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: Wed Nov 13 12:46:57 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