Atomistry » Magnesium » PDB 6ggi-6gog » 6ggi
Atomistry »
  Magnesium »
    PDB 6ggi-6gog »
      6ggi »

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

Go back to Magnesium Binding Sites List in 6ggi
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

Go back to Magnesium Binding Sites List in 6ggi
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

Go back to Magnesium Binding Sites List in 6ggi
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

Go back to Magnesium Binding Sites List in 6ggi
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

Go back to Magnesium Binding Sites List in 6ggi
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

Go back to Magnesium Binding Sites List in 6ggi
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

Go back to Magnesium Binding Sites List in 6ggi
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

Go back to Magnesium Binding Sites List in 6ggi
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

Go back to Magnesium Binding Sites List in 6ggi
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy