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Cobalt in PDB 5ero: Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate

Enzymatic activity of Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate

All present enzymatic activity of Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate:
2.5.1.29;

Protein crystallography data

The structure of Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate, PDB code: 5ero was solved by M.Chen, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.85 / 2.55
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 103.577, 216.122, 129.234, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.6

Cobalt Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate (pdb code 5ero). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 12 binding sites of Cobalt where determined in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate, PDB code: 5ero:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 12 in 5ero

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Cobalt binding site 1 out of 12 in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate


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 Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co801

b:38.9
occ:1.00
 O10 A:210804 2.0 50.6 1.0
O3 A:210804 2.0 53.2 1.0
O A:HOH918 2.0 44.3 1.0
OD2 A:ASP605 2.0 43.7 1.0
O A:HOH923 2.1 39.9 1.0
O A:HOH926 2.2 41.8 1.0
CG A:ASP605 3.2 32.3 1.0
P1 A:210804 3.2 39.5 1.0
P8 A:210804 3.2 38.7 1.0
C7 A:210804 3.5 39.6 1.0
O A:HOH908 3.6 45.8 1.0
O14 A:210804 3.6 53.7 1.0
OD1 A:ASP605 3.7 48.6 1.0
O5 A:210804 3.8 44.6 1.0
NZ A:LYS629 3.9 49.7 1.0
OD1 A:ASP624 4.1 39.1 1.0
O A:ASP605 4.1 38.0 1.0
OD1 A:ASP606 4.2 39.5 1.0
O12 A:210804 4.2 42.1 1.0
O9 A:210804 4.2 41.0 1.0
ND2 A:ASN609 4.3 41.6 1.0
O A:HOH928 4.3 36.1 1.0
OD2 A:ASP624 4.4 44.4 1.0
CB A:ASP605 4.4 32.6 1.0
O2 A:210804 4.4 41.0 1.0
CE A:LYS619 4.4 55.4 1.0
C A:ASP605 4.5 35.6 1.0
NE2 A:GLN602 4.5 41.9 1.0
CG A:ASP624 4.7 43.4 1.0
CE A:LYS629 4.7 38.7 1.0
CO A:CO803 4.7 37.2 1.0
NZ A:LYS619 4.8 46.7 1.0
OE1 A:GLU623 4.9 54.6 1.0
N A:ASP606 5.0 35.9 1.0

Cobalt binding site 2 out of 12 in 5ero

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Cobalt binding site 2 out of 12 in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate


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 Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co802

b:41.0
occ:1.00
 O A:HOH913 1.9 45.8 1.0
OD1 A:ASP474 2.0 39.4 1.0
O A:HOH911 2.0 44.3 1.0
O9 A:210804 2.0 41.0 1.0
OD2 A:ASP478 2.1 33.6 1.0
O A:HOH903 2.1 36.5 1.0
CG A:ASP474 2.9 36.1 1.0
CG A:ASP478 3.0 37.4 1.0
CO A:CO803 3.0 37.2 1.0
OD2 A:ASP474 3.2 34.3 1.0
OD1 A:ASP478 3.2 33.9 1.0
P8 A:210804 3.3 38.7 1.0
O12 A:210804 3.6 42.1 1.0
OE2 A:GLU627 4.0 43.0 1.0
O A:HOH928 4.1 36.1 1.0
OE1 A:GLN536 4.2 52.7 1.0
C16 A:210804 4.2 41.4 1.0
CB A:ASP474 4.2 39.0 1.0
O10 A:210804 4.3 50.6 1.0
CB A:ASP478 4.4 26.7 1.0
OD2 A:ASP539 4.5 48.6 1.0
C7 A:210804 4.5 39.6 1.0
NZ A:LYS629 4.5 49.7 1.0
NZ A:LYS561 4.5 55.2 1.0
O A:HOH905 4.5 30.6 1.0
NE2 A:GLN536 4.6 31.6 1.0
O A:ASP474 4.6 33.9 1.0
O5 A:210804 4.6 44.6 1.0
OE1 A:GLU627 4.7 44.5 1.0
CD A:GLU627 4.7 38.7 1.0
CD A:GLN536 4.8 34.7 1.0
CA A:ASP474 4.8 27.1 1.0

Cobalt binding site 3 out of 12 in 5ero

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Cobalt binding site 3 out of 12 in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate


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 Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co803

b:37.2
occ:1.00
 O A:HOH928 1.9 36.1 1.0
O A:HOH905 2.0 30.6 1.0
OD2 A:ASP474 2.0 34.3 1.0
O9 A:210804 2.0 41.0 1.0
O5 A:210804 2.1 44.6 1.0
OD2 A:ASP478 2.2 33.6 1.0
CG A:ASP474 3.0 36.1 1.0
CO A:CO802 3.0 41.0 1.0
P8 A:210804 3.1 38.7 1.0
OD1 A:ASP474 3.3 39.4 1.0
CG A:ASP478 3.3 37.4 1.0
P1 A:210804 3.3 39.5 1.0
C7 A:210804 3.6 39.6 1.0
O10 A:210804 3.6 50.6 1.0
C16 A:210804 3.7 41.4 1.0
CB A:ASP478 3.9 26.7 1.0
O A:HOH911 4.0 44.3 1.0
O A:HOH923 4.0 39.9 1.0
NZ A:LYS619 4.2 46.7 1.0
O3 A:210804 4.2 53.2 1.0
OE1 A:GLU627 4.2 44.5 1.0
CB A:ASP474 4.3 39.0 1.0
O A:ASP474 4.3 33.9 1.0
OD1 A:ASP478 4.4 33.9 1.0
O12 A:210804 4.4 42.1 1.0
O2 A:210804 4.4 41.0 1.0
OG A:SER480 4.5 29.5 1.0
O A:HOH913 4.5 45.8 1.0
C A:ASP474 4.6 24.2 1.0
OE2 A:GLU623 4.6 59.3 1.0
OD1 A:ASP475 4.6 35.0 1.0
CO A:CO801 4.7 38.9 1.0
O A:HOH903 4.8 36.5 1.0
CD A:GLU627 5.0 38.7 1.0
O14 A:210804 5.0 53.7 1.0
N A:ASP475 5.0 24.8 1.0

Cobalt binding site 4 out of 12 in 5ero

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Cobalt binding site 4 out of 12 in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate


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 Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co805

b:0.4
occ:1.00
 OD1 A:ASP447 2.2 41.8 1.0
O A:HOH965 3.0 65.5 1.0
CG A:ASP447 3.3 41.0 1.0
OD2 A:ASP447 3.7 47.5 1.0
O A:ASP443 4.1 49.6 1.0
CB A:ASP447 4.5 35.1 1.0
CA A:ASP447 4.7 51.8 1.0
N A:ASP447 4.9 51.4 1.0
C A:ASP443 4.9 49.8 1.0

Cobalt binding site 5 out of 12 in 5ero

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Cobalt binding site 5 out of 12 in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate


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 Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co801

b:37.8
occ:1.00
 O9 B:210804 1.9 50.0 1.0
O5 B:210804 2.0 46.4 1.0
O B:HOH915 2.0 37.2 1.0
O B:HOH922 2.0 43.9 1.0
OD2 B:ASP605 2.1 46.1 1.0
O B:HOH930 2.3 42.4 1.0
CG B:ASP605 3.1 45.0 1.0
P1 B:210804 3.2 42.7 1.0
P8 B:210804 3.3 40.1 1.0
OD1 B:ASP605 3.4 46.3 1.0
C7 B:210804 3.6 28.2 1.0
O14 B:210804 3.7 42.7 1.0
O B:HOH901 3.7 50.1 1.0
O3 B:210804 3.8 46.8 1.0
NZ B:LYS629 3.9 42.5 1.0
OD1 B:ASP606 4.1 40.6 1.0
O10 B:210804 4.1 44.5 1.0
OD1 B:ASP624 4.1 53.1 1.0
OD2 B:ASP624 4.3 51.0 1.0
ND2 B:ASN609 4.3 45.9 1.0
O B:HOH907 4.3 40.5 1.0
O12 B:210804 4.3 34.5 1.0
O B:ASP605 4.3 42.2 1.0
CB B:ASP605 4.4 43.0 1.0
CE B:LYS619 4.4 55.9 1.0
O2 B:210804 4.4 43.1 1.0
NE2 B:GLN602 4.5 31.3 1.0
C B:ASP605 4.6 35.8 1.0
CG B:ASP624 4.6 48.3 1.0
CE B:LYS629 4.7 32.6 1.0
NZ B:LYS619 4.7 38.6 1.0
CO B:CO803 4.8 40.4 1.0
OE1 B:GLU623 5.0 51.1 1.0
N B:ASP606 5.0 32.9 1.0

Cobalt binding site 6 out of 12 in 5ero

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Cobalt binding site 6 out of 12 in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate


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 Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co802

b:44.5
occ:1.00
 O B:HOH908 1.9 41.8 1.0
OD2 B:ASP474 1.9 40.0 1.0
O B:HOH906 2.0 39.8 1.0
O B:HOH902 2.0 32.3 1.0
OD2 B:ASP478 2.1 43.3 1.0
O10 B:210804 2.1 44.5 1.0
CG B:ASP474 2.9 41.4 1.0
CG B:ASP478 2.9 47.5 1.0
CO B:CO803 3.1 40.4 1.0
OD1 B:ASP478 3.1 41.0 1.0
OD1 B:ASP474 3.1 36.1 1.0
P8 B:210804 3.3 40.1 1.0
O12 B:210804 3.5 34.5 1.0
OE2 B:GLU627 3.8 47.0 1.0
O B:HOH907 4.0 40.5 1.0
OE1 B:GLN536 4.2 57.3 1.0
C16 B:210804 4.2 39.1 1.0
CB B:ASP474 4.3 24.8 1.0
OD2 B:ASP539 4.3 55.4 1.0
CB B:ASP478 4.3 30.9 1.0
O9 B:210804 4.3 50.0 1.0
C7 B:210804 4.4 28.2 1.0
NZ B:LYS629 4.4 42.5 1.0
NZ B:LYS561 4.5 39.9 1.0
NE2 B:GLN536 4.5 33.6 1.0
CD B:GLU627 4.5 51.1 1.0
O3 B:210804 4.6 46.8 1.0
OE1 B:GLU627 4.6 50.2 1.0
O B:ASP474 4.6 33.0 1.0
CD B:GLN536 4.7 46.2 1.0
N22 B:210804 4.8 40.9 1.0
CA B:ASP474 4.9 22.9 1.0
CG B:ASP539 4.9 59.4 1.0
CE B:LYS629 4.9 32.6 1.0
O B:HOH903 5.0 30.6 1.0

Cobalt binding site 7 out of 12 in 5ero

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Cobalt binding site 7 out of 12 in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate


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 Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co803

b:40.4
occ:1.00
 O3 B:210804 2.0 46.8 1.0
OD1 B:ASP474 2.0 36.1 1.0
O B:HOH907 2.0 40.5 1.0
O10 B:210804 2.0 44.5 1.0
OD2 B:ASP478 2.2 43.3 1.0
O B:HOH903 2.3 30.6 1.0
CG B:ASP474 3.0 41.4 1.0
CO B:CO802 3.1 44.5 1.0
P8 B:210804 3.3 40.1 1.0
CG B:ASP478 3.3 47.5 1.0
P1 B:210804 3.3 42.7 1.0
OD2 B:ASP474 3.4 40.0 1.0
C7 B:210804 3.6 28.2 1.0
CB B:ASP478 3.8 30.9 1.0
C16 B:210804 3.8 39.1 1.0
O9 B:210804 3.8 50.0 1.0
O B:HOH922 4.0 43.9 1.0
O5 B:210804 4.1 46.4 1.0
OE1 B:GLU627 4.2 50.2 1.0
O B:HOH902 4.2 32.3 1.0
O B:ASP474 4.2 33.0 1.0
NZ B:LYS619 4.2 38.6 1.0
OG B:SER480 4.3 30.9 1.0
CB B:ASP474 4.4 24.8 1.0
OD1 B:ASP478 4.4 41.0 1.0
O2 B:210804 4.4 43.1 1.0
OD1 B:ASP475 4.5 38.1 1.0
O12 B:210804 4.5 34.5 1.0
C B:ASP474 4.5 24.1 1.0
OE2 B:GLU623 4.6 53.3 1.0
O B:HOH906 4.7 39.8 1.0
NH1 B:ARG483 4.7 38.0 1.0
CO B:CO801 4.8 37.8 1.0
O B:HOH908 4.8 41.8 1.0
CD B:GLU627 4.9 51.1 1.0
N B:ASP475 4.9 23.2 1.0
OE2 B:GLU627 4.9 47.0 1.0

Cobalt binding site 8 out of 12 in 5ero

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Cobalt binding site 8 out of 12 in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate


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 Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co805

b:61.8
occ:1.00
 OD2 B:ASP453 2.0 85.1 1.0
CG B:ASP453 2.9 57.5 1.0
OD1 B:ASP453 3.3 75.5 1.0
CB B:ASP453 4.2 64.2 1.0

Cobalt binding site 9 out of 12 in 5ero

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Cobalt binding site 9 out of 12 in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co801

b:72.0
occ:1.00
 O12 C:210804 2.1 94.8 1.0
O3 C:210804 2.2 77.6 1.0
OD2 C:ASP605 2.4 76.9 1.0
P8 C:210804 3.4 99.0 1.0
O C:HOH901 3.5 94.8 1.0
CG C:ASP605 3.5 87.0 1.0
OD1 C:ASP624 3.6 89.5 1.0
P1 C:210804 3.6 91.8 1.0
C7 C:210804 3.9 88.5 1.0
O9 C:210804 3.9 76.0 1.0
OD1 C:ASP606 4.0 74.7 1.0
OD2 C:ASP624 4.0 70.6 1.0
OD1 C:ASP605 4.0 88.7 1.0
O14 C:210804 4.0 96.8 1.0
CG C:ASP624 4.2 84.5 1.0
O C:ASP605 4.3 70.8 1.0
ND2 C:ASN609 4.3 85.8 1.0
NZ C:LYS619 4.4 83.7 1.0
CE C:LYS629 4.4 87.5 1.0
CD C:LYS629 4.5 73.9 1.0
O2 C:210804 4.5 91.0 1.0
C C:ASP605 4.5 77.6 1.0
O5 C:210804 4.6 84.4 1.0
CB C:ASP605 4.6 86.0 1.0
O10 C:210804 4.6 83.7 1.0
NE2 C:GLN602 4.7 65.8 1.0
OE1 C:GLU623 4.7 89.9 1.0
CE C:LYS619 4.8 98.7 1.0
N C:ASP606 4.8 69.4 1.0
CB C:ASN609 4.8 84.3 1.0
CG C:ASN609 4.9 77.2 1.0
CA C:ASP606 4.9 69.3 1.0
CO C:CO802 5.0 71.7 1.0

Cobalt binding site 10 out of 12 in 5ero

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Cobalt binding site 10 out of 12 in the Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of Elongation Domain of Phomopsis Amygdali Fusicoccadiene Synthase Complexed with Cobalt Ions and Pamidronate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co802

b:71.7
occ:1.00
 OD2 C:ASP474 1.9 58.9 1.0
O9 C:210804 2.5 76.0 1.0
OD2 C:ASP478 2.5 70.8 1.0
O5 C:210804 2.7 84.4 1.0
CG C:ASP474 3.0 56.6 1.0
CO C:CO803 3.4 54.6 1.0
OD1 C:ASP474 3.5 61.2 1.0
CG C:ASP478 3.5 63.8 1.0
P1 C:210804 3.7 91.8 1.0
O3 C:210804 3.8 77.6 1.0
CB C:ASP478 3.8 62.2 1.0
P8 C:210804 3.8 99.0 1.0
OE1 C:GLU627 4.0 87.6 1.0
OE2 C:GLU623 4.0 97.6 1.0
O C:ASP474 4.1 47.9 1.0
OG C:SER480 4.2 51.3 1.0
C7 C:210804 4.2 88.5 1.0
CB C:ASP474 4.3 50.2 1.0
OD1 C:ASP475 4.4 59.6 1.0
C C:ASP474 4.4 45.8 1.0
C16 C:210804 4.5 80.4 1.0
O12 C:210804 4.5 94.8 1.0
NZ C:LYS619 4.6 83.7 1.0
CD C:GLU627 4.7 87.7 1.0
OD1 C:ASP478 4.7 66.3 1.0
N C:ASP475 4.8 40.0 1.0
O C:HOH902 4.8 51.4 1.0
CD C:GLU623 4.9 89.2 1.0
CA C:ASP474 4.9 41.4 1.0
OE1 C:GLU623 4.9 89.9 1.0
O10 C:210804 5.0 83.7 1.0
OE2 C:GLU627 5.0 77.1 1.0
CA C:ASP475 5.0 42.0 1.0
CO C:CO801 5.0 72.0 1.0

Reference:

M.Chen, W.K.Chou, T.Toyomasu, D.E.Cane, D.W.Christianson. Structure and Function of Fusicoccadiene Synthase, A Hexameric Bifunctional Diterpene Synthase. Acs Chem.Biol. V. 11 889 2016.
ISSN: ESSN 1554-8937
PubMed: 26734760
DOI: 10.1021/ACSCHEMBIO.5B00960
Page generated: Tue Jul 30 17:50:42 2024

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