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Magnesium in PDB 6ggi: Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene

Enzymatic activity of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene

All present enzymatic activity of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene:
4.2.3.146;

Protein crystallography data

The structure of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene, PDB code: 6ggi was solved by R.Driller, S.Janke, M.Fuchs, E.Warner, A.R.Mhashal, D.T.Major, M.Christmann, T.Brueck, B.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.74 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.885, 98.722, 105.862, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20

Other elements in 6ggi:

The structure of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Potassium (K) 2 atoms
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene (pdb code 6ggi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene, PDB code: 6ggi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6ggi

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Magnesium binding site 1 out of 9 in the Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:21.6
occ:1.00
 O12 A:PPV406 2.1 19.8 1.0
OD2 A:ASP110 2.1 18.3 1.0
O11 A:PPV406 2.1 18.7 1.0
O A:HOH548 2.2 20.6 1.0
O A:HOH556 2.2 18.7 1.0
O A:HOH562 2.3 18.5 1.0
CG A:ASP110 3.1 21.8 1.0
MG A:MG403 3.1 19.6 1.0
P2 A:PPV406 3.2 18.3 1.0
P1 A:PPV406 3.2 20.0 1.0
OD1 A:ASP110 3.4 20.4 1.0
OPP A:PPV406 3.4 17.3 1.0
O22 A:PPV406 3.7 15.7 1.0
O A:HOH625 3.9 22.4 1.0
O21 A:PPV406 4.0 19.8 1.0
NH1 A:ARG227 4.0 24.9 1.0
NH2 A:ARG294 4.1 20.5 1.0
O A:HOH544 4.2 16.8 1.0
O A:HOH564 4.3 18.7 1.0
OE2 A:GLU228 4.4 16.1 1.0
O A:HOH553 4.4 27.8 1.0
O32 A:PPV406 4.4 18.1 1.0
O31 A:PPV406 4.4 16.7 1.0
O A:HOH558 4.5 18.0 1.0
O A:HOH547 4.5 17.2 1.0
CB A:ASP110 4.5 18.3 1.0
FAL A:EXW407 4.5 44.3 1.0
OD1 A:ASP111 4.6 23.9 1.0
NE2 A:GLN233 4.6 24.5 1.0
O A:ASP110 4.6 20.5 1.0
MG A:MG402 4.8 16.6 1.0

Magnesium binding site 2 out of 9 in 6ggi

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Magnesium binding site 2 out of 9 in the Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:16.6
occ:1.00
 O21 A:PPV406 2.0 19.8 1.0
O22 A:PPV406 2.0 15.7 1.0
OE2 A:GLU228 2.1 16.1 1.0
OD1 A:ASN220 2.1 15.7 1.0
O A:HOH515 2.1 15.6 1.0
OG A:SER224 2.3 18.1 1.0
CD A:GLU228 3.1 21.5 1.0
CB A:SER224 3.1 16.1 1.0
CG A:ASN220 3.2 15.6 1.0
P1 A:PPV406 3.2 20.0 1.0
P2 A:PPV406 3.3 18.3 1.0
OPP A:PPV406 3.4 17.3 1.0
OE1 A:GLU228 3.5 19.8 1.0
ND2 A:ASN220 3.7 16.8 1.0
O A:HOH547 3.9 17.2 1.0
O A:HOH548 3.9 20.6 1.0
O A:ASN220 4.0 14.2 1.0
O11 A:PPV406 4.0 18.7 1.0
NH2 A:ARG177 4.1 15.8 1.0
O12 A:PPV406 4.2 19.8 1.0
O32 A:PPV406 4.3 18.1 1.0
CG A:GLU228 4.3 20.8 1.0
C A:ASN220 4.3 17.0 1.0
O31 A:PPV406 4.4 16.7 1.0
OD1 A:ASP221 4.4 15.3 1.0
CB A:ASN220 4.4 11.6 1.0
NH2 A:ARG227 4.5 20.9 1.0
CA A:SER224 4.5 16.9 1.0
N A:ASP221 4.8 14.1 1.0
MG A:MG401 4.8 21.6 1.0
CA A:ASP221 4.8 13.1 1.0
NH1 A:ARG227 4.8 24.9 1.0
C A:SER224 5.0 19.5 1.0
CA A:ASN220 5.0 12.3 1.0
CE1 A:TYR295 5.0 16.6 1.0

Magnesium binding site 3 out of 9 in 6ggi

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Magnesium binding site 3 out of 9 in the Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:19.6
occ:1.00
 O A:HOH564 1.9 18.7 1.0
OD1 A:ASP110 2.0 20.4 1.0
O A:HOH562 2.1 18.5 1.0
O A:HOH518 2.1 17.9 1.0
O A:HOH544 2.1 16.8 1.0
O12 A:PPV406 2.1 19.8 1.0
CG A:ASP110 2.9 21.8 1.0
MG A:MG401 3.1 21.6 1.0
OD2 A:ASP110 3.3 18.3 1.0
P2 A:PPV406 3.4 18.3 1.0
O32 A:PPV406 3.7 18.1 1.0
O A:HOH558 3.7 18.0 1.0
OD2 A:ASP180 4.1 18.6 1.0
OD1 A:ASP153 4.1 20.3 1.0
O A:HOH625 4.1 22.4 1.0
O A:HOH547 4.2 17.2 1.0
CAN A:EXW407 4.3 40.0 1.0
CB A:ASP110 4.3 18.3 1.0
O A:ASP180 4.3 19.4 1.0
O A:HOH548 4.3 20.6 1.0
OD1 A:ASP180 4.3 21.3 1.0
O22 A:PPV406 4.4 15.7 1.0
OPP A:PPV406 4.5 17.3 1.0
NH1 A:ARG177 4.5 16.3 1.0
CG A:ASP180 4.6 21.4 1.0
O11 A:PPV406 4.8 18.7 1.0
FAL A:EXW407 4.9 44.3 1.0
O A:HOH556 4.9 18.7 1.0
CAK A:EXW407 4.9 26.7 1.0
CAM A:EXW407 4.9 21.7 1.0
CAO A:EXW407 5.0 30.0 1.0

Magnesium binding site 4 out of 9 in 6ggi

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Magnesium binding site 4 out of 9 in the Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:37.6
occ:1.00
 O A:TYR134 2.1 23.3 1.0
O A:HOH536 2.1 28.1 1.0
O A:GLU131 2.2 29.7 1.0
O A:HOH587 2.2 25.6 1.0
C A:TYR134 3.3 24.4 1.0
C A:GLU131 3.4 28.6 1.0
CA A:GLU131 3.9 28.1 1.0
CA A:GLY135 4.0 23.8 1.0
C A:GLY135 4.0 29.1 1.0
N A:GLY135 4.1 27.4 1.0
O A:HOH637 4.2 39.1 1.0
O A:GLY135 4.2 25.3 1.0
N A:TYR134 4.3 21.0 1.0
O A:LYS132 4.3 24.5 1.0
OE2 A:GLU131 4.4 38.4 1.0
CA A:TYR134 4.4 21.9 1.0
C A:LYS132 4.4 29.9 1.0
N A:LYS132 4.5 23.3 1.0
N A:PRO136 4.6 32.4 1.0
CB A:GLU131 4.6 29.2 1.0
O A:CYS130 4.6 25.3 1.0
CA A:LYS132 4.8 28.3 1.0
N A:TYR133 4.9 22.8 1.0

Magnesium binding site 5 out of 9 in 6ggi

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Magnesium binding site 5 out of 9 in the Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:35.8
occ:1.00
 OD2 A:ASP301 2.0 33.1 1.0
OE1 A:GLU72 2.1 28.7 1.0
O A:HOH534 2.2 31.5 1.0
O A:HOH526 2.2 31.3 1.0
CG A:ASP301 3.0 35.1 1.0
CD A:GLU72 3.1 30.6 1.0
OD1 A:ASP301 3.3 34.2 1.0
OE2 A:GLU72 3.4 36.1 1.0
O A:HOH552 3.6 35.1 1.0
NZ A:LYS293 3.9 37.8 1.0
CB A:ASP301 4.3 31.5 1.0
CG A:GLU72 4.4 29.9 1.0
CE A:LYS293 4.8 36.5 1.0
O A:HOH618 5.0 27.4 1.0

Magnesium binding site 6 out of 9 in 6ggi

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Magnesium binding site 6 out of 9 in the Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:19.9
occ:1.00
 O11 B:PPV405 2.1 19.0 1.0
OD2 B:ASP110 2.1 19.4 1.0
O22 B:PPV405 2.1 20.0 1.0
O B:HOH577 2.1 18.7 1.0
O B:HOH571 2.2 22.8 1.0
O B:HOH553 2.3 18.5 1.0
CG B:ASP110 3.1 19.9 1.0
MG B:MG402 3.2 17.7 1.0
P1 B:PPV405 3.2 17.7 1.0
P2 B:PPV405 3.3 19.3 1.0
OD1 B:ASP110 3.4 17.0 1.0
OPP B:PPV405 3.5 16.6 1.0
O21 B:PPV405 3.7 14.4 1.0
O B:HOH621 4.0 21.5 1.0
O32 B:PPV405 4.0 15.9 1.0
NH1 B:ARG227 4.1 22.3 1.0
NH2 B:ARG294 4.2 18.9 1.0
O B:HOH522 4.4 25.4 1.0
O B:HOH512 4.4 16.1 1.0
OE2 B:GLU228 4.4 15.6 1.0
O B:HOH538 4.4 18.9 1.0
CB B:ASP110 4.4 18.2 1.0
O12 B:PPV405 4.5 17.2 1.0
O31 B:PPV405 4.5 16.2 1.0
O B:HOH534 4.5 16.0 1.0
OD1 B:ASP111 4.6 28.5 1.0
O B:ASP110 4.6 23.8 1.0
O B:HOH546 4.6 16.2 1.0
NE2 B:GLN233 4.6 31.4 1.0
MG B:MG403 4.8 16.4 1.0
C B:ASP110 4.9 25.5 1.0

Magnesium binding site 7 out of 9 in 6ggi

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Magnesium binding site 7 out of 9 in the Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:17.7
occ:1.00
 OD1 B:ASP110 2.0 17.0 1.0
O B:HOH534 2.0 16.0 1.0
O11 B:PPV405 2.1 19.0 1.0
O B:HOH512 2.1 16.1 1.0
O B:HOH531 2.2 19.6 1.0
O B:HOH553 2.2 18.5 1.0
CG B:ASP110 3.0 19.9 1.0
MG B:MG401 3.2 19.9 1.0
OD2 B:ASP110 3.3 19.4 1.0
P1 B:PPV405 3.3 17.7 1.0
O31 B:PPV405 3.5 16.2 1.0
O B:HOH538 3.8 18.9 1.0
OD2 B:ASP180 4.1 18.9 1.0
O B:HOH621 4.1 21.5 1.0
O21 B:PPV405 4.2 14.4 1.0
O B:HOH546 4.2 16.2 1.0
OD1 B:ASP153 4.2 24.8 1.0
O B:ASP180 4.3 17.8 1.0
CB B:ASP110 4.3 18.2 1.0
O B:HOH577 4.4 18.7 1.0
OD1 B:ASP180 4.4 21.5 1.0
O B:HOH603 4.4 31.1 1.0
CAI B:EXW406 4.5 32.6 1.0
OPP B:PPV405 4.5 16.6 1.0
NH1 B:ARG177 4.5 14.8 1.0
CG B:ASP180 4.6 19.0 1.0
O22 B:PPV405 4.8 20.0 1.0
O B:HOH571 4.9 22.8 1.0

Magnesium binding site 8 out of 9 in 6ggi

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Magnesium binding site 8 out of 9 in the Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:16.4
occ:1.00
 O32 B:PPV405 2.0 15.9 1.0
OE2 B:GLU228 2.0 15.6 1.0
O21 B:PPV405 2.1 14.4 1.0
O B:HOH525 2.1 16.2 1.0
OD1 B:ASN220 2.1 17.2 1.0
OG B:SER224 2.2 15.0 1.0
CD B:GLU228 3.1 19.9 1.0
CB B:SER224 3.1 16.8 1.0
P2 B:PPV405 3.2 19.3 1.0
CG B:ASN220 3.2 12.6 1.0
P1 B:PPV405 3.3 17.7 1.0
OPP B:PPV405 3.4 16.6 1.0
OE1 B:GLU228 3.5 16.3 1.0
ND2 B:ASN220 3.7 15.4 1.0
O B:HOH546 3.9 16.2 1.0
NH2 B:ARG177 4.0 17.0 1.0
O B:ASN220 4.0 14.8 1.0
O22 B:PPV405 4.0 20.0 1.0
O B:HOH577 4.1 18.7 1.0
O11 B:PPV405 4.3 19.0 1.0
O31 B:PPV405 4.3 16.2 1.0
O12 B:PPV405 4.4 17.2 1.0
CG B:GLU228 4.4 20.2 1.0
OD1 B:ASP221 4.4 15.0 1.0
C B:ASN220 4.4 14.4 1.0
CB B:ASN220 4.5 13.2 1.0
CA B:SER224 4.5 14.0 1.0
NH2 B:ARG227 4.6 18.6 1.0
CA B:ASP221 4.8 13.2 1.0
N B:ASP221 4.8 13.6 1.0
MG B:MG401 4.8 19.9 1.0
NH1 B:ARG227 4.8 22.3 1.0
C B:SER224 5.0 20.3 1.0

Magnesium binding site 9 out of 9 in 6ggi

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Magnesium binding site 9 out of 9 in the Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of COTB2 in Complex with 2-Fluoro-3,7,18- Dolabellatriene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:32.6
occ:1.00
 O B:HOH594 2.0 35.5 1.0
O B:HOH556 2.1 28.4 1.0
O B:HOH527 2.1 30.9 1.0
O B:HOH517 2.2 35.9 1.0
OG B:SER244 2.2 26.5 1.0
CB B:SER244 3.2 26.0 1.0
OD1 B:ASP242 4.0 26.1 1.0
OD2 B:ASP242 4.1 28.6 1.0
OD2 B:ASP12 4.2 31.9 1.0
OD1 B:ASP12 4.2 30.3 1.0
O B:HOH632 4.4 35.0 1.0
CG B:ASP242 4.5 31.0 1.0
O B:HOH622 4.5 42.0 1.0
CA B:SER244 4.5 25.4 1.0
CG B:ASP12 4.7 35.5 1.0
C B:SER244 4.8 27.4 1.0
O B:SER244 4.8 30.8 1.0

Reference:

R.Driller, S.Janke, M.Fuchs, E.Warner, A.R.Mhashal, D.T.Major, M.Christmann, T.Bruck, B.Loll. Towards A Comprehensive Understanding of the Structural Dynamics of A Bacterial Diterpene Synthase During Catalysis. Nat Commun V. 9 3971 2018.
ISSN: ESSN 2041-1723
PubMed: 30266969
DOI: 10.1038/S41467-018-06325-8
Page generated: Tue Oct 1 01:10:24 2024

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