Fluorine in PDB 7z6k: Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate

Enzymatic activity of Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate

All present enzymatic activity of Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate:
2.3.2.10;

Protein crystallography data

The structure of Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate, PDB code: 7z6k was solved by I.Li De La Sierra-Gallay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.95 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.22, 101.13, 46.05, 90, 102.57, 90
R / Rfree (%) 19.7 / 22.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate (pdb code 7z6k). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate, PDB code: 7z6k:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7z6k

Go back to Fluorine Binding Sites List in 7z6k
Fluorine binding site 1 out of 3 in the Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F7

b:64.1
occ:1.00
 F B:A5L7 0.0 64.1 1.0
C2' B:A5L7 1.4 64.8 1.0
C3' B:A5L7 2.3 68.3 1.0
C1' B:A5L7 2.4 65.5 1.0
O2 B:CFL8 2.5 59.8 1.0
N9 B:A5L7 2.8 65.2 1.0
C8 B:A5L7 2.9 64.1 1.0
O4' B:A5L7 3.0 71.9 1.0
C2 B:CFL8 3.1 59.3 1.0
C4' B:A5L7 3.3 71.4 1.0
O3' B:A5L7 3.5 66.3 1.0
N3 B:CFL8 3.5 63.1 1.0
O1P B:CFL8 3.9 57.7 1.0
O4' B:CFL8 3.9 56.0 1.0
C4 B:A5L7 4.0 65.9 1.0
N1 B:CFL8 4.0 58.0 1.0
O5' B:CFL8 4.1 54.1 1.0
N7 B:A5L7 4.1 64.2 1.0
P B:CFL8 4.1 63.7 1.0
C5' B:A5L7 4.1 75.6 1.0
C1' B:CFL8 4.5 54.3 1.0
C4 B:CFL8 4.6 59.6 1.0
C5 B:A5L7 4.6 64.3 1.0
N4 B:CFL9 4.7 51.4 1.0
C5' B:CFL8 4.7 54.4 1.0
N3 B:CFL9 4.8 55.7 1.0
C4' B:CFL8 4.8 53.4 1.0
N3 B:A5L7 4.9 64.0 1.0
F B:CFL8 4.9 54.1 1.0
C4 B:CFL9 5.0 50.6 1.0

Fluorine binding site 2 out of 3 in 7z6k

Go back to Fluorine Binding Sites List in 7z6k
Fluorine binding site 2 out of 3 in the Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F8

b:54.1
occ:1.00
 F B:CFL8 0.0 54.1 1.0
C2' B:CFL8 1.4 52.5 1.0
C3' B:CFL8 2.4 49.9 1.0
C1' B:CFL8 2.4 54.3 1.0
O2 B:CFL8 2.5 59.8 1.0
N1 B:CFL8 2.7 58.0 1.0
C2 B:CFL8 2.8 59.3 1.0
O4' B:CFL9 3.2 42.5 1.0
OG A:SER300 3.2 45.2 1.0
O4' B:CFL8 3.2 56.0 1.0
O2 B:CFL9 3.3 50.5 1.0
O3' B:CFL8 3.3 42.4 1.0
C4' B:CFL8 3.4 53.4 1.0
C2 B:CFL9 3.5 50.0 1.0
N1 B:A9Z10 3.6 42.3 1.0
C6 B:CFL8 3.8 58.8 1.0
N1 B:CFL9 3.8 45.0 1.0
N3 B:CFL8 3.9 63.1 1.0
O5' B:CFL9 4.0 42.2 1.0
C1' B:CFL9 4.0 42.8 1.0
C2 B:A9Z10 4.1 43.1 1.0
N3 B:CFL9 4.2 55.7 1.0
C5' B:CFL9 4.2 44.5 1.0
O5' B:CFL8 4.3 54.1 1.0
C4' B:CFL9 4.3 40.5 1.0
C6 B:A9Z10 4.3 43.1 1.0
P B:CFL9 4.3 44.1 1.0
N6 B:A9Z10 4.4 44.0 1.0
C5' B:CFL8 4.5 54.4 1.0
CB A:SER300 4.6 44.5 1.0
C6 B:CFL9 4.7 48.5 1.0
C5 B:CFL8 4.7 57.9 1.0
C4 B:CFL8 4.7 59.6 1.0
O1P B:CFL9 4.9 44.0 1.0
C4 B:CFL9 4.9 50.6 1.0
F B:A5L7 4.9 64.1 1.0

Fluorine binding site 3 out of 3 in 7z6k

Go back to Fluorine Binding Sites List in 7z6k
Fluorine binding site 3 out of 3 in the Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Weissella Viridescens Femxvv Non-Ribosomal Amino Acid Transferase in Complex with A Peptidyl-Xna Conjugate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F9

b:40.1
occ:1.00
 F B:CFL9 0.0 40.1 1.0
C2' B:CFL9 1.4 41.8 1.0
C1' B:CFL9 2.4 42.8 1.0
C3' B:CFL9 2.4 37.9 1.0
N1 B:CFL9 2.5 45.0 1.0
C2 B:CFL9 3.1 50.0 1.0
C6 B:CFL9 3.2 48.5 1.0
O3' B:CFL9 3.2 37.0 1.0
CB A:PRO268 3.3 27.1 1.0
O2 B:CFL9 3.4 50.5 1.0
CG A:PRO268 3.4 28.2 1.0
O4' B:CFL9 3.4 42.5 1.0
C4' B:CFL9 3.6 40.5 1.0
N3 B:CFL9 4.0 55.7 1.0
C5 B:CFL9 4.0 50.2 1.0
CE1 A:TYR269 4.1 35.7 1.0
CE1 A:PHE304 4.1 39.4 1.0
CD A:PRO268 4.1 26.3 1.0
CD1 A:PHE304 4.3 39.0 1.0
C4 B:CFL9 4.4 50.6 1.0
P B:A9Z10 4.5 39.2 1.0
CD1 A:TYR269 4.5 32.6 1.0
OP1 B:A9Z10 4.5 36.5 1.0
O5' B:CFL9 4.5 42.2 1.0
CZ A:PHE304 4.6 37.5 1.0
C5' B:CFL9 4.7 44.5 1.0
CA A:PRO268 4.7 27.7 1.0
CG A:PHE304 5.0 36.4 1.0

Reference:

L.Rietmeyer, I.Li De La Sierra-Gallay, G.Schepers, D.Dorchene, L.Iannazzo, D.Patin, T.Touze, H.Van Tilbeurgh, P.Herdewijn, M.Etheve-Quelquejeu, M.Fonvielle. Amino-Acyl Txna As Inhibitors or Amino Acid Donors in Peptide Synthesis. Nucleic Acids Res. V. 50 11415 2022.
ISSN: ESSN 1362-4962
PubMed: 36350642
DOI: 10.1093/NAR/GKAC1023
Page generated: Wed Apr 5 02:00:00 2023

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