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Cobalt in PDB 3ojk: Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution

Enzymatic activity of Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution

All present enzymatic activity of Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution:
1.13.11.15;

Protein crystallography data

The structure of Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution, PDB code: 3ojk was solved by A.J.Fielding, E.G.Kovaleva, E.R.Farquhar, J.D.Lipscomb, L.Que Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.96 / 1.68
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.102, 150.395, 95.941, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.2

Other elements in 3ojk:

The structure of Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Calcium (Ca) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution (pdb code 3ojk). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution, PDB code: 3ojk:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 3ojk

Go back to Cobalt Binding Sites List in 3ojk
Cobalt binding site 1 out of 4 in the Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co500

b:18.1
occ:1.00
 O8 A:4NC601 2.1 16.2 0.8
OE1 A:GLU267 2.1 14.6 1.0
NE2 A:HIS214 2.1 17.1 1.0
NE2 A:HIS155 2.1 14.8 1.0
O7 A:4NC601 2.2 15.1 0.8
O A:HOH906 2.4 8.5 1.0
C2 A:4NC601 2.9 17.9 0.8
C1 A:4NC601 2.9 15.5 0.8
CE1 A:HIS214 3.0 17.4 1.0
CE1 A:HIS155 3.0 16.0 1.0
CD A:GLU267 3.1 17.4 1.0
CD2 A:HIS155 3.2 16.5 1.0
CD2 A:HIS214 3.2 15.5 1.0
OE2 A:GLU267 3.6 17.6 1.0
NE2 A:HIS200 3.8 22.8 1.0
ND1 A:HIS214 4.1 17.3 1.0
OH A:TYR257 4.1 16.9 1.0
ND1 A:HIS155 4.2 15.6 1.0
C3 A:4NC601 4.2 17.8 0.8
CG A:HIS155 4.2 16.5 1.0
CG A:HIS214 4.3 17.9 1.0
C6 A:4NC601 4.3 14.2 0.8
CG A:GLU267 4.4 17.4 1.0
CB A:ALA216 4.5 16.2 1.0
CE1 A:HIS200 4.5 19.7 1.0
CB A:GLU267 4.6 15.4 1.0
ND2 A:ASN157 4.6 22.5 1.0
CE1 A:TYR257 4.6 14.2 1.0
CB A:ASN157 4.7 18.5 1.0
CD1 A:TYR269 4.8 16.3 1.0
CZ A:TYR257 4.9 16.5 1.0
CD2 A:HIS200 4.9 22.9 1.0
CE1 A:TYR269 4.9 17.0 1.0

Cobalt binding site 2 out of 4 in 3ojk

Go back to Cobalt Binding Sites List in 3ojk
Cobalt binding site 2 out of 4 in the Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co500

b:16.5
occ:1.00
 O B:HOH777 2.0 11.8 1.0
OE1 B:GLU267 2.1 12.8 1.0
O B:HOH778 2.2 19.4 1.0
NE2 B:HIS155 2.2 14.2 1.0
NE2 B:HIS214 2.2 13.3 1.0
O B:HOH951 2.3 7.8 1.0
CE1 B:HIS214 3.0 13.9 1.0
CD2 B:HIS155 3.1 15.6 1.0
CD B:GLU267 3.1 16.9 1.0
CE1 B:HIS155 3.1 15.2 1.0
CD2 B:HIS214 3.2 12.4 1.0
OE2 B:GLU267 3.6 17.6 1.0
NE2 B:HIS200 3.8 16.9 1.0
OH B:TYR257 4.1 13.8 1.0
O B:HOH898 4.2 17.9 1.0
ND1 B:HIS214 4.2 15.2 1.0
ND1 B:HIS155 4.2 13.7 1.0
CG B:HIS155 4.3 14.5 1.0
CG B:HIS214 4.3 15.1 1.0
CG B:GLU267 4.4 13.3 1.0
ND2 B:ASN157 4.5 20.1 1.0
CE1 B:HIS200 4.5 16.1 1.0
CB B:GLU267 4.5 12.4 1.0
CE1 B:TYR257 4.5 13.9 1.0
CB B:ALA216 4.6 14.2 1.0
CB B:ASN157 4.7 16.6 1.0
CZ B:TYR257 4.8 15.0 1.0
CD2 B:HIS200 4.9 20.0 1.0
CD1 B:TYR269 5.0 14.5 1.0

Cobalt binding site 3 out of 4 in 3ojk

Go back to Cobalt Binding Sites List in 3ojk
Cobalt binding site 3 out of 4 in the Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co500

b:14.8
occ:1.00
 OE1 C:GLU267 2.0 12.6 1.0
O8 C:4NC601 2.0 12.4 0.8
NE2 C:HIS155 2.1 11.3 1.0
NE2 C:HIS214 2.1 12.2 1.0
O7 C:4NC601 2.2 16.3 0.8
O C:HOH919 2.3 8.0 1.0
C2 C:4NC601 2.8 19.6 0.8
C1 C:4NC601 2.9 16.5 0.8
CE1 C:HIS214 3.0 13.4 1.0
CE1 C:HIS155 3.0 13.8 1.0
CD C:GLU267 3.1 14.0 1.0
CD2 C:HIS155 3.1 11.1 1.0
CD2 C:HIS214 3.2 13.9 1.0
OE2 C:GLU267 3.5 13.4 1.0
NE2 C:HIS200 3.8 16.9 1.0
OH C:TYR257 4.1 12.7 1.0
ND1 C:HIS155 4.2 10.4 1.0
ND1 C:HIS214 4.2 13.6 1.0
C3 C:4NC601 4.2 19.1 0.8
C6 C:4NC601 4.2 14.3 0.8
CG C:HIS155 4.2 12.1 1.0
CG C:HIS214 4.3 12.3 1.0
CG C:GLU267 4.3 12.1 1.0
CB C:GLU267 4.5 12.0 1.0
CB C:ALA216 4.5 12.2 1.0
CE1 C:HIS200 4.5 16.8 1.0
CE1 C:TYR257 4.6 11.0 1.0
ND2 C:ASN157 4.7 22.1 1.0
CB C:ASN157 4.7 14.7 1.0
CZ C:TYR257 4.8 12.2 1.0
CD2 C:HIS200 4.8 16.1 1.0
CD1 C:TYR269 4.9 14.9 1.0

Cobalt binding site 4 out of 4 in 3ojk

Go back to Cobalt Binding Sites List in 3ojk
Cobalt binding site 4 out of 4 in the Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of Co-Substituted Homoprotocatechuate 2,3-Dioxygenase in Complex with 4-Nitrocatechol at 1.68 Ang Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co500

b:14.3
occ:1.00
 OE1 D:GLU267 2.0 12.2 1.0
NE2 D:HIS155 2.1 11.1 1.0
O8 D:4NC601 2.1 13.6 0.8
NE2 D:HIS214 2.1 11.6 1.0
O7 D:4NC601 2.2 15.0 0.8
O D:HOH954 2.3 9.2 1.0
C2 D:4NC601 2.9 17.3 0.8
C1 D:4NC601 2.9 15.7 0.8
CE1 D:HIS155 3.0 13.8 1.0
CE1 D:HIS214 3.1 10.2 1.0
CD D:GLU267 3.1 11.4 1.0
CD2 D:HIS155 3.2 10.8 1.0
CD2 D:HIS214 3.2 10.4 1.0
OE2 D:GLU267 3.5 13.7 1.0
NE2 D:HIS200 3.8 16.0 1.0
OH D:TYR257 4.1 13.8 1.0
ND1 D:HIS155 4.2 12.3 1.0
ND1 D:HIS214 4.2 11.3 1.0
CG D:HIS155 4.3 12.5 1.0
C3 D:4NC601 4.3 16.3 0.8
CG D:HIS214 4.3 10.9 1.0
C6 D:4NC601 4.3 12.8 0.8
CG D:GLU267 4.3 11.7 1.0
CE1 D:HIS200 4.5 15.0 1.0
CB D:GLU267 4.5 10.7 1.0
CB D:ALA216 4.5 12.2 1.0
CE1 D:TYR257 4.6 11.3 1.0
ND2 D:ASN157 4.6 17.1 1.0
CB D:ASN157 4.7 14.6 1.0
CZ D:TYR257 4.8 12.2 1.0
CD1 D:TYR269 4.9 11.9 1.0
CD2 D:HIS200 4.9 16.5 1.0
CE1 D:TYR269 5.0 13.7 1.0

Reference:

A.J.Fielding, E.G.Kovaleva, E.R.Farquhar, J.D.Lipscomb, L.Que. A Hyperactive Cobalt-Substituted Extradiol-Cleaving Catechol Dioxygenase. J.Biol.Inorg.Chem. V. 16 341 2011.
ISSN: ISSN 0949-8257
PubMed: 21153851
DOI: 10.1007/S00775-010-0732-0
Page generated: Tue Jul 30 16:23:10 2024

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