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Magnesium in PDB 9c7l: Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate

Enzymatic activity of Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate

All present enzymatic activity of Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate:
4.2.3.7;

Protein crystallography data

The structure of Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate, PDB code: 9c7l was solved by R.Prem Kumar, W.H.Ellenburg, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 2.20
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 181.521, 181.521, 55.763, 90, 90, 120
R / Rfree (%) 18.5 / 21.3

Other elements in 9c7l:

The structure of Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate also contains other interesting chemical elements:

Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate (pdb code 9c7l). 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 Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate, PDB code: 9c7l:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 9c7l

Go back to Magnesium Binding Sites List in 9c7l
Magnesium binding site 1 out of 3 in the Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate


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 Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:70.7
occ:1.00
 O A:HOH537 2.1 57.9 1.0
O A:HOH639 2.3 64.6 1.0
O2B A:FPF401 2.3 70.4 1.0
OD2 A:ASP80 2.4 51.9 1.0
O2A A:FPF401 2.5 62.8 1.0
O A:HOH588 3.0 60.7 1.0
MG A:MG404 3.3 75.9 1.0
CG A:ASP80 3.4 46.9 1.0
OD1 A:ASP84 3.4 69.8 1.0
P2 A:FPF401 3.7 67.5 1.0
OD1 A:ASP80 3.7 51.8 1.0
P1 A:FPF401 3.8 63.5 1.0
O A:HOH600 3.9 64.0 1.0
O A:HOH614 3.9 67.0 1.0
O3A A:FPF401 4.0 69.5 1.0
F A:FPF401 4.1 79.5 1.0
CG A:ASP84 4.1 66.5 1.0
OD2 A:ASP84 4.2 75.7 1.0
O A:ASP80 4.3 41.3 1.0
O A:HOH662 4.4 70.0 1.0
O1B A:FPF401 4.4 73.3 1.0
OD1 A:ASP81 4.6 53.7 1.0
O1A A:FPF401 4.7 68.4 1.0
CB A:ASP80 4.7 38.2 1.0
NH2 A:ARG314 4.7 57.7 1.0
O3B A:FPF401 4.7 63.7 1.0
C A:ASP80 4.8 41.4 1.0
NH1 A:ARG314 4.8 65.4 1.0
O1 A:FPF401 5.0 73.8 1.0

Magnesium binding site 2 out of 3 in 9c7l

Go back to Magnesium Binding Sites List in 9c7l
Magnesium binding site 2 out of 3 in the Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate


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 Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:61.7
occ:1.00
 OD1 A:ASN219 2.4 55.5 1.0
O1A A:FPF401 2.5 68.4 1.0
OG A:SER223 2.6 60.3 1.0
OE2 A:GLU227 2.7 67.1 1.0
O3A A:FPF401 2.7 69.5 1.0
O A:HOH547 2.8 62.0 1.0
P1 A:FPF401 3.1 63.5 1.0
CG A:ASN219 3.5 54.4 1.0
CD A:GLU227 3.6 71.0 1.0
CB A:SER223 3.7 58.4 1.0
OD1 A:ASP220 3.8 54.2 1.0
O1 A:FPF401 3.8 73.8 1.0
O A:ASN219 4.0 52.9 1.0
NH2 A:ARG173 4.0 63.3 1.0
OE1 A:GLU227 4.0 73.9 1.0
ND2 A:ASN219 4.2 56.2 1.0
O A:HOH504 4.2 59.3 1.0
P2 A:FPF401 4.2 67.5 1.0
C A:ASN219 4.4 53.5 1.0
O2A A:FPF401 4.4 62.8 1.0
O1B A:FPF401 4.5 73.3 1.0
CA A:ASP220 4.6 49.6 1.0
CB A:ASN219 4.6 49.2 1.0
O A:HOH572 4.7 60.5 1.0
N A:ASP220 4.7 48.0 1.0
C1 A:FPF401 4.7 72.0 1.0
O A:HOH538 4.7 64.9 1.0
CG A:GLU227 4.8 67.7 1.0
O3B A:FPF401 4.9 63.7 1.0
CG A:ASP220 4.9 51.0 1.0
CZ A:ARG173 4.9 62.0 1.0
ND2 A:ASN235 5.0 58.7 1.0

Magnesium binding site 3 out of 3 in 9c7l

Go back to Magnesium Binding Sites List in 9c7l
Magnesium binding site 3 out of 3 in the Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate


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 Pentalenene Synthase Variant F76A Complexed with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:75.9
occ:1.00
 OD1 A:ASP80 2.5 51.8 1.0
O A:HOH588 2.5 60.7 1.0
O A:HOH662 2.6 70.0 1.0
O A:HOH614 2.7 67.0 1.0
O A:HOH642 2.9 63.3 1.0
O2A A:FPF401 2.9 62.8 1.0
MG A:MG402 3.3 70.7 1.0
CG A:ASP80 3.3 46.9 1.0
O A:HOH625 3.5 64.6 1.0
OD2 A:ASP80 3.5 51.9 1.0
O A:HOH639 3.8 64.6 1.0
O A:HOH538 4.1 64.9 1.0
P1 A:FPF401 4.2 63.5 1.0
O1A A:FPF401 4.4 68.4 1.0
OH A:TYR150 4.4 47.0 1.0
CE2 A:TYR150 4.4 45.8 1.0
O A:ASP80 4.4 41.3 1.0
F A:FPF401 4.5 79.5 1.0
OE1 A:GLU153 4.6 69.7 1.0
CZ A:TYR150 4.7 53.5 1.0
CB A:ASP80 4.7 38.2 1.0
OD1 A:ASP84 4.9 69.8 1.0
O1 A:FPF401 4.9 73.8 1.0
O A:HOH537 4.9 57.9 1.0

Reference:

R.P.Kumar, J.O.Matos, B.Y.Black, W.H.Ellenburg, J.Chen, M.Patterson, J.A.Gehtman, D.L.Theobald, I.J.Krauss, D.D.Oprian. Crystal Structure of Caryolan-1-Ol Synthase, A Sesquiterpene Synthase Catalyzing An Initial Anti-Markovnikov Cyclization Reaction. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 39400323
DOI: 10.1021/ACS.BIOCHEM.4C00547
Page generated: Fri Aug 15 23:43:58 2025

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