Fluorine in PDB 8enk: Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp

Enzymatic activity of Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp

All present enzymatic activity of Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp:
3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp, PDB code: 8enk was solved by Y.Xie, Y.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.72 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.534, 96.786, 126.18, 90, 90, 90
R / Rfree (%) 22.4 / 25.3

Other elements in 8enk:

The structure of Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp (pdb code 8enk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp, PDB code: 8enk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8enk

Go back to Fluorine Binding Sites List in 8enk
Fluorine binding site 1 out of 6 in the Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp


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 UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:49.3
occ:1.00
 F1 A:BEF1001 0.0 49.3 1.0
BE A:BEF1001 1.5 50.2 1.0
O1B A:ADP1000 2.3 51.4 1.0
F3 A:BEF1001 2.5 49.3 1.0
F2 A:BEF1001 2.5 51.3 1.0
NH1 A:ARG380 2.8 49.9 1.0
NH2 A:ARG377 2.9 45.2 1.0
NH2 A:ARG380 3.2 49.5 1.0
O A:HOH1105 3.3 48.7 1.0
O A:HOH1106 3.3 50.1 1.0
NH1 A:ARG377 3.3 44.9 1.0
CZ A:ARG380 3.4 51.9 1.0
CZ A:ARG377 3.6 46.9 1.0
N A:GLY92 3.6 51.6 1.0
PB A:ADP1000 3.7 48.0 1.0
O A:HOH1103 4.0 44.5 1.0
CA A:GLY92 4.1 52.4 1.0
N A:GLY350 4.3 49.0 1.0
O2B A:ADP1000 4.3 47.5 1.0
CA A:GLY350 4.4 45.0 1.0
O3A A:ADP1000 4.4 50.9 1.0
C A:SER91 4.5 54.6 1.0
CA A:SER91 4.5 54.6 1.0
MG A:MG1002 4.5 50.5 1.0
CB A:SER91 4.7 53.6 1.0
O3B A:ADP1000 4.7 53.2 1.0
NE A:ARG380 4.7 52.0 1.0
O A:HOH1108 4.7 49.9 1.0
O A:HOH1107 4.8 50.0 1.0
C A:GLY350 4.8 47.7 1.0
O A:GLY350 4.8 43.2 1.0
OE2 A:GLU197 4.8 44.3 1.0
O1A A:ADP1000 4.9 52.4 1.0
NE A:ARG377 4.9 50.6 1.0
NZ A:LYS95 5.0 51.3 1.0

Fluorine binding site 2 out of 6 in 8enk

Go back to Fluorine Binding Sites List in 8enk
Fluorine binding site 2 out of 6 in the Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp


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 UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:51.3
occ:1.00
 F2 A:BEF1001 0.0 51.3 1.0
BE A:BEF1001 1.6 50.2 1.0
F3 A:BEF1001 2.5 49.3 1.0
F1 A:BEF1001 2.5 49.3 1.0
O1B A:ADP1000 2.5 51.4 1.0
O A:HOH1107 2.6 50.0 1.0
O A:HOH1105 3.1 48.7 1.0
NZ A:LYS95 3.1 51.3 1.0
O A:HOH1106 3.2 50.1 1.0
O A:HOH1108 3.2 49.9 1.0
CE A:LYS95 3.4 52.2 1.0
PB A:ADP1000 3.6 48.0 1.0
CB A:ALA229 3.9 51.1 1.0
O3B A:ADP1000 4.0 53.2 1.0
O2B A:ADP1000 4.0 47.5 1.0
OE2 A:GLU197 4.1 44.3 1.0
MG A:MG1002 4.1 50.5 1.0
N A:GLY92 4.2 51.6 1.0
CA A:SER91 4.3 54.6 1.0
N A:ALA229 4.5 51.0 1.0
CE1 A:HIS373 4.5 49.1 1.0
ND1 A:HIS373 4.5 48.6 1.0
NH2 A:ARG377 4.6 45.2 1.0
CA A:ALA229 4.8 50.0 1.0
OE1 A:GLU197 4.8 43.6 1.0
OG A:SER91 4.8 51.7 1.0
O A:HOH1103 4.8 44.5 1.0
C A:SER91 4.8 54.6 1.0
CB A:SER91 4.8 53.6 1.0
CD A:GLU197 4.8 44.9 1.0
O A:HOH1102 4.9 47.2 1.0
O3A A:ADP1000 5.0 50.9 1.0
CD A:LYS95 5.0 53.8 1.0

Fluorine binding site 3 out of 6 in 8enk

Go back to Fluorine Binding Sites List in 8enk
Fluorine binding site 3 out of 6 in the Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp


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 UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:49.3
occ:1.00
 F3 A:BEF1001 0.0 49.3 1.0
BE A:BEF1001 1.5 50.2 1.0
MG A:MG1002 2.1 50.5 1.0
O A:HOH1103 2.4 44.5 1.0
F2 A:BEF1001 2.5 51.3 1.0
O1B A:ADP1000 2.5 51.4 1.0
F1 A:BEF1001 2.5 49.3 1.0
O A:HOH1108 2.5 49.9 1.0
O2B A:ADP1000 2.8 47.5 1.0
O A:HOH1102 3.0 47.2 1.0
PB A:ADP1000 3.1 48.0 1.0
OE2 A:GLU197 3.3 44.3 1.0
O A:HOH1105 3.5 48.7 1.0
CA A:GLY350 3.7 45.0 1.0
O A:HOH1107 3.9 50.0 1.0
N A:GLY350 4.2 49.0 1.0
NH2 A:ARG380 4.2 49.5 1.0
O A:HOH1101 4.2 50.6 1.0
O3A A:ADP1000 4.2 50.9 1.0
O A:GLY350 4.3 43.2 1.0
O3B A:ADP1000 4.3 53.2 1.0
O1A A:ADP1000 4.3 52.4 1.0
C A:GLY350 4.4 47.7 1.0
CD A:GLU197 4.5 44.9 1.0
CE A:LYS95 4.6 52.2 1.0
NZ A:LYS95 4.6 51.3 1.0
NH1 A:ARG377 4.7 44.9 1.0
PA A:ADP1000 4.8 49.9 1.0
NH1 A:ARG380 4.9 49.9 1.0
O A:HOH1106 4.9 50.1 1.0
NH2 A:ARG377 4.9 45.2 1.0

Fluorine binding site 4 out of 6 in 8enk

Go back to Fluorine Binding Sites List in 8enk
Fluorine binding site 4 out of 6 in the Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp


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 UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:54.5
occ:1.00
 F1 B:BEF1001 0.0 54.5 1.0
BE B:BEF1001 1.5 53.8 1.0
O2B B:ADP1000 2.3 52.9 1.0
F3 B:BEF1001 2.6 51.3 1.0
NH2 B:ARG377 2.6 57.0 1.0
F2 B:BEF1001 2.6 53.6 1.0
NH1 B:ARG380 2.8 56.2 1.0
NH2 B:ARG380 3.0 50.9 1.0
O B:HOH1102 3.2 52.5 1.0
NH1 B:ARG377 3.3 50.5 1.0
O B:HOH1105 3.3 60.2 1.0
CZ B:ARG380 3.3 56.6 1.0
CZ B:ARG377 3.3 52.1 1.0
N B:GLY92 3.4 55.3 1.0
PB B:ADP1000 3.8 51.8 1.0
CA B:GLY92 3.9 54.5 1.0
O B:HOH1103 4.1 50.9 1.0
CA B:GLY350 4.1 52.5 1.0
N B:GLY350 4.2 51.7 1.0
C B:SER91 4.3 58.0 1.0
O3A B:ADP1000 4.4 52.8 1.0
O1B B:ADP1000 4.5 50.5 1.0
CB B:SER91 4.5 61.2 1.0
CA B:SER91 4.5 58.5 1.0
MG B:MG1002 4.5 54.9 1.0
NE B:ARG377 4.6 57.6 1.0
NE B:ARG380 4.6 54.1 1.0
C B:GLY350 4.7 47.6 1.0
O3B B:ADP1000 4.7 53.4 1.0
O B:HOH1109 4.8 55.9 1.0
O B:GLY350 4.8 48.0 1.0
OE2 B:GLU197 4.8 57.5 1.0
CB B:ALA376 4.9 62.8 1.0
O2A B:ADP1000 4.9 52.7 1.0
OG B:SER91 5.0 63.2 1.0

Fluorine binding site 5 out of 6 in 8enk

Go back to Fluorine Binding Sites List in 8enk
Fluorine binding site 5 out of 6 in the Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp


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 UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:53.6
occ:1.00
 F2 B:BEF1001 0.0 53.6 1.0
BE B:BEF1001 1.6 53.8 1.0
F3 B:BEF1001 2.5 51.3 1.0
O2B B:ADP1000 2.5 52.9 1.0
F1 B:BEF1001 2.6 54.5 1.0
O B:HOH1109 2.6 55.9 1.0
O B:HOH1105 2.9 60.2 1.0
O B:HOH1102 3.2 52.5 1.0
NZ B:LYS95 3.3 57.8 1.0
CE B:LYS95 3.5 56.7 1.0
PB B:ADP1000 3.6 51.8 1.0
N B:GLY92 3.6 55.3 1.0
CA B:SER91 3.7 58.5 1.0
CB B:ALA229 3.8 62.0 1.0
O B:HOH1106 3.9 56.2 1.0
O3B B:ADP1000 3.9 53.4 1.0
CB B:SER91 4.1 61.2 1.0
OG B:SER91 4.2 63.2 1.0
C B:SER91 4.2 58.0 1.0
O1B B:ADP1000 4.2 50.5 1.0
OE2 B:GLU197 4.2 57.5 1.0
NH2 B:ARG377 4.3 57.0 1.0
MG B:MG1002 4.4 54.9 1.0
N B:ALA229 4.6 65.7 1.0
ND1 B:HIS373 4.6 61.3 1.0
CE1 B:HIS373 4.6 61.8 1.0
CA B:GLY92 4.7 54.5 1.0
N B:SER91 4.7 61.4 1.0
CA B:ALA229 4.8 63.8 1.0
O B:LYS90 4.8 58.8 1.0
O3A B:ADP1000 5.0 52.8 1.0
O B:HOH1103 5.0 50.9 1.0

Fluorine binding site 6 out of 6 in 8enk

Go back to Fluorine Binding Sites List in 8enk
Fluorine binding site 6 out of 6 in the Crystal Structure of UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp


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 UAP56 in Complex with THO1, the Yeast Homolog of Human Sarnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:51.3
occ:1.00
 F3 B:BEF1001 0.0 51.3 1.0
BE B:BEF1001 1.5 53.8 1.0
MG B:MG1002 2.1 54.9 1.0
O2B B:ADP1000 2.3 52.9 1.0
F2 B:BEF1001 2.5 53.6 1.0
F1 B:BEF1001 2.6 54.5 1.0
O B:HOH1103 2.7 50.9 1.0
O B:HOH1106 2.7 56.2 1.0
O1B B:ADP1000 2.9 50.5 1.0
O B:HOH1104 3.1 57.7 1.0
PB B:ADP1000 3.1 51.8 1.0
O B:HOH1102 3.3 52.5 1.0
OE2 B:GLU197 3.3 57.5 1.0
O B:HOH1109 3.5 55.9 1.0
CA B:GLY350 3.5 52.5 1.0
N B:GLY350 4.1 51.7 1.0
O B:HOH1101 4.2 50.6 1.0
O3B B:ADP1000 4.2 53.4 1.0
O3A B:ADP1000 4.3 52.8 1.0
NH2 B:ARG380 4.3 50.9 1.0
O B:GLY350 4.4 48.0 1.0
CE B:LYS95 4.5 56.7 1.0
C B:GLY350 4.5 47.6 1.0
CD B:GLU197 4.5 56.6 1.0
O B:HOH1105 4.5 60.2 1.0
NH2 B:ARG377 4.6 57.0 1.0
O2A B:ADP1000 4.6 52.7 1.0
NH1 B:ARG377 4.8 50.5 1.0
NZ B:LYS95 4.8 57.8 1.0
N B:GLY92 4.9 55.3 1.0
OD1 B:ASP196 5.0 51.8 1.0

Reference:

Y.Xie, Y.Ren. Structural Basis For High Order Complex of Sarnp and DDX39B to Facilitate Mrnp Assembly Cell Rep 2023.
ISSN: ESSN 2211-1247
Page generated: Fri Aug 2 18:14:57 2024

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