Fluorine in PDB 8d0g: Human SARM1 Tir Domain Bound to Nb-3-Adprp

Enzymatic activity of Human SARM1 Tir Domain Bound to Nb-3-Adprp

All present enzymatic activity of Human SARM1 Tir Domain Bound to Nb-3-Adprp:
3.2.2.6;

Protein crystallography data

The structure of Human SARM1 Tir Domain Bound to Nb-3-Adprp, PDB code: 8d0g 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) 35.69 / 1.99
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 86.953, 117.429, 33.271, 90, 90, 90
R / Rfree (%) 18.9 / 23.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human SARM1 Tir Domain Bound to Nb-3-Adprp (pdb code 8d0g). 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-3-Adprp, PDB code: 8d0g:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8d0g

Go back to Fluorine Binding Sites List in 8d0g
Fluorine binding site 1 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adprp


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-3-Adprp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:25.5
occ:1.00
 F09 A:Q1X801 0.0 25.5 1.0
C08 A:Q1X801 1.3 21.4 1.0
F11 A:Q1X801 2.2 19.6 1.0
F10 A:Q1X801 2.2 21.4 1.0
C07 A:Q1X801 2.3 17.3 1.0
O A:HOH905 3.6 21.4 1.0
CA A:VAL595 3.6 18.7 1.0
N06 A:Q1X801 3.6 20.0 1.0
CG1 A:VAL595 3.8 19.4 1.0
O A:ASP594 3.9 16.5 1.0
O A:HOH902 4.1 26.6 1.0
CB A:VAL595 4.1 18.8 1.0
N A:VAL595 4.3 18.0 1.0
C A:ASP594 4.3 16.8 1.0
O A:VAL595 4.4 26.8 1.0
C A:VAL595 4.4 21.9 1.0
O12 A:Q1X801 4.5 21.1 1.0
C05 A:Q1X801 4.6 19.7 1.0
CG B:GLU686 4.7 22.9 1.0
NH2 A:ARG570 4.7 24.6 1.0

Fluorine binding site 2 out of 6 in 8d0g

Go back to Fluorine Binding Sites List in 8d0g
Fluorine binding site 2 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adprp


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-3-Adprp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:21.4
occ:1.00
 F10 A:Q1X801 0.0 21.4 1.0
C08 A:Q1X801 1.4 21.4 1.0
F11 A:Q1X801 2.2 19.6 1.0
F09 A:Q1X801 2.2 25.5 1.0
C07 A:Q1X801 2.3 17.3 1.0
N06 A:Q1X801 2.7 20.0 1.0
O A:HOH905 3.3 21.4 1.0
CD2 A:LEU598 3.5 14.7 1.0
O A:ASP594 3.6 16.5 1.0
O A:LEU598 3.8 19.8 1.0
CB A:LEU598 3.8 15.8 1.0
C05 A:Q1X801 3.9 19.7 1.0
CG A:LEU598 4.0 16.4 1.0
C A:ASP594 4.3 16.8 1.0
O12 A:Q1X801 4.4 21.1 1.0
C A:LEU598 4.6 17.6 1.0
CA A:LEU598 4.7 18.4 1.0
CA A:VAL595 4.7 18.7 1.0
CB A:ASP594 4.8 13.6 1.0
N A:VAL595 4.9 18.0 1.0
N03 A:Q1X801 4.9 20.6 1.0
C04 A:Q1X801 5.0 19.3 1.0

Fluorine binding site 3 out of 6 in 8d0g

Go back to Fluorine Binding Sites List in 8d0g
Fluorine binding site 3 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adprp


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-3-Adprp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:19.6
occ:1.00
 F11 A:Q1X801 0.0 19.6 1.0
C08 A:Q1X801 1.4 21.4 1.0
F10 A:Q1X801 2.2 21.4 1.0
F09 A:Q1X801 2.2 25.5 1.0
C07 A:Q1X801 2.4 17.3 1.0
N06 A:Q1X801 2.8 20.0 1.0
NH2 A:ARG570 3.1 24.6 1.0
O12 A:Q1X801 3.2 21.1 1.0
C05 A:Q1X801 3.3 19.7 1.0
CB A:ASP594 3.6 13.6 1.0
OD2 A:ASP594 3.7 18.8 1.0
CG A:ASP594 3.7 15.9 1.0
O A:ASP594 3.7 16.5 1.0
C A:ASP594 3.8 16.8 1.0
N A:VAL595 4.0 18.0 1.0
CA A:VAL595 4.1 18.7 1.0
CG1 A:VAL595 4.1 19.4 1.0
CZ A:ARG570 4.2 26.1 1.0
CA A:ASP594 4.3 18.9 1.0
OD1 A:ASP594 4.3 15.5 1.0
C57 A:Q1X801 4.4 17.4 1.0
CD2 A:LEU598 4.4 14.7 1.0
N03 A:Q1X801 4.5 20.6 1.0
CB A:VAL595 4.8 18.8 1.0
O A:HOH905 4.8 21.4 1.0
NH1 A:ARG570 4.9 29.5 1.0
CB A:LEU598 4.9 15.8 1.0
C56 A:Q1X801 4.9 17.2 1.0

Fluorine binding site 4 out of 6 in 8d0g

Go back to Fluorine Binding Sites List in 8d0g
Fluorine binding site 4 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adprp


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-3-Adprp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:22.2
occ:1.00
 F09 B:Q1X801 0.0 22.2 1.0
C08 B:Q1X801 1.4 22.4 1.0
F11 B:Q1X801 2.2 19.8 1.0
F10 B:Q1X801 2.2 24.3 1.0
C07 B:Q1X801 2.3 20.6 1.0
N06 B:Q1X801 2.9 19.0 1.0
NH2 B:ARG570 2.9 23.9 1.0
O12 B:Q1X801 3.2 19.4 1.0
C05 B:Q1X801 3.3 20.9 1.0
CG B:ASP594 3.7 21.2 1.0
OD2 B:ASP594 3.8 21.0 1.0
CB B:ASP594 3.8 18.4 1.0
C B:ASP594 3.9 18.6 1.0
CG1 B:VAL595 3.9 17.7 1.0
O B:ASP594 4.0 17.4 1.0
N B:VAL595 4.0 21.3 1.0
CA B:VAL595 4.1 20.8 1.0
CZ B:ARG570 4.1 29.3 1.0
OD1 B:ASP594 4.3 17.6 1.0
CA B:ASP594 4.5 17.4 1.0
N03 B:Q1X801 4.5 17.3 1.0
C57 B:Q1X801 4.6 16.8 1.0
CD2 B:LEU598 4.6 15.7 1.0
CB B:VAL595 4.6 19.7 1.0
O B:HOH918 4.7 20.5 1.0
NH1 B:ARG570 4.8 28.4 1.0
NE B:ARG570 4.9 26.4 1.0

Fluorine binding site 5 out of 6 in 8d0g

Go back to Fluorine Binding Sites List in 8d0g
Fluorine binding site 5 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adprp


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-3-Adprp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:24.3
occ:1.00
 F10 B:Q1X801 0.0 24.3 1.0
C08 B:Q1X801 1.4 22.4 1.0
F11 B:Q1X801 2.2 19.8 1.0
F09 B:Q1X801 2.2 22.2 1.0
C07 B:Q1X801 2.3 20.6 1.0
O B:HOH918 3.6 20.5 1.0
N06 B:Q1X801 3.6 19.0 1.0
CA B:VAL595 3.7 20.8 1.0
CG1 B:VAL595 3.9 17.7 1.0
O B:ASP594 4.2 17.4 1.0
O A:HOH952 4.2 21.0 1.0
CB B:VAL595 4.3 19.7 1.0
N B:VAL595 4.4 21.3 1.0
C B:ASP594 4.5 18.6 1.0
O B:VAL595 4.5 22.8 1.0
CG A:GLU686 4.5 21.6 1.0
C B:VAL595 4.5 23.7 1.0
C05 B:Q1X801 4.6 20.9 1.0
O12 B:Q1X801 4.7 19.4 1.0
NH2 B:ARG570 4.7 23.9 1.0

Fluorine binding site 6 out of 6 in 8d0g

Go back to Fluorine Binding Sites List in 8d0g
Fluorine binding site 6 out of 6 in the Human SARM1 Tir Domain Bound to Nb-3-Adprp


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-3-Adprp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:19.8
occ:1.00
 F11 B:Q1X801 0.0 19.8 1.0
C08 B:Q1X801 1.4 22.4 1.0
F09 B:Q1X801 2.2 22.2 1.0
F10 B:Q1X801 2.2 24.3 1.0
C07 B:Q1X801 2.4 20.6 1.0
N06 B:Q1X801 2.8 19.0 1.0
O B:HOH918 3.3 20.5 1.0
O B:ASP594 3.6 17.4 1.0
CD2 B:LEU598 3.6 15.7 1.0
CB B:LEU598 3.8 13.2 1.0
O B:LEU598 3.8 19.5 1.0
C05 B:Q1X801 4.0 20.9 1.0
CG B:LEU598 4.1 16.7 1.0
C B:ASP594 4.2 18.6 1.0
O12 B:Q1X801 4.5 19.4 1.0
C B:LEU598 4.6 18.4 1.0
CA B:VAL595 4.7 20.8 1.0
CB B:ASP594 4.7 18.4 1.0
CA B:LEU598 4.7 14.8 1.0
N B:VAL595 4.8 21.3 1.0
CA B:ASP594 4.9 17.4 1.0
N03 B:Q1X801 5.0 17.3 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 17:19:16 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy