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Manganese in PDB 6onm: Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate

Enzymatic activity of Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate

All present enzymatic activity of Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate:
4.2.3.20;

Protein crystallography data

The structure of Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate, PDB code: 6onm was solved by R.Prem Kumar, B.R.Morehouse, Q.Yu, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.810, 85.810, 217.620, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.1

Other elements in 6onm:

The structure of Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate (pdb code 6onm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate, PDB code: 6onm:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 6onm

Go back to Manganese Binding Sites List in 6onm
Manganese binding site 1 out of 3 in the Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:68.8
occ:1.00
 O2B A:MWG704 2.0 71.8 1.0
OD2 A:ASP343 2.3 67.1 1.0
OD2 A:ASP347 2.6 77.3 1.0
O2A A:MWG704 2.6 69.1 1.0
CG A:ASP347 3.2 74.8 1.0
PB A:MWG704 3.3 79.3 1.0
OD1 A:ASP347 3.3 72.3 1.0
CG A:ASP343 3.3 66.2 1.0
PA A:MWG704 3.5 76.2 1.0
OD1 A:ASP343 3.6 67.3 1.0
O3A A:MWG704 3.6 78.1 1.0
MN A:MN702 3.7 71.6 1.0
O1A A:MWG704 3.7 91.5 1.0
O3B A:MWG704 4.0 69.0 1.0
O1B A:MWG704 4.4 72.3 1.0
CB A:ASP347 4.6 74.2 1.0
CB A:ASP343 4.7 61.0 1.0
O A:HOH813 4.7 72.9 1.0
OD1 A:ASP344 4.8 74.9 1.0
O A:ASP343 4.8 62.9 1.0
NZ A:LYS504 4.9 72.1 1.0

Manganese binding site 2 out of 3 in 6onm

Go back to Manganese Binding Sites List in 6onm
Manganese binding site 2 out of 3 in the Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:71.6
occ:1.00
 OD2 A:ASP347 2.3 77.3 1.0
OD1 A:ASP343 2.4 67.3 1.0
O2B A:MWG704 2.6 71.8 1.0
CG A:ASP347 3.3 74.8 1.0
O1B A:MWG704 3.3 72.3 1.0
CG A:ASP343 3.4 66.2 1.0
OE1 A:GLU422 3.5 72.2 1.0
PB A:MWG704 3.6 79.3 1.0
CB A:ASP347 3.6 74.2 1.0
MN A:MN701 3.7 68.8 1.0
OD2 A:ASP343 3.7 67.1 1.0
CE1 A:TYR419 3.9 57.6 1.0
CD1 A:TYR419 4.1 58.4 1.0
OD1 A:ASP347 4.4 72.3 1.0
O3B A:MWG704 4.5 69.0 1.0
O A:ASP343 4.5 62.9 1.0
NZ A:LYS504 4.6 72.1 1.0
CD A:GLU422 4.7 76.6 1.0
CB A:ASP343 4.7 61.0 1.0
O3A A:MWG704 4.7 78.1 1.0
CZ A:TYR419 4.7 55.7 1.0
CA A:ASP347 4.9 72.7 1.0
N A:ASP347 4.9 64.4 1.0

Manganese binding site 3 out of 3 in 6onm

Go back to Manganese Binding Sites List in 6onm
Manganese binding site 3 out of 3 in the Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn703

b:78.0
occ:1.00
 OD2 A:ASP488 1.9 66.3 1.0
O1A A:MWG704 2.1 91.5 1.0
O3B A:MWG704 2.5 69.0 1.0
CG A:ASP488 3.1 67.2 1.0
PA A:MWG704 3.4 76.2 1.0
OD1 A:ASP488 3.6 70.5 1.0
PB A:MWG704 3.7 79.3 1.0
O3A A:MWG704 3.9 78.1 1.0
NZ A:LYS504 4.0 72.1 1.0
O1 A:MWG704 4.1 88.8 1.0
O A:ASP488 4.2 69.2 1.0
OD1 A:ASP489 4.2 62.6 1.0
NH1 A:ARG485 4.2 52.9 1.0
CB A:ASP488 4.3 58.3 1.0
O2B A:MWG704 4.4 71.8 1.0
C A:ASP488 4.5 60.2 1.0
OG1 A:THR492 4.5 92.2 1.0
CD A:LYS504 4.5 77.7 1.0
O2A A:MWG704 4.5 69.1 1.0
CE A:LYS504 4.8 71.1 1.0
O1B A:MWG704 4.8 72.3 1.0
N A:ASP489 4.9 58.5 1.0
CA A:ASP488 5.0 57.1 1.0

Reference:

B.R.Morehouse, R.P.Kumar, J.O.Matos, Q.Yu, A.Bannister, K.Malik, J.S.Temme, I.J.Krauss, D.D.Oprian. Direct Evidence of An Enzyme-Generated Lpp Intermediate in (+)-Limonene Synthase Using A Fluorinated Gpp Substrate Analog. Acs Chem.Biol. V. 14 2035 2019.
ISSN: ESSN 1554-8937
PubMed: 31433159
DOI: 10.1021/ACSCHEMBIO.9B00514
Page generated: Sun Oct 6 05:46:46 2024

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