Fluorine in PDB 7a6d: Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol

Enzymatic activity of Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol

All present enzymatic activity of Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol:
2.4.2.29;

Protein crystallography data

The structure of Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol, PDB code: 7a6d was solved by D.Nguyen, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.79 / 1.59
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 127.868, 127.868, 115.189, 90, 90, 120
R / Rfree (%) 14.8 / 17.8

Other elements in 7a6d:

The structure of Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol (pdb code 7a6d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol, PDB code: 7a6d:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7a6d

Go back to Fluorine Binding Sites List in 7a6d
Fluorine binding site 1 out of 4 in the Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:35.0
occ:1.00
F2 A:R1E407 0.0 35.0 1.0
C2 A:R1E407 1.4 36.0 1.0
F1 A:R1E407 2.1 37.0 1.0
C3 A:R1E407 2.4 35.6 1.0
C1 A:R1E407 2.4 38.5 1.0
HA A:PRO56 2.6 24.1 1.0
HG21 A:VAL59 2.9 26.1 1.0
HB A:VAL59 3.0 24.0 1.0
HB3 A:PRO56 3.1 27.9 1.0
HE3 A:TRP95 3.2 24.3 1.0
HG11 A:VAL59 3.4 26.6 1.0
HD13 A:ILE67 3.4 28.2 1.0
C4 A:R1E407 3.5 40.1 1.0
CA A:PRO56 3.5 20.1 1.0
C A:R1E407 3.6 41.7 1.0
CG2 A:VAL59 3.6 21.8 1.0
CB A:VAL59 3.6 20.0 1.0
HG21 A:ILE67 3.7 24.0 1.0
CB A:PRO56 3.7 23.2 1.0
O2 A:R1E407 3.8 43.2 1.0
CE3 A:TRP95 3.8 20.2 1.0
HG23 A:VAL59 3.8 26.1 1.0
CG1 A:VAL59 3.9 22.1 1.0
HB2 A:TRP95 3.9 25.6 1.0
HD12 A:ILE67 4.0 28.2 1.0
HZ3 A:TRP95 4.1 24.6 1.0
HG12 A:VAL59 4.1 26.6 1.0
O1 A:R1E407 4.2 45.3 1.0
CD1 A:ILE67 4.2 23.5 1.0
HB2 A:PRO56 4.2 27.9 1.0
CZ3 A:TRP95 4.3 20.5 1.0
N A:PRO56 4.3 20.8 1.0
O A:PRO56 4.4 21.0 1.0
HG22 A:VAL59 4.4 26.1 1.0
C A:PRO56 4.5 19.8 1.0
CD2 A:TRP95 4.6 20.4 1.0
CG2 A:ILE67 4.6 20.0 1.0
O A:LYS55 4.6 20.7 1.0
HD11 A:ILE67 4.7 28.2 1.0
HD3 A:PRO56 4.7 26.7 1.0
C A:LYS55 4.7 21.1 1.0
H A:VAL59 4.8 23.6 1.0
HG13 A:VAL59 4.8 26.6 1.0
HG23 A:ILE67 4.8 24.0 1.0
CB A:TRP95 4.8 21.3 1.0
CG A:PRO56 4.9 23.8 1.0
CD A:PRO56 4.9 22.2 1.0
O A:MET93 4.9 26.3 1.0
HB3 A:MET93 4.9 31.5 1.0
HA2 A:GLY46 5.0 35.2 1.0

Fluorine binding site 2 out of 4 in 7a6d

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Fluorine binding site 2 out of 4 in the Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:37.0
occ:1.00
F1 A:R1E407 0.0 37.0 1.0
C2 A:R1E407 1.4 36.0 1.0
F2 A:R1E407 2.1 35.0 1.0
C3 A:R1E407 2.4 35.6 1.0
C1 A:R1E407 2.4 38.5 1.0
HA2 A:GLY46 2.9 35.2 1.0
O1 A:R1E407 2.9 45.3 1.0
HG21 A:VAL59 3.0 26.1 1.0
C A:R1E407 3.1 41.7 1.0
HD12 A:ILE67 3.3 28.2 1.0
HG21 A:ILE67 3.3 24.0 1.0
HA3 A:GLY46 3.4 35.2 1.0
C4 A:R1E407 3.4 40.1 1.0
HG11 A:VAL59 3.4 26.6 1.0
HD13 A:ILE67 3.6 28.2 1.0
CA A:GLY46 3.6 29.3 1.0
C3 A:GOL404 3.8 57.4 1.0
CD1 A:ILE67 3.9 23.5 1.0
CG2 A:VAL59 3.9 21.8 1.0
C2 A:GOL404 4.0 56.7 1.0
O2 A:GOL404 4.0 57.9 1.0
HB A:VAL59 4.2 24.0 1.0
CG1 A:VAL59 4.2 22.1 1.0
CG2 A:ILE67 4.3 20.0 1.0
HE2 A:MET93 4.3 49.6 1.0
HB A:ILE67 4.3 25.8 1.0
O2 A:R1E407 4.4 43.2 1.0
CB A:VAL59 4.4 20.0 1.0
O A:GLY46 4.4 38.9 1.0
HG23 A:VAL59 4.4 26.1 1.0
HG22 A:VAL59 4.4 26.1 1.0
HA A:PRO56 4.5 24.1 1.0
C A:GLY46 4.5 34.2 1.0
HD11 A:ILE67 4.5 28.2 1.0
N A:GLY46 4.5 25.5 1.0
HG22 A:ILE67 4.6 24.0 1.0
HE1 A:MET93 4.7 49.6 1.0
HB2 A:PRO44 4.7 27.8 1.0
HG12 A:VAL59 4.7 26.6 1.0
CB A:ILE67 4.7 21.5 1.0
O3 A:GOL404 4.7 56.2 1.0
HG23 A:ILE67 4.9 24.0 1.0
HG13 A:VAL59 4.9 26.6 1.0
CG1 A:ILE67 4.9 21.5 1.0
H A:GLY46 4.9 30.6 1.0
CE A:MET93 4.9 41.4 1.0

Fluorine binding site 3 out of 4 in 7a6d

Go back to Fluorine Binding Sites List in 7a6d
Fluorine binding site 3 out of 4 in the Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:50.3
occ:0.50
F A:RGN408 0.0 50.3 0.5
C2 A:RGN408 1.4 48.0 0.5
F1 A:RGN408 2.1 51.4 0.5
HB3 A:GLU57 2.3 24.8 1.0
C3 A:RGN408 2.3 45.5 0.5
C1 A:RGN408 2.4 44.9 0.5
HA A:GLU57 3.0 24.1 1.0
CB A:GLU57 3.1 20.6 1.0
C4 A:RGN408 3.2 43.2 0.5
HB2 A:GLU57 3.4 24.8 1.0
C A:RGN408 3.4 43.0 0.5
CA A:GLU57 3.5 20.1 1.0
N A:GLU57 3.9 21.0 1.0
H A:GLU57 3.9 25.2 1.0
OE1 A:GLU57 4.1 25.4 1.0
O A:HOH652 4.3 29.5 1.0
CG A:GLU57 4.3 24.0 1.0
CD A:GLU57 4.5 25.3 1.0
O1 A:RGN408 4.5 41.6 0.5
O A:RGN408 4.6 43.7 0.5
HG2 A:PRO56 4.6 28.6 1.0
HB2 A:PRO56 4.6 27.9 1.0
C A:PRO56 4.7 19.8 1.0
O A:HOH602 4.7 24.4 1.0
HG3 A:GLU57 4.7 28.8 1.0
C A:GLU57 4.9 19.4 1.0
HB3 A:ARG60 5.0 24.0 1.0

Fluorine binding site 4 out of 4 in 7a6d

Go back to Fluorine Binding Sites List in 7a6d
Fluorine binding site 4 out of 4 in the Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Trna-Guanine Transglycosylase C158S/C281S/Y330C/H333A Mutant in Complex with Rac-Trans-4,4-Difluorocyclopentane-1,2-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:51.4
occ:0.50
F1 A:RGN408 0.0 51.4 0.5
C2 A:RGN408 1.4 48.0 0.5
F A:RGN408 2.1 50.3 0.5
C1 A:RGN408 2.3 44.9 0.5
C3 A:RGN408 2.4 45.5 0.5
HA A:GLU57 2.9 24.1 1.0
C A:RGN408 3.1 43.0 0.5
HG2 A:ARG60 3.4 24.8 1.0
HB3 A:ARG60 3.4 24.0 1.0
C4 A:RGN408 3.4 43.2 0.5
HB3 A:GLU57 3.6 24.8 1.0
CA A:GLU57 3.8 20.1 1.0
HB2 A:ARG60 3.8 24.0 1.0
CB A:ARG60 3.9 20.0 1.0
CB A:GLU57 4.1 20.6 1.0
CG A:ARG60 4.1 20.6 1.0
HB2 A:GLU57 4.1 24.8 1.0
O A:HOH688 4.3 37.8 1.0
N A:GLU57 4.4 21.0 1.0
O A:RGN408 4.5 43.7 0.5
HG3 A:ARG60 4.5 24.8 1.0
O A:PRO56 4.6 21.0 1.0
O1 A:RGN408 4.6 41.6 0.5
C A:PRO56 4.7 19.8 1.0
H A:GLU57 4.8 25.2 1.0
C A:GLU57 4.8 19.4 1.0
O A:GLU57 4.8 20.7 1.0
HB2 A:PRO56 4.9 27.9 1.0

Reference:

D.Nguyen, X.Xie, S.Jakobi, F.Terwesten, A.Metz, T.X.P.Nguyen, V.A.Palchykov, A.Heine, K.Reuter, G.Klebe. Targeting A Cryptic Pocket in A Protein-Protein Contact By Disulfide-Induced Rupture of A Homodimeric Interface Acs Chem.Biol. 2021.
ISSN: ESSN 1554-8937
DOI: 10.1021/ACSCHEMBIO.1C00296
Page generated: Sat Jul 10 14:00:40 2021

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