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: Wed Apr 5 02:09:57 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy