Atomistry » Manganese » PDB 6oe2-6q9f » 6onm
Atomistry »
  Manganese »
    PDB 6oe2-6q9f »
      6onm »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy