Cobalt in PDB 2d2x: Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase

The structure of Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase, PDB code: 2d2x was solved by E.Nango, T.Kumasaka, N.Tanaka, K.Kakinuma, T.Eguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.77 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.510, 70.350, 82.984, 90.00, 117.84, 90.00
R / Rfree (%)	19.1 / 22.8

The binding sites of Cobalt atom in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase (pdb code 2d2x). 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 2-Deoxy-Scyllo-Inosose Synthase, PDB code: 2d2x:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase


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 2-Deoxy-Scyllo-Inosose Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Co601 b:12.5 occ:1.00 OE1 A:GLU183 2.2 12.0 1.0 NE2 A:HIS246 2.2 14.6 1.0 NE2 A:HIS262 2.2 12.6 1.0 O A:HOH773 2.4 16.2 1.0 O A:HOH774 2.4 27.3 1.0 O A:HOH801 2.4 9.2 1.0 CD2 A:HIS262 3.0 11.2 1.0 CE1 A:HIS246 3.1 15.7 1.0 CD A:GLU183 3.2 13.0 1.0 CD2 A:HIS246 3.2 14.8 1.0 CE1 A:HIS262 3.4 10.9 1.0 OE2 A:GLU183 3.7 11.7 1.0 O A:HOH776 3.9 37.1 1.0 OD2 A:ASP135 4.0 13.5 1.0 O A:HOH775 4.1 25.6 1.0 CG A:HIS262 4.2 12.8 1.0 ND1 A:HIS246 4.2 15.7 1.0 CG A:HIS246 4.4 15.6 1.0 ND1 A:HIS262 4.4 14.0 1.0 CG1 A:ILE266 4.4 17.8 1.0 CG A:GLU183 4.4 11.9 1.0 CD1 A:ILE266 4.8 20.7 1.0 NZ A:LYS186 4.9 7.5 1.0 O A:HOH800 5.0 23.2 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase


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 2-Deoxy-Scyllo-Inosose Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Co603 b:23.0 occ:0.50 OD1 A:ASP42 2.6 12.0 1.0 N A:GLY103 2.8 14.2 1.0 N A:THR106 3.1 10.8 1.0 CA A:GLY103 3.2 11.5 1.0 C A:GLY103 3.3 12.8 1.0 OG1 A:THR106 3.3 8.1 1.0 O A:GLY103 3.5 12.3 1.0 CB A:THR106 3.6 7.5 1.0 N A:LEU105 3.6 12.9 1.0 CB A:LEU105 3.6 13.8 1.0 O3 A:GOL607 3.7 19.0 1.0 CG A:ASP42 3.8 13.4 1.0 N A:GLY104 3.9 13.0 1.0 C A:GLY102 3.9 14.2 1.0 CA A:LEU105 3.9 13.0 1.0 CA A:THR106 3.9 8.9 1.0 C A:LEU105 4.0 11.9 1.0 O A:HOH659 4.1 20.3 1.0 O A:HOH714 4.2 39.1 1.0 CA A:GLY102 4.2 12.6 1.0 CG A:LEU105 4.3 14.7 1.0 C A:GLY104 4.4 13.5 1.0 OD2 A:ASP42 4.4 12.5 1.0 C3 A:GOL607 4.5 27.6 1.0 CD2 A:LEU105 4.6 19.8 1.0 CG2 A:VAL45 4.7 15.2 1.0 CA A:GLY104 4.7 12.8 1.0 O A:GLY102 4.9 12.4 1.0 CB A:ASP42 5.0 12.0 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase


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 2-Deoxy-Scyllo-Inosose Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Co604 b:25.2 occ:0.50 O A:HOH630 2.8 9.3 1.0 OE1 A:GLU235 2.8 16.9 1.0 O A:GLY239 2.9 13.3 1.0 O A:HOH631 3.0 17.7 1.0 OE2 A:GLU243 3.2 24.9 1.0 CB A:GLU235 3.6 15.4 1.0 CG A:GLU243 3.7 18.2 1.0 CD A:GLU235 3.8 16.1 1.0 C A:GLY239 3.9 14.7 1.0 CD A:GLU243 3.9 21.8 1.0 CB A:PHE242 4.0 12.5 1.0 CG A:GLU235 4.1 15.6 1.0 O A:HOH799 4.2 18.2 1.0 CA A:LEU240 4.2 15.9 1.0 O A:GLU235 4.3 15.7 1.0 N A:GLU243 4.4 14.1 1.0 C A:PHE242 4.4 12.3 1.0 N A:PHE242 4.5 12.9 1.0 N A:LEU240 4.5 14.2 1.0 CA A:PHE242 4.5 13.2 1.0 C A:LEU240 4.6 16.8 1.0 O A:LEU240 4.7 14.2 1.0 CD1 A:PHE242 4.7 12.9 1.0 CA A:GLU235 4.7 17.2 1.0 CB A:GLU243 4.9 15.6 1.0 CG A:PHE242 4.9 12.1 1.0 O A:PHE242 4.9 12.0 1.0 CA A:GLY239 4.9 13.5 1.0 OE2 A:GLU235 4.9 15.2 1.0 C A:GLU235 5.0 17.3 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of 2-Deoxy-Scyllo-Inosose Synthase


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 2-Deoxy-Scyllo-Inosose Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Co602 b:14.8 occ:1.00 OE1 B:GLU183 2.1 14.2 1.0 NE2 B:HIS246 2.2 12.3 1.0 NE2 B:HIS262 2.3 10.6 1.0 C3 B:GOL606 2.5 38.8 1.0 C2 B:GOL606 2.7 38.9 1.0 O2 B:GOL606 2.8 36.3 1.0 O B:HOH788 2.8 20.4 1.0 CD2 B:HIS262 3.0 8.0 1.0 CE1 B:HIS246 3.1 14.1 1.0 CD B:GLU183 3.1 12.8 1.0 CD2 B:HIS246 3.3 12.7 1.0 O3 B:GOL606 3.4 42.5 1.0 CE1 B:HIS262 3.4 12.0 1.0 OE2 B:GLU183 3.6 13.5 1.0 C1 B:GOL606 3.8 35.3 1.0 OD2 B:ASP135 4.0 13.0 1.0 ND1 B:HIS246 4.2 15.9 1.0 CG B:HIS262 4.3 11.5 1.0 CG B:GLU183 4.3 11.9 1.0 ND1 B:HIS262 4.4 13.8 1.0 CG B:HIS246 4.4 14.8 1.0 CG1 B:ILE266 4.4 15.0 1.0 O1 B:GOL606 4.5 31.1 1.0 CD1 B:ILE266 4.7 17.9 1.0

E.Nango, T.Kumasaka, T.Hirayama, N.Tanaka, T.Eguchi. Structure of 2-Deoxy-Scyllo-Inosose Synthase, A Key Enzyme in the Biosynthesis of 2-Deoxystreptamine-Containing Aminoglycoside Antibiotics, in Complex with A Mechanism-Based Inhibitor and Nad+ Proteins V. 70 517 2008.
ISSN: ISSN 0887-3585
PubMed: 17879343
DOI: 10.1002/PROT.21526