Cobalt in PDB 3h9a: Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form

The structure of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic Form, PDB code: 3h9a 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)	30.34 / 2.04
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.252, 47.198, 62.906, 89.05, 77.27, 82.28
R / Rfree (%)	20.6 / 26.2

The structure of Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic 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 Triclinic Form (pdb code 3h9a). 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 Triclinic Form, PDB code: 3h9a:
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 Triclinic 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 Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co244 b:39.5 occ:1.00 NE2 A:HIS52 2.3 12.6 1.0 NE2 A:HIS50 2.3 19.7 1.0 O A:HOH346 2.3 25.9 1.0 OE1 A:GLN56 2.4 10.8 1.0 NE2 A:HIS91 2.4 9.8 1.0 O A:HOH335 2.9 40.0 1.0 CE1 A:HIS50 3.1 19.9 1.0 CD A:GLN56 3.2 10.0 1.0 CD2 A:HIS52 3.2 13.3 1.0 CE1 A:HIS52 3.2 13.4 1.0 CE1 A:HIS91 3.3 8.9 1.0 CD2 A:HIS50 3.4 19.0 1.0 CD2 A:HIS91 3.5 9.1 1.0 NE2 A:GLN56 3.5 10.6 1.0 ND1 A:HIS50 4.3 19.4 1.0 ND1 A:HIS52 4.3 13.5 1.0 CG A:HIS52 4.4 13.0 1.0 ND1 A:HIS91 4.4 9.1 1.0 CG A:GLN56 4.4 9.5 1.0 CG A:HIS50 4.5 18.3 1.0 NZ A:LYS107 4.5 18.9 1.0 CG A:HIS91 4.5 9.7 1.0 CB A:GLN56 4.6 8.8 1.0 CD A:LYS107 4.9 17.1 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic 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 Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co245 b:15.6 occ:1.00 O2 A:PPY246 2.0 15.7 1.0 OE1 A:GLN168 2.2 9.8 1.0 O3 A:PPY246 2.2 17.7 1.0 NE2 A:HIS162 2.2 11.5 1.0 NE2 A:HIS202 2.2 7.9 1.0 NE2 A:HIS164 2.2 10.2 1.0 C1 A:PPY246 2.7 18.4 1.0 C2 A:PPY246 2.8 17.5 1.0 CE1 A:HIS162 3.0 11.9 1.0 CE1 A:HIS202 3.0 7.5 1.0 CD A:GLN168 3.2 10.4 1.0 CD2 A:HIS164 3.2 10.9 1.0 CE1 A:HIS164 3.2 9.6 1.0 CD2 A:HIS202 3.3 6.9 1.0 CD2 A:HIS162 3.3 11.4 1.0 NE2 A:GLN168 3.5 12.4 1.0 O1 A:PPY246 4.0 17.9 1.0 ND1 A:HIS162 4.2 11.3 1.0 CE1 A:PHE218 4.2 8.8 1.0 ND1 A:HIS202 4.2 6.0 1.0 C3 A:PPY246 4.3 19.8 1.0 ND1 A:HIS164 4.4 10.0 1.0 CG A:HIS202 4.4 7.6 1.0 CG A:HIS164 4.4 10.6 1.0 CG A:HIS162 4.4 11.3 1.0 CG A:GLN168 4.5 10.3 1.0 C2' A:PPY246 4.7 21.8 1.0 CZ A:PHE218 4.8 9.1 1.0 CB A:GLN168 4.8 9.6 1.0 NE A:ARG222 4.9 17.0 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic 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 Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Co244 b:60.7 occ:1.00 NE2 B:HIS91 2.2 19.7 1.0 NE2 B:HIS52 2.4 22.6 1.0 OE1 B:GLN56 2.4 19.1 1.0 NE2 B:HIS50 2.5 24.7 1.0 CE1 B:HIS91 3.0 19.2 1.0 CD B:GLN56 3.3 18.2 1.0 CE1 B:HIS52 3.3 22.8 1.0 CD2 B:HIS50 3.3 24.3 1.0 CD2 B:HIS91 3.3 19.0 1.0 CD2 B:HIS52 3.4 22.8 1.0 CE1 B:HIS50 3.5 24.5 1.0 NE2 B:GLN56 3.6 18.3 1.0 ND1 B:HIS91 4.2 18.4 1.0 CG B:HIS91 4.4 18.8 1.0 ND1 B:HIS52 4.4 22.9 1.0 CG B:HIS50 4.5 23.9 1.0 CE B:LYS107 4.5 28.3 1.0 CG B:HIS52 4.5 22.9 1.0 ND1 B:HIS50 4.5 24.4 1.0 NZ B:LYS107 4.5 29.5 1.0 CG B:GLN56 4.6 18.1 1.0 CB B:GLN56 4.7 17.8 1.0 CD B:LYS107 4.9 27.5 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Bacb, An Enzyme Involved in Bacilysin Synthesis, in Triclinic 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 Triclinic Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Co245 b:23.6 occ:1.00 O2 B:PPY246 2.0 21.9 1.0 NE2 B:HIS202 2.2 14.9 1.0 NE2 B:HIS162 2.2 11.7 1.0 O3 B:PPY246 2.3 23.6 1.0 OE1 B:GLN168 2.3 13.4 1.0 NE2 B:HIS164 2.3 13.9 1.0 C1 B:PPY246 2.8 22.5 1.0 C2 B:PPY246 2.9 22.6 1.0 CE1 B:HIS162 3.1 11.4 1.0 CE1 B:HIS202 3.1 14.8 1.0 CD2 B:HIS202 3.1 13.6 1.0 CD B:GLN168 3.2 14.1 1.0 CE1 B:HIS164 3.2 13.2 1.0 CD2 B:HIS164 3.3 13.9 1.0 CD2 B:HIS162 3.3 11.6 1.0 NE2 B:GLN168 3.4 14.3 1.0 O1 B:PPY246 4.0 21.7 1.0 ND1 B:HIS162 4.2 11.2 1.0 ND1 B:HIS202 4.2 14.0 1.0 CG B:HIS202 4.3 13.9 1.0 CE1 B:PHE218 4.3 15.9 1.0 ND1 B:HIS164 4.4 13.0 1.0 C3 B:PPY246 4.4 23.8 1.0 CG B:HIS162 4.4 12.5 1.0 CG B:HIS164 4.4 13.8 1.0 CG B:GLN168 4.6 14.2 1.0 CE B:MSE159 4.6 21.0 1.0 C2' B:PPY246 4.7 26.0 1.0 CB B:GLN168 4.9 14.9 1.0 CZ B:PHE218 4.9 16.1 1.0

M.Rajavel, B.Gopal. Analysis of Multiple Crystal Forms of Bacillus Subtilis Bacb Suggests A Role For A Metal Ion As A Nucleant For Crystallization Acta Crystallogr.,Sect.D V. 66 635 2010.
ISSN: ISSN 0907-4449
PubMed: 20445239
DOI: 10.1107/S0907444910006682