.0 NE2 B:HIS91 2.2 8.0 1.0 NE2 B:HIS50 2.2 16.2 1.0 NE2 B:HIS52 2.3 11.4 1.0 O B:HOH267 2.6 35.4 1.0 CD B:GLN56 3.1 8.7 1.0 CD2 B:HIS52 3.1 11.1 1.0 CD2 B:HIS50 3.2 15.8 1.0 CE1 B:HIS91 3.2 7.3 1.0 CD2 B:HIS91 3.2 7.4 1.0 CE1 B:HIS50 3.3 16.1 1.0 CE1 B:HIS52 3.3 11.2 1.0 NE2 B:GLN56 3.4 8.8 1.0 ND1 B:HIS91 4.3 7.3 1.0 CG B:HIS91 4.3 7.6 1.0 CG B:HIS52 4.3 11.2 1.0 CG B:HIS50 4.3 14.8 1.0 CD B:LYS107 4.3 21.4 1.0 ND1 B:HIS50 4.4 15.7 1.0 ND1 B:HIS52 4.4 11.0 1.0 CG B:GLN56 4.4 8.9 1.0 CB B:GLN56 4.7 9.4 1.0 O B:HOH268 4.8 14.5 1.0 NZ B:LYS107 4.9 23.1 1.0 CG B:LYS107 4.9 20.0 1.0 CE B:LYS107 4.9 22.0 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form


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 Bacb, An Enzyme Involved in Bacilysin Synthesis, in Tetragonal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Co245 b:22.0 occ:1.00 O2 B:PPY246 1.9 14.1 1.0 NE2 B:HIS202 2.1 10.3 1.0 O3 B:PPY246 2.2 14.7 1.0 OE1 B:GLN168 2.3 10.6 1.0 NE2 B:HIS164 2.3 10.2 1.0 NE2 B:HIS162 2.5 14.4 1.0 C1 B:PPY246 2.7 14.6 1.0 C2 B:PPY246 2.8 14.8 1.0 CE1 B:HIS202 3.1 10.0 1.0 CD B:GLN168 3.1 10.1 1.0 CD2 B:HIS202 3.1 9.9 1.0 CE1 B:HIS164 3.2 10.9 1.0 CE1 B:HIS162 3.2 15.1 1.0 CD2 B:HIS164 3.2 10.9 1.0 NE2 B:GLN168 3.3 9.3 1.0 CD2 B:HIS162 3.5 14.7 1.0 O1 B:PPY246 3.9 14.2 1.0 ND1 B:HIS202 4.2 10.1 1.0 C3 B:PPY246 4.3 16.3 1.0 CG B:HIS202 4.3 10.1 1.0 ND1 B:HIS164 4.3 11.5 1.0 CE1 B:PHE218 4.3 9.1 1.0 ND1 B:HIS162 4.4 14.9 1.0 CG B:HIS164 4.4 11.6 1.0 CG B:GLN168 4.5 10.2 1.0 CG B:HIS162 4.6 14.4 1.0 C2' B:PPY246 4.6 17.8 1.0 CZ B:PHE218 4.8 9.3 1.0 CB B:GLN168 4.9 11.1 1.0 NE B:ARG222 4.9 19.1 1.0 C1' B:PPY246 4.9 17.2 1.0

M.Rajavel, A.Mitra, B.Gopal. Role of Bacillus Subtilis Bacb in the Synthesis of Bacilysin J.Biol.Chem. V. 284 31882 2009.
ISSN: ISSN 0021-9258
PubMed: 19776011
DOI: 10.1074/JBC.M109.014522