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Magnesium in PDB 4rnq: Crystal Structure of Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline

Enzymatic activity of Crystal Structure of Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline

All present enzymatic activity of Crystal Structure of Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline:
4.2.3.61;

Protein crystallography data

The structure of Crystal Structure of Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline, PDB code: 4rnq was solved by H.J.Koo, C.M.Crenshaw, C.Starks, H.P.Spielmann, J.Chappell, J.P.Noel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.07 / 2.47
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 126.750, 126.750, 124.300, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline (pdb code 4rnq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline, PDB code: 4rnq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4rnq

Go back to Magnesium Binding Sites List in 4rnq
Magnesium binding site 1 out of 3 in the Crystal Structure of Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline


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 Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:87.8
occ:1.00
 O3 A:DPO606 2.4 0.4 0.6
O22 A:A4S604 2.6 0.2 0.5
OD2 A:ASP301 2.8 83.3 1.0
OD2 A:ASP305 3.0 0.2 1.0
OE2 A:GLU379 3.1 99.1 1.0
CG A:ASP301 3.5 83.6 1.0
CG A:ASP305 3.6 0.6 1.0
CB A:ASP305 3.7 0.6 1.0
MG A:MG602 3.7 85.8 1.0
OD1 A:ASP301 3.8 86.2 1.0
CE1 A:TYR376 3.8 72.6 1.0
O A:ASP301 3.8 83.6 1.0
P21 A:A4S604 3.9 0.4 0.5
P1 A:DPO606 3.9 0.8 0.6
O24 A:A4S604 4.0 0.6 0.5
CD1 A:TYR376 4.0 74.3 1.0
CD A:GLU379 4.3 92.8 1.0
O19 A:A4S604 4.5 0.3 0.5
O2 A:DPO606 4.5 0.8 0.6
CZ A:TYR376 4.5 72.8 1.0
CA A:ASP305 4.5 0.1 1.0
CB A:ASP301 4.6 79.3 1.0
CA A:ASP301 4.6 76.8 1.0
C A:ASP301 4.6 78.4 1.0
O4 A:DPO606 4.6 0.8 0.6
OD1 A:ASP305 4.7 0.9 1.0
N A:ASP305 4.7 97.0 1.0
CG A:TYR376 4.8 77.4 1.0
O1 A:DPO606 4.9 0.9 0.6
CB A:PHE304 4.9 86.7 1.0
OE1 A:GLU379 5.0 91.8 1.0
OH A:TYR376 5.0 65.1 1.0

Magnesium binding site 2 out of 3 in 4rnq

Go back to Magnesium Binding Sites List in 4rnq
Magnesium binding site 2 out of 3 in the Crystal Structure of Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline


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 Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:85.8
occ:1.00
 O18 A:A4S604 2.1 0.4 0.5
O5 A:DPO606 2.1 0.6 0.6
OD1 A:ASP301 2.3 86.2 1.0
OD2 A:ASP305 2.4 0.2 1.0
P17 A:A4S604 2.9 0.9 0.5
P2 A:DPO606 2.9 0.1 0.6
O3 A:DPO606 2.9 0.4 0.6
O19 A:A4S604 3.0 0.3 0.5
O4 A:DPO606 3.0 0.8 0.6
O7 A:DPO606 3.2 0.6 0.6
CG A:ASP301 3.2 83.6 1.0
CG A:ASP305 3.3 0.6 1.0
O22 A:A4S604 3.3 0.2 0.5
O16 A:A4S604 3.4 0.2 0.5
OD2 A:ASP301 3.4 83.3 1.0
P1 A:DPO606 3.6 0.8 0.6
P21 A:A4S604 3.7 0.4 0.5
CB A:ASP305 3.7 0.6 1.0
MG A:MG601 3.7 87.8 1.0
NH2 A:ARG264 4.1 75.1 1.0
O1 A:DPO606 4.2 0.9 0.6
O20 A:A4S604 4.3 0.9 0.5
OD1 A:ASP305 4.3 0.9 1.0
O6 A:DPO606 4.3 0.9 0.6
C15 A:A4S604 4.5 0.4 0.5
O A:ASP301 4.5 83.6 1.0
OD1 A:ASP302 4.5 87.2 1.0
C14 A:A4S604 4.5 87.0 0.5
CB A:ASP301 4.6 79.3 1.0
CZ A:ARG264 4.7 77.3 1.0
NH1 A:ARG264 4.7 79.2 1.0
O24 A:A4S604 4.7 0.6 0.5
O2 A:DPO606 4.8 0.8 0.6
O23 A:A4S604 4.8 0.7 0.5
C A:ASP301 4.9 78.4 1.0
N09 A:1GA605 4.9 82.0 0.6
OE2 A:GLU452 5.0 0.5 1.0

Magnesium binding site 3 out of 3 in 4rnq

Go back to Magnesium Binding Sites List in 4rnq
Magnesium binding site 3 out of 3 in the Crystal Structure of Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline


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 Tobacco 5-Epi-Aristolochene Synthase (Teas) with Anilinogeranyl Diphosphate (Agpp) and Geraniline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:98.1
occ:1.00
 OG1 A:THR448 2.5 89.3 1.0
O23 A:A4S604 2.6 0.7 0.5
O1 A:DPO606 2.8 0.9 0.6
OE1 A:GLU452 3.4 0.8 1.0
OD2 A:ASP444 3.5 78.8 1.0
O6 A:DPO606 3.5 0.9 0.6
OD1 A:ASP445 3.5 72.9 1.0
O20 A:A4S604 3.6 0.9 0.5
CG A:ASP444 3.8 77.4 1.0
CB A:THR448 3.8 88.5 1.0
OD1 A:ASP444 3.8 89.0 1.0
O A:ASP444 3.9 60.6 1.0
P21 A:A4S604 4.1 0.4 0.5
NH2 A:ARG441 4.1 54.0 1.0
P1 A:DPO606 4.3 0.8 0.6
CG2 A:THR448 4.3 76.5 1.0
C A:ASP444 4.3 57.7 1.0
CA A:ASP445 4.4 59.5 1.0
CD A:GLU452 4.4 0.2 1.0
O A:THR448 4.4 93.0 1.0
P17 A:A4S604 4.6 0.9 0.5
P2 A:DPO606 4.6 0.1 0.6
N A:ASP445 4.6 56.3 1.0
O19 A:A4S604 4.6 0.3 0.5
CG A:ASP445 4.7 67.1 1.0
OE2 A:GLU452 4.7 0.5 1.0
O5 A:DPO606 4.7 0.6 0.6
CB A:ASP444 4.7 59.5 1.0
O4 A:DPO606 4.8 0.8 0.6
O2 A:DPO606 4.9 0.8 0.6
O22 A:A4S604 4.9 0.2 0.5
CA A:THR448 4.9 94.8 1.0
C A:THR448 4.9 93.4 1.0

Reference:

K.A.Rising, C.M.Crenshaw, H.J.Koo, T.Subramanian, K.A.Chehade, C.Starks, K.D.Allen, D.A.Andres, H.P.Spielmann, J.P.Noel, J.Chappell. Formation of A Novel Macrocyclic Alkaloid From the Unnatural Farnesyl Diphosphate Analogue Anilinogeranyl Diphosphate By 5-Epi-Aristolochene Synthase. Acs Chem.Biol. 2015.
ISSN: ESSN 1554-8937
PubMed: 25897591
DOI: 10.1021/ACSCHEMBIO.5B00145
Page generated: Tue Aug 20 03:14:18 2024

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