Cobalt in PDB 3gob: Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa

The structure of Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa, PDB code: 3gob was solved by T.J.Rydel, E.J.Sturman, F.Moshiri, G.R.Brown, Y.Qi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.05
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	81.010, 81.010, 161.050, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa also contains other interesting chemical elements:

Iron	(Fe)	6 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Cobalt atom in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa (pdb code 3gob). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa, PDB code: 3gob:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa


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 Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Co502 b:36.7 occ:1.00 O A:HOH862 2.1 42.3 1.0 OD1 A:ASP294 2.1 30.6 1.0 OD2 A:ASP294 2.2 35.6 1.0 NE2 A:HIS160 2.2 33.9 1.0 NE2 A:HIS165 2.3 35.1 1.0 CG A:ASP294 2.5 33.5 1.0 OD1 A:ASN154 2.5 28.3 1.0 CE1 A:HIS165 3.0 36.8 1.0 CD2 A:HIS160 3.1 31.8 1.0 CE1 A:HIS160 3.2 33.5 1.0 CG A:ASN154 3.3 30.7 1.0 ND2 A:ASN154 3.4 28.4 1.0 CD2 A:HIS165 3.5 35.9 1.0 CB A:ASP294 4.0 35.7 1.0 ND1 A:HIS165 4.2 35.8 1.0 CG A:HIS160 4.3 33.0 1.0 ND1 A:HIS160 4.3 34.3 1.0 CG A:HIS165 4.5 38.5 1.0 CB A:ASN154 4.7 27.0 1.0 O A:HOH1027 4.8 37.7 1.0 O A:ASN154 4.8 28.8 1.0 CA A:ASP294 4.8 36.5 1.0 CG1 A:VAL164 4.8 33.5 1.0

Cobalt binding site 2 out of 8 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa


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 Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa within 5.0Å range: probe atom residue distance (Å) B Occ A:Co602 b:55.3 occ:1.00 NE2 A:HIS65 2.5 40.6 1.0 CD2 A:HIS65 3.2 39.4 1.0 CE1 A:HIS65 3.6 41.9 1.0 O A:HOH1165 4.0 44.2 1.0 O A:HOH1117 4.1 59.2 1.0 CG A:HIS65 4.5 40.4 1.0 ND1 A:HIS65 4.6 41.6 1.0 CB A:ASP76 4.8 36.8 1.0

Cobalt binding site 3 out of 8 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa


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 Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa within 5.0Å range: probe atom residue distance (Å) B Occ B:Co502 b:42.0 occ:1.00 NE2 B:HIS165 2.0 32.6 1.0 OD2 B:ASP294 2.0 36.9 1.0 NE2 B:HIS160 2.1 39.8 1.0 O B:HOH863 2.4 31.8 1.0 OD1 B:ASP294 2.4 40.6 1.0 CG B:ASP294 2.5 38.8 1.0 CE1 B:HIS165 2.9 35.4 1.0 CE1 B:HIS160 3.0 39.3 1.0 CD2 B:HIS165 3.1 36.3 1.0 CD2 B:HIS160 3.1 38.7 1.0 OD1 B:ASN154 3.5 35.6 1.0 O B:HOH986 3.9 48.9 1.0 CB B:ASP294 4.0 37.5 1.0 ND1 B:HIS165 4.1 36.4 1.0 ND1 B:HIS160 4.2 39.1 1.0 CG B:HIS165 4.2 38.0 1.0 CG B:HIS160 4.2 40.1 1.0 CG B:ASN154 4.3 35.0 1.0 ND2 B:ASN154 4.4 32.5 1.0 O B:ALA289 4.8 48.4 1.0 CA B:ASP294 4.9 38.9 1.0

Cobalt binding site 4 out of 8 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa


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 Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa within 5.0Å range: probe atom residue distance (Å) B Occ B:Co602 b:64.7 occ:1.00 NE2 B:HIS65 2.1 55.1 1.0 O B:HOH797 2.2 48.7 1.0 CE1 B:HIS65 2.5 52.9 1.0 CD2 B:HIS65 3.4 51.9 1.0 ND1 B:HIS65 3.8 51.2 1.0 CG B:HIS65 4.2 50.5 1.0 CG1 B:VAL82 4.8 40.1 1.0 CB B:VAL82 4.9 38.2 1.0 O B:ASN63 4.9 50.9 1.0 CG2 B:VAL82 4.9 37.6 1.0

Cobalt binding site 5 out of 8 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa within 5.0Å range: probe atom residue distance (Å) B Occ C:Co502 b:54.2 occ:1.00 NE2 C:HIS165 2.2 48.4 1.0 OD2 C:ASP294 2.2 44.0 1.0 O C:HOH864 2.3 57.9 1.0 OD1 C:ASP294 2.4 47.3 1.0 NE2 C:HIS160 2.5 59.0 1.0 CG C:ASP294 2.7 44.2 1.0 CE1 C:HIS165 2.8 48.5 1.0 CD2 C:HIS160 3.2 58.2 1.0 CD2 C:HIS165 3.4 50.5 1.0 OD1 C:ASN154 3.4 37.3 1.0 CE1 C:HIS160 3.7 58.5 1.0 ND1 C:HIS165 4.1 49.8 1.0 CB C:ASP294 4.2 43.5 1.0 CG C:ASN154 4.2 35.5 1.0 ND2 C:ASN154 4.3 37.1 1.0 CG C:HIS165 4.3 50.8 1.0 CG C:HIS160 4.4 57.6 1.0 ND1 C:HIS160 4.6 58.2 1.0 CG1 C:VAL164 4.9 42.2 1.0

Cobalt binding site 6 out of 8 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa within 5.0Å range: probe atom residue distance (Å) B Occ C:Co602 b:59.2 occ:1.00 O C:HOH870 2.2 36.6 1.0 O C:HOH1092 2.3 58.3 1.0 NE2 C:HIS65 2.3 46.5 1.0 CD2 C:HIS65 3.1 42.5 1.0 CE1 C:HIS65 3.5 45.8 1.0 O C:HOH996 3.7 35.8 1.0 CG C:HIS65 4.4 43.7 1.0 ND1 C:HIS65 4.5 45.1 1.0 CB C:ASP76 4.7 34.1 1.0 O C:ASN63 5.0 49.0 1.0

Cobalt binding site 7 out of 8 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa within 5.0Å range: probe atom residue distance (Å) B Occ C:Co603 b:70.9 occ:1.00 NE2 C:HIS83 2.4 42.5 1.0 CD2 C:HIS83 3.1 40.3 1.0 O C:HOH1023 3.4 54.8 1.0 CE1 C:HIS83 3.5 41.9 1.0 CG C:HIS83 4.3 39.7 1.0 ND1 C:HIS83 4.5 41.5 1.0 O C:ASN84 4.5 36.7 1.0 CA C:PRO85 4.6 40.4 1.0 C C:ASN84 5.0 38.0 1.0

Cobalt binding site 8 out of 8 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dcsa within 5.0Å range: probe atom residue distance (Å) B Occ C:Co604 b:76.9 occ:1.00 ND1 C:HIS86 2.5 42.6 1.0 CB A:CYS320 2.7 52.7 1.0 O A:HOH985 2.8 61.2 1.0 SG A:CYS320 2.9 60.4 1.0 CG C:HIS86 3.1 43.5 1.0 CB C:HIS86 3.2 43.1 1.0 CE1 C:HIS86 3.6 43.9 1.0 O A:HOH1121 3.8 56.0 1.0 CA C:HIS86 4.0 45.2 1.0 CA A:CYS320 4.0 50.5 1.0 N A:CYS320 4.2 50.1 1.0 CD2 C:HIS86 4.3 42.4 1.0 NE2 C:HIS86 4.5 42.4 1.0 CA A:GLY159 4.5 35.4 1.0 N C:GLY87 4.5 49.4 1.0 OG A:SER319 4.6 50.8 1.0 O A:HOH895 4.6 73.2 1.0 C C:HIS86 4.7 47.2 1.0 CG A:ARG176 5.0 89.0 1.0

R.L.D'ordine, T.J.Rydel, M.J.Storek, E.J.Sturman, F.Moshiri, R.K.Bartlett, G.R.Brown, R.J.Eilers, C.Dart, Y.Qi, S.Flasinski, S.J.Franklin. Dicamba Monooxygenase: Structural Insights Into A Dynamic Rieske Oxygenase That Catalyzes An Exocyclic Monooxygenation. J.Mol.Biol. V. 392 481 2009.
ISSN: ISSN 0022-2836
PubMed: 19616009
DOI: 10.1016/J.JMB.2009.07.022