Fluorine in PDB 7z6a: 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: 7z6a 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) 41.44 / 1.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.9, 100.88, 44.29, 90, 110.65, 90
R / Rfree (%) 19.8 / 23

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 7z6a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 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: 7z6a:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 7z6a

Go back to Fluorine Binding Sites List in 7z6a
Fluorine binding site 1 out of 7 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:F1

b:76.2
occ:1.00
 F B:GF21 0.0 76.2 1.0
C2' B:GF21 1.4 77.4 1.0
C3' B:GF21 2.4 80.6 1.0
C1' B:GF21 2.4 72.3 1.0
O3' B:GF21 2.6 84.0 1.0
CG2 A:THR297 2.9 68.0 1.0
O5' B:GF22 3.1 83.0 1.0
C4' B:GF21 3.1 76.5 1.0
O4' B:GF21 3.2 74.8 1.0
O4' B:GF22 3.2 77.9 1.0
P B:GF22 3.5 85.9 1.0
N9 B:GF21 3.6 68.0 1.0
OG1 A:THR297 3.6 69.6 1.0
C4' B:GF22 3.9 78.0 1.0
CB A:THR297 3.9 65.0 1.0
C5' B:GF22 4.0 81.7 1.0
C4 B:GF21 4.1 67.9 1.0
N3 B:GF21 4.2 66.9 1.0
OP2 B:GF22 4.3 84.3 1.0
C1' B:GF22 4.4 78.0 1.0
C8 B:GF22 4.6 73.2 1.0
C5' B:GF21 4.6 76.3 1.0
OP1 B:GF22 4.6 80.8 1.0
C8 B:GF21 4.6 66.7 1.0
CA A:THR297 4.8 58.7 1.0
N9 B:GF22 4.9 74.3 1.0
CG2 A:VAL303 4.9 48.6 1.0

Fluorine binding site 2 out of 7 in 7z6a

Go back to Fluorine Binding Sites List in 7z6a
Fluorine binding site 2 out of 7 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:F2

b:85.1
occ:1.00
 F B:GF22 0.0 85.1 1.0
C2' B:GF22 1.4 83.0 1.0
C1' B:GF22 2.4 78.0 1.0
C3' B:GF22 2.4 80.1 1.0
O3' B:GF22 2.6 80.1 1.0
N9 B:GF22 3.3 74.3 1.0
N3 B:GF22 3.3 73.5 1.0
O4' B:GF22 3.4 77.9 1.0
C4' B:GF22 3.5 78.0 1.0
C4 B:GF22 3.5 74.0 1.0
C2 B:GF22 4.5 74.3 1.0
C8 B:GF22 4.5 73.2 1.0
C5' B:GF22 4.6 81.7 1.0
N2 B:GF22 4.9 72.9 1.0
C5 B:GF22 4.9 71.4 1.0

Fluorine binding site 3 out of 7 in 7z6a

Go back to Fluorine Binding Sites List in 7z6a
Fluorine binding site 3 out of 7 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:F5

b:82.3
occ:1.00
 F2' B:CFZ5 0.0 82.3 1.0
C2' B:CFZ5 1.4 83.9 1.0
C1' B:CFZ5 2.4 83.3 1.0
C3' B:CFZ5 2.4 85.8 1.0
O3' B:CFZ5 2.6 85.8 1.0
C4' B:CFZ5 3.2 87.5 1.0
O4' B:CFZ5 3.2 89.5 1.0
O2 B:CFZ5 3.5 75.9 1.0
N1 B:CFZ5 3.5 79.5 1.0
O4' B:CFZ6 3.5 85.0 1.0
O5' B:CFZ6 3.6 88.1 1.0
P B:CFZ6 3.8 91.9 1.0
C2 B:CFZ5 3.9 76.3 1.0
C5' B:CFZ6 4.3 84.4 1.0
C4' B:CFZ6 4.3 83.0 1.0
C6 B:CFZ6 4.5 77.8 1.0
C6 B:CFZ5 4.6 78.7 1.0
C1' B:CFZ6 4.6 80.0 1.0
C5' B:CFZ5 4.7 86.8 1.0
O2P B:CFZ6 4.7 83.5 1.0
O1P B:CFZ6 4.8 73.8 1.0

Fluorine binding site 4 out of 7 in 7z6a

Go back to Fluorine Binding Sites List in 7z6a
Fluorine binding site 4 out of 7 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 4 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:F6

b:80.2
occ:1.00
 F2' B:CFZ6 0.0 80.2 1.0
C2' B:CFZ6 1.4 79.1 1.0
C3' B:CFZ6 2.4 80.4 1.0
C1' B:CFZ6 2.4 80.0 1.0
O3' B:CFZ6 2.7 83.7 1.0
C4' B:CFZ6 3.0 83.0 1.0
O4' B:CFZ6 3.0 85.0 1.0
O4' B:AF27 3.4 79.3 1.0
N1 B:CFZ6 3.6 76.6 1.0
O2 B:CFZ6 3.8 73.6 1.0
C2 B:CFZ6 4.1 74.8 1.0
C1' B:AF27 4.3 73.2 1.0
P B:AF27 4.3 89.3 1.0
C4' B:AF27 4.4 76.6 1.0
C5' B:CFZ6 4.4 84.4 1.0
C6 B:CFZ6 4.6 77.8 1.0
O5' B:AF27 4.7 82.8 1.0
C8 B:AF27 4.8 70.0 1.0
OP2 B:AF27 4.9 83.3 1.0
N9 B:AF27 4.9 71.7 1.0
C5' B:AF27 4.9 76.1 1.0

Fluorine binding site 5 out of 7 in 7z6a

Go back to Fluorine Binding Sites List in 7z6a
Fluorine binding site 5 out of 7 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 5 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:68.6
occ:1.00
 F B:AF27 0.0 68.6 1.0
C2' B:AF27 1.4 71.8 1.0
C3' B:AF27 2.4 72.1 1.0
C1' B:AF27 2.4 73.2 1.0
O3' B:AF27 2.7 64.8 1.0
O4' B:AF27 3.1 79.3 1.0
C4' B:AF27 3.1 76.6 1.0
N9 B:AF27 3.6 71.7 1.0
O4' B:CFZ8 3.9 60.1 1.0
N3 B:AF27 4.1 63.3 1.0
C4 B:AF27 4.2 68.1 1.0
P B:CFZ8 4.2 68.1 1.0
O5' B:CFZ8 4.2 69.4 1.0
C5' B:AF27 4.5 76.1 1.0
C4' B:CFZ8 4.5 61.5 1.0
N2 B:GF21 4.6 72.9 1.0
C5' B:CFZ8 4.6 62.7 1.0
C8 B:AF27 4.8 70.0 1.0
O2P B:CFZ8 4.9 69.8 1.0

Fluorine binding site 6 out of 7 in 7z6a

Go back to Fluorine Binding Sites List in 7z6a
Fluorine binding site 6 out of 7 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 6 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:54.0
occ:1.00
 F2' B:CFZ8 0.0 54.0 1.0
C2' B:CFZ8 1.4 57.5 1.0
C3' B:CFZ8 2.4 58.9 1.0
C1' B:CFZ8 2.4 60.3 1.0
O3' B:CFZ8 2.7 60.9 1.0
O4' B:CFZ8 3.1 60.1 1.0
C4' B:CFZ8 3.1 61.5 1.0
O A:SER300 3.2 44.0 1.0
N1 B:CFZ8 3.7 56.1 1.0
CG1 A:VAL303 3.8 43.3 1.0
O2 B:CFZ8 3.8 54.6 1.0
CA A:SER300 4.0 51.6 1.0
CB A:SER300 4.0 50.4 1.0
N A:PHE304 4.0 33.0 1.0
C A:SER300 4.0 47.5 1.0
CB A:VAL303 4.1 42.0 1.0
CB A:PHE304 4.1 35.7 1.0
OG A:SER300 4.1 59.7 1.0
C2 B:CFZ8 4.2 52.9 1.0
O4' B:CFZ9 4.2 44.3 1.0
P B:CFZ9 4.2 62.2 1.0
C5' B:CFZ9 4.3 54.5 1.0
O5' B:CFZ9 4.4 55.8 1.0
CA A:PHE304 4.5 32.7 1.0
C5' B:CFZ8 4.5 62.7 1.0
C A:VAL303 4.7 33.3 1.0
C6 B:CFZ8 4.7 59.7 1.0
C4' B:CFZ9 4.7 54.0 1.0
O2P B:CFZ9 4.8 56.2 1.0
CA A:VAL303 4.9 37.8 1.0
O A:HOH622 4.9 46.1 1.0

Fluorine binding site 7 out of 7 in 7z6a

Go back to Fluorine Binding Sites List in 7z6a
Fluorine binding site 7 out of 7 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 7 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:45.6
occ:1.00
 F2' B:CFZ9 0.0 45.6 1.0
C2' B:CFZ9 1.4 48.0 1.0
C3' B:CFZ9 2.3 49.1 1.0
C1' B:CFZ9 2.4 47.6 1.0
O3' B:CFZ9 2.5 52.4 1.0
C4' B:CFZ9 2.9 54.0 1.0
CB A:PRO268 3.0 25.4 1.0
O4' B:CFZ9 3.1 44.3 1.0
CE1 A:PHE304 3.3 33.1 1.0
CZ A:PHE304 3.4 33.1 1.0
N1 B:CFZ9 3.6 46.7 1.0
CG A:PRO268 3.6 25.2 1.0
O2 B:CFZ9 3.7 42.8 1.0
CD1 A:PHE304 3.8 37.9 1.0
CE2 A:PHE304 3.9 31.8 1.0
P B:A9Z10 4.0 59.5 1.0
C2 B:CFZ9 4.1 50.9 1.0
OP2 B:A9Z10 4.2 45.7 1.0
CG A:PHE304 4.2 35.6 1.0
CD2 A:PHE304 4.3 34.6 1.0
C5' B:CFZ9 4.4 54.5 1.0
CA A:PRO268 4.5 21.8 1.0
C6 B:CFZ9 4.6 50.0 1.0
O A:HOH587 4.7 26.8 1.0
O5' B:A9Z10 4.8 50.5 1.0
CD A:PRO268 4.9 24.0 1.0
OP1 B:A9Z10 4.9 52.2 1.0
C A:PRO268 5.0 22.9 1.0
O B:HOH103 5.0 41.6 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: Fri Aug 2 16:05:56 2024

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