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Fluorine in PDB 1pfv: Methionyl-Trna Synthetase From Escherichia Coli Complexed with Difluoromethionine

Enzymatic activity of Methionyl-Trna Synthetase From Escherichia Coli Complexed with Difluoromethionine

All present enzymatic activity of Methionyl-Trna Synthetase From Escherichia Coli Complexed with Difluoromethionine:
6.1.1.10;

Protein crystallography data

The structure of Methionyl-Trna Synthetase From Escherichia Coli Complexed with Difluoromethionine, PDB code: 1pfv was solved by T.Crepin, E.Schmitt, Y.Mechulam, P.B.Sampson, M.D.Vaughan, J.F.Honek, S.Blanquet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.573, 45.221, 86.068, 90.00, 107.37, 90.00
R / Rfree (%) 18.6 / 20.3

Other elements in 1pfv:

The structure of Methionyl-Trna Synthetase From Escherichia Coli Complexed with Difluoromethionine also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Methionyl-Trna Synthetase From Escherichia Coli Complexed with Difluoromethionine (pdb code 1pfv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Methionyl-Trna Synthetase From Escherichia Coli Complexed with Difluoromethionine, PDB code: 1pfv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 1pfv

Go back to Fluorine Binding Sites List in 1pfv
Fluorine binding site 1 out of 2 in the Methionyl-Trna Synthetase From Escherichia Coli Complexed with Difluoromethionine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Methionyl-Trna Synthetase From Escherichia Coli Complexed with Difluoromethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F553

b:14.3
occ:1.00
FZ1 A:2FM553 0.0 14.3 1.0
CE A:2FM553 1.3 10.6 1.0
FZ2 A:2FM553 2.2 13.3 1.0
SD A:2FM553 2.6 9.9 1.0
CG A:2FM553 3.0 12.4 1.0
O A:ALA256 3.1 7.9 1.0
C A:ALA256 3.1 9.2 1.0
CD1 A:LEU13 3.2 11.4 1.0
CG A:LEU13 3.2 7.4 1.0
CB A:ALA256 3.4 10.8 1.0
N A:PRO257 3.5 9.2 1.0
CB A:LEU13 3.7 8.7 1.0
CA A:PRO257 3.8 8.4 1.0
CA A:ALA256 3.8 9.3 1.0
CZ A:TYR260 4.3 5.7 1.0
CD A:PRO257 4.3 9.5 1.0
OH A:TYR260 4.3 7.0 1.0
N A:LEU13 4.4 8.0 1.0
OD2 A:ASP52 4.4 12.2 1.0
CB A:2FM553 4.4 13.6 1.0
CE2 A:TYR260 4.6 5.6 1.0
CE1 A:TYR260 4.6 6.5 1.0
CB A:PRO257 4.6 9.9 1.0
CD2 A:LEU13 4.6 8.4 1.0
CA A:LEU13 4.7 7.8 1.0
C A:PRO257 4.9 8.7 1.0
CG A:ASP52 4.9 10.7 1.0
CZ3 A:TRP253 4.9 16.6 1.0

Fluorine binding site 2 out of 2 in 1pfv

Go back to Fluorine Binding Sites List in 1pfv
Fluorine binding site 2 out of 2 in the Methionyl-Trna Synthetase From Escherichia Coli Complexed with Difluoromethionine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Methionyl-Trna Synthetase From Escherichia Coli Complexed with Difluoromethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F553

b:13.3
occ:1.00
FZ2 A:2FM553 0.0 13.3 1.0
CE A:2FM553 1.3 10.6 1.0
FZ1 A:2FM553 2.2 14.3 1.0
SD A:2FM553 2.6 9.9 1.0
CG A:2FM553 3.2 12.4 1.0
CZ3 A:TRP253 3.2 16.6 1.0
N A:PRO257 3.4 9.2 1.0
CD A:PRO257 3.5 9.5 1.0
CA A:PRO257 3.6 8.4 1.0
CB A:PRO257 3.6 9.9 1.0
CB A:ALA256 3.7 10.8 1.0
C A:ALA256 3.8 9.2 1.0
CE1 A:HIS301 3.8 8.8 1.0
CE3 A:TRP253 3.8 14.6 1.0
NE2 A:HIS301 3.9 7.4 1.0
CH2 A:TRP253 4.1 18.0 1.0
CG A:PRO257 4.2 12.2 1.0
OH A:TYR260 4.3 7.0 1.0
O A:ALA256 4.3 7.9 1.0
CA A:ALA256 4.4 9.3 1.0
CE1 A:TYR260 4.4 6.5 1.0
CZ A:TYR260 4.5 5.7 1.0
CB A:2FM553 4.5 13.6 1.0
ND1 A:HIS301 4.9 7.2 1.0
CD2 A:HIS301 4.9 8.1 1.0

Reference:

T.Crepin, E.Schmitt, Y.Mechulam, P.B.Sampson, M.D.Vaughan, J.F.Honek, S.Blanquet. Use of Analogues of Methionine and Methionyl Adenylate to Sample Conformational Changes During Catalysis in Escherichia Coli Methionyl-Trna Synthetase. J.Mol.Biol. V. 332 59 2003.
ISSN: ISSN 0022-2836
PubMed: 12946347
DOI: 10.1016/S0022-2836(03)00917-3
Page generated: Sun Dec 13 11:31:52 2020

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