Fluorine in PDB 8d0f: Human SARM1 Tir Domain Bound to Nb-2-Adpr

Enzymatic activity of Human SARM1 Tir Domain Bound to Nb-2-Adpr

All present enzymatic activity of Human SARM1 Tir Domain Bound to Nb-2-Adpr:
3.2.2.6;

Protein crystallography data

The structure of Human SARM1 Tir Domain Bound to Nb-2-Adpr, PDB code: 8d0f was solved by M.A.Bratkowski, P.Mathur, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.08 / 1.74
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 32.94, 86.363, 115.757, 90, 90, 90
R / Rfree (%) 21.3 / 25.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human SARM1 Tir Domain Bound to Nb-2-Adpr (pdb code 8d0f). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human SARM1 Tir Domain Bound to Nb-2-Adpr, PDB code: 8d0f:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8d0f

Go back to Fluorine Binding Sites List in 8d0f
Fluorine binding site 1 out of 6 in the Human SARM1 Tir Domain Bound to Nb-2-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human SARM1 Tir Domain Bound to Nb-2-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:26.1
occ:1.00
 F48 A:Q0U801 0.0 26.1 1.0
C47 A:Q0U801 1.4 25.7 1.0
F50 A:Q0U801 2.2 21.0 1.0
F49 A:Q0U801 2.3 24.2 1.0
C46 A:Q0U801 2.4 25.7 1.0
N45 A:Q0U801 2.9 21.6 1.0
NH2 A:ARG570 2.9 24.1 1.0
O51 A:Q0U801 3.2 23.5 1.0
C44 A:Q0U801 3.3 23.2 1.0
OD2 A:ASP594 3.5 22.8 1.0
CG A:ASP594 3.5 22.1 1.0
CB A:ASP594 3.6 17.4 1.0
C A:ASP594 3.8 20.9 1.0
N A:VAL595 3.9 19.6 1.0
O A:ASP594 3.9 17.3 1.0
CG1 A:VAL595 3.9 23.0 1.0
CA A:VAL595 4.0 19.1 1.0
CZ A:ARG570 4.1 36.1 1.0
OD1 A:ASP594 4.1 19.3 1.0
CA A:ASP594 4.3 18.6 1.0
C38 A:Q0U801 4.3 20.9 1.0
CD2 A:LEU598 4.3 16.7 1.0
N43 A:Q0U801 4.4 22.5 1.0
O A:HOH913 4.5 23.8 1.0
CB A:VAL595 4.7 17.2 1.0
NH1 A:ARG570 4.8 36.7 1.0
CB A:LEU598 4.8 18.1 1.0
C37 A:Q0U801 4.8 19.1 1.0
OE2 B:GLU686 4.9 42.9 1.0
NE A:ARG570 4.9 31.1 1.0

Fluorine binding site 2 out of 6 in 8d0f

Go back to Fluorine Binding Sites List in 8d0f
Fluorine binding site 2 out of 6 in the Human SARM1 Tir Domain Bound to Nb-2-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human SARM1 Tir Domain Bound to Nb-2-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:24.2
occ:1.00
 F49 A:Q0U801 0.0 24.2 1.0
C47 A:Q0U801 1.4 25.7 1.0
F50 A:Q0U801 2.2 21.0 1.0
F48 A:Q0U801 2.3 26.1 1.0
C46 A:Q0U801 2.4 25.7 1.0
O A:HOH913 3.4 23.8 1.0
CA A:VAL595 3.5 19.1 1.0
CG1 A:VAL595 3.6 23.0 1.0
O A:HOH914 3.7 24.9 1.0
N45 A:Q0U801 3.7 21.6 1.0
OE2 B:GLU686 3.9 42.9 1.0
CB A:VAL595 4.0 17.2 1.0
O A:ASP594 4.0 17.3 1.0
CD B:GLU686 4.0 40.6 1.0
OE1 B:GLU686 4.1 36.6 1.0
N A:VAL595 4.1 19.6 1.0
C A:ASP594 4.3 20.9 1.0
C A:VAL595 4.4 22.1 1.0
O A:VAL595 4.4 25.2 1.0
O B:HOH915 4.5 30.3 1.0
O51 A:Q0U801 4.6 23.5 1.0
C44 A:Q0U801 4.6 23.2 1.0
NH2 A:ARG570 4.7 24.1 1.0
O B:HOH902 4.7 24.1 1.0
CG B:GLU686 4.8 27.0 1.0
CB B:GLU686 5.0 22.9 1.0

Fluorine binding site 3 out of 6 in 8d0f

Go back to Fluorine Binding Sites List in 8d0f
Fluorine binding site 3 out of 6 in the Human SARM1 Tir Domain Bound to Nb-2-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human SARM1 Tir Domain Bound to Nb-2-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:21.0
occ:1.00
 F50 A:Q0U801 0.0 21.0 1.0
C47 A:Q0U801 1.4 25.7 1.0
F48 A:Q0U801 2.2 26.1 1.0
F49 A:Q0U801 2.2 24.2 1.0
C46 A:Q0U801 2.4 25.7 1.0
N45 A:Q0U801 2.8 21.6 1.0
O A:HOH913 3.1 23.8 1.0
O A:ASP594 3.6 17.3 1.0
CD2 A:LEU598 3.6 16.7 1.0
O A:LEU598 3.6 21.4 1.0
CB A:LEU598 3.7 18.1 1.0
CG A:LEU598 3.9 15.3 1.0
C44 A:Q0U801 3.9 23.2 1.0
C A:ASP594 4.1 20.9 1.0
C A:LEU598 4.4 19.9 1.0
O51 A:Q0U801 4.5 23.5 1.0
CA A:VAL595 4.5 19.1 1.0
CA A:LEU598 4.6 16.4 1.0
CB A:ASP594 4.6 17.4 1.0
N A:VAL595 4.7 19.6 1.0
CA A:ASP594 4.9 18.6 1.0
N43 A:Q0U801 4.9 22.5 1.0

Fluorine binding site 4 out of 6 in 8d0f

Go back to Fluorine Binding Sites List in 8d0f
Fluorine binding site 4 out of 6 in the Human SARM1 Tir Domain Bound to Nb-2-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human SARM1 Tir Domain Bound to Nb-2-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:21.5
occ:1.00
 F48 B:Q0U801 0.0 21.5 1.0
C47 B:Q0U801 1.4 22.9 1.0
F49 B:Q0U801 2.2 25.0 1.0
F50 B:Q0U801 2.2 27.5 1.0
C46 B:Q0U801 2.4 25.1 1.0
N45 B:Q0U801 2.8 20.0 1.0
O B:HOH909 3.3 26.1 1.0
CD2 B:LEU598 3.6 17.1 1.0
O B:LEU598 3.6 22.3 1.0
O B:ASP594 3.6 17.9 1.0
CB B:LEU598 3.7 17.8 1.0
C44 B:Q0U801 4.0 19.7 1.0
CG B:LEU598 4.0 16.6 1.0
C B:ASP594 4.2 19.8 1.0
C B:LEU598 4.4 22.7 1.0
O51 B:Q0U801 4.5 22.0 1.0
CA B:LEU598 4.6 22.3 1.0
CA B:VAL595 4.7 25.8 1.0
CB B:ASP594 4.7 20.8 1.0
N B:VAL595 4.8 24.2 1.0
N43 B:Q0U801 4.9 21.9 1.0
C52 B:Q0U801 5.0 20.2 1.0
CA B:ASP594 5.0 19.8 1.0

Fluorine binding site 5 out of 6 in 8d0f

Go back to Fluorine Binding Sites List in 8d0f
Fluorine binding site 5 out of 6 in the Human SARM1 Tir Domain Bound to Nb-2-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human SARM1 Tir Domain Bound to Nb-2-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:25.0
occ:1.00
 F49 B:Q0U801 0.0 25.0 1.0
C47 B:Q0U801 1.4 22.9 1.0
F48 B:Q0U801 2.2 21.5 1.0
F50 B:Q0U801 2.3 27.5 1.0
C46 B:Q0U801 2.4 25.1 1.0
N45 B:Q0U801 2.8 20.0 1.0
NH2 B:ARG570 2.8 24.6 1.0
O51 B:Q0U801 3.2 22.0 1.0
C44 B:Q0U801 3.2 19.7 1.0
OD2 B:ASP594 3.5 20.2 1.0
CG B:ASP594 3.6 20.2 1.0
CB B:ASP594 3.6 20.8 1.0
C B:ASP594 3.9 19.8 1.0
O B:ASP594 3.9 17.9 1.0
N B:VAL595 4.0 24.2 1.0
CZ B:ARG570 4.1 31.4 1.0
OD1 B:ASP594 4.2 19.8 1.0
CG1 B:VAL595 4.2 19.6 1.0
CA B:VAL595 4.2 25.8 1.0
CD2 B:LEU598 4.2 17.1 1.0
C40 B:Q0U801 4.3 20.9 1.0
N43 B:Q0U801 4.4 21.9 1.0
CA B:ASP594 4.4 19.8 1.0
O B:HOH909 4.7 26.1 1.0
CB B:LEU598 4.8 17.8 1.0
NH1 B:ARG570 4.9 31.6 1.0
C39 B:Q0U801 4.9 21.1 1.0
CB B:VAL595 4.9 20.3 1.0
NE B:ARG570 4.9 32.8 1.0
OE2 A:GLU686 5.0 42.8 1.0

Fluorine binding site 6 out of 6 in 8d0f

Go back to Fluorine Binding Sites List in 8d0f
Fluorine binding site 6 out of 6 in the Human SARM1 Tir Domain Bound to Nb-2-Adpr


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human SARM1 Tir Domain Bound to Nb-2-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:27.5
occ:1.00
 F50 B:Q0U801 0.0 27.5 1.0
C47 B:Q0U801 1.4 22.9 1.0
F48 B:Q0U801 2.2 21.5 1.0
F49 B:Q0U801 2.3 25.0 1.0
C46 B:Q0U801 2.4 25.1 1.0
O B:HOH909 3.6 26.1 1.0
CA B:VAL595 3.6 25.8 1.0
N45 B:Q0U801 3.6 20.0 1.0
CG1 B:VAL595 3.8 19.6 1.0
O A:HOH905 3.9 28.5 1.0
CD A:GLU686 3.9 37.7 1.0
OE2 A:GLU686 3.9 42.8 1.0
O B:ASP594 4.1 17.9 1.0
OE1 A:GLU686 4.1 34.6 1.0
CB B:VAL595 4.2 20.3 1.0
N B:VAL595 4.2 24.2 1.0
O A:HOH922 4.4 30.0 1.0
C B:ASP594 4.4 19.8 1.0
CG A:GLU686 4.4 25.9 1.0
C B:VAL595 4.5 22.9 1.0
O B:VAL595 4.6 26.9 1.0
C44 B:Q0U801 4.6 19.7 1.0
NH2 B:ARG570 4.6 24.6 1.0
O51 B:Q0U801 4.6 22.0 1.0

Reference:

M.Bratkowski, T.C.Burdett, J.Danao, X.Wang, P.Mathur, W.Gu, J.A.Beckstead, S.Talreja, Y.S.Yang, G.Danko, J.H.Park, M.Walton, S.P.Brown, C.M.Tegley, P.R.B.Joseph, C.H.Reynolds, S.Sambashivan. Uncompetitive, Adduct-Forming SARM1 Inhibitors Are Neuroprotective in Preclinical Models of Nerve Injury and Disease. Neuron V. 110 3711 2022.
ISSN: ISSN 0896-6273
PubMed: 36087583
DOI: 10.1016/J.NEURON.2022.08.017
Page generated: Fri Aug 2 17:18:58 2024

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