Atomistry » Fluorine » PDB 6zqs-7adg » 7a6d
Atomistry »
  Fluorine »
    PDB 6zqs-7adg »
      7a6d »

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

Go back to Fluorine Binding Sites List in 7a6d
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: Fri Aug 2 05:30:33 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy