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Cobalt in PDB 3gb4: Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba

Protein crystallography data

The structure of Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba, PDB code: 3gb4 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 (°) 81.550, 81.550, 161.290, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Other elements in 3gb4:

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

Iron (Fe) 6 atoms
Chlorine (Cl) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba (pdb code 3gb4). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba, PDB code: 3gb4:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in 3gb4

Go back to Cobalt Binding Sites List in 3gb4
Cobalt binding site 1 out of 7 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba


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 Dicamba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co502

b:40.0
occ:1.00
 NE2 A:HIS165 2.2 30.4 1.0
OD2 A:ASP294 2.2 42.8 1.0
NE2 A:HIS160 2.2 35.0 1.0
OD1 A:ASP294 2.4 42.6 1.0
O A:HOH700 2.5 36.7 1.0
CG A:ASP294 2.6 41.7 1.0
CE1 A:HIS165 3.1 32.6 1.0
CD2 A:HIS160 3.2 34.2 1.0
CD2 A:HIS165 3.2 29.5 1.0
CE1 A:HIS160 3.2 36.0 1.0
OD1 A:ASN154 3.6 37.8 1.0
O A:HOH1015 4.0 43.9 1.0
CB A:ASP294 4.1 39.0 1.0
ND1 A:HIS165 4.2 32.5 1.0
CG A:HIS165 4.3 33.5 1.0
ND1 A:HIS160 4.3 35.2 1.0
CG A:HIS160 4.3 35.6 1.0
CG A:ASN154 4.5 34.9 1.0
ND2 A:ASN154 4.5 33.7 1.0
O A:ALA289 4.8 43.7 1.0
CA A:ASP294 4.9 40.1 1.0
CG1 A:VAL164 4.9 32.1 1.0

Cobalt binding site 2 out of 7 in 3gb4

Go back to Cobalt Binding Sites List in 3gb4
Cobalt binding site 2 out of 7 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba


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 Dicamba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co602

b:66.8
occ:1.00
 NE2 A:HIS65 2.0 52.5 1.0
O A:HOH930 2.4 62.8 1.0
CE1 A:HIS65 2.4 49.0 1.0
CD2 A:HIS65 3.3 46.9 1.0
ND1 A:HIS65 3.7 48.0 1.0
CG A:HIS65 4.2 47.7 1.0
O A:ASN63 4.7 52.5 1.0

Cobalt binding site 3 out of 7 in 3gb4

Go back to Cobalt Binding Sites List in 3gb4
Cobalt binding site 3 out of 7 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba


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 Dicamba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co502

b:40.4
occ:1.00
 OD2 B:ASP294 2.2 46.7 1.0
NE2 B:HIS165 2.2 38.2 1.0
O B:HOH701 2.2 56.2 1.0
OD1 B:ASP294 2.3 46.0 1.0
NE2 B:HIS160 2.3 47.0 1.0
CG B:ASP294 2.5 44.3 1.0
CD2 B:HIS160 3.1 47.7 1.0
CE1 B:HIS165 3.1 37.9 1.0
CD2 B:HIS165 3.2 36.9 1.0
CE1 B:HIS160 3.3 47.1 1.0
OD1 B:ASN154 3.5 38.3 1.0
CB B:ASP294 4.0 44.4 1.0
ND1 B:HIS165 4.3 38.4 1.0
ND2 B:ASN154 4.3 38.0 1.0
CG B:ASN154 4.3 36.4 1.0
CG B:HIS160 4.3 48.1 1.0
CG B:HIS165 4.3 38.9 1.0
ND1 B:HIS160 4.4 45.9 1.0
O B:ALA289 4.7 50.4 1.0
CD1 B:LEU290 4.8 51.1 1.0
CA B:ASP294 4.8 43.4 1.0

Cobalt binding site 4 out of 7 in 3gb4

Go back to Cobalt Binding Sites List in 3gb4
Cobalt binding site 4 out of 7 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba


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 Dicamba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co602

b:63.0
occ:1.00
 O B:HOH921 2.3 34.1 1.0
NE2 B:HIS65 2.4 45.1 1.0
CD2 B:HIS65 3.1 40.1 1.0
CE1 B:HIS65 3.5 45.1 1.0
CG B:HIS65 4.4 42.5 1.0
ND1 B:HIS65 4.5 43.3 1.0
CB B:ASP76 4.7 37.6 1.0

Cobalt binding site 5 out of 7 in 3gb4

Go back to Cobalt Binding Sites List in 3gb4
Cobalt binding site 5 out of 7 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba


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 Dicamba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co603

b:82.3
occ:1.00
 NE2 B:HIS83 2.3 43.0 1.0
O B:HOH1130 2.6 61.4 1.0
O B:HOH941 2.8 52.2 1.0
CD2 B:HIS83 3.1 41.2 1.0
O B:HOH1096 3.2 66.5 1.0
CE1 B:HIS83 3.4 42.0 1.0
CG B:HIS83 4.3 41.1 1.0
ND1 B:HIS83 4.4 41.5 1.0
O B:ASN84 4.5 36.9 1.0
CA B:PRO85 4.5 40.5 1.0

Cobalt binding site 6 out of 7 in 3gb4

Go back to Cobalt Binding Sites List in 3gb4
Cobalt binding site 6 out of 7 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba


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 Dicamba within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co502

b:40.6
occ:1.00
 O C:HOH703 2.1 39.7 1.0
NE2 C:HIS165 2.2 35.3 1.0
NE2 C:HIS160 2.2 32.0 1.0
OD1 C:ASP294 2.3 33.4 1.0
OD2 C:ASP294 2.4 39.3 1.0
OD1 C:ASN154 2.6 32.8 1.0
CG C:ASP294 2.6 37.9 1.0
CE1 C:HIS165 3.0 36.3 1.0
CE1 C:HIS160 3.2 31.4 1.0
CD2 C:HIS160 3.2 30.3 1.0
CG C:ASN154 3.3 32.9 1.0
ND2 C:ASN154 3.3 29.9 1.0
CD2 C:HIS165 3.4 34.7 1.0
CB C:ASP294 4.1 38.1 1.0
ND1 C:HIS165 4.2 37.0 1.0
ND1 C:HIS160 4.3 32.7 1.0
CG C:HIS160 4.4 31.4 1.0
CG C:HIS165 4.4 37.4 1.0
O C:HOH934 4.7 40.7 1.0
CB C:ASN154 4.8 29.7 1.0
O C:ASN154 4.8 30.1 1.0
CG1 C:VAL164 4.9 34.8 1.0

Cobalt binding site 7 out of 7 in 3gb4

Go back to Cobalt Binding Sites List in 3gb4
Cobalt binding site 7 out of 7 in the Crystal Structure of Dicamba Monooxygenase with Non-Heme Cobalt and Dicamba


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 Dicamba within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co602

b:56.5
occ:1.00
 NE2 C:HIS65 2.4 38.8 1.0
CD2 C:HIS65 3.2 37.1 1.0
CE1 C:HIS65 3.5 40.5 1.0
O C:HOH1159 4.0 50.1 1.0
O C:HOH1138 4.0 64.2 1.0
CG C:HIS65 4.4 38.7 1.0
ND1 C:HIS65 4.6 38.0 1.0
CB C:ASP76 4.7 39.3 1.0

Reference:

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
Page generated: Tue Jul 30 16:00:53 2024

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