Fluorine in PDB 8d0i: Human SARM1 Bound to An Nb-3 Eadpr Adduct

Enzymatic activity of Human SARM1 Bound to An Nb-3 Eadpr Adduct

All present enzymatic activity of Human SARM1 Bound to An Nb-3 Eadpr Adduct:
3.2.2.6;

Protein crystallography data

The structure of Human SARM1 Bound to An Nb-3 Eadpr Adduct, PDB code: 8d0i 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) 39.40 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 33.273, 78.797, 116.975, 90, 90, 90
R / Rfree (%) 17.4 / 21.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human SARM1 Bound to An Nb-3 Eadpr Adduct (pdb code 8d0i). 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 Bound to An Nb-3 Eadpr Adduct, PDB code: 8d0i:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8d0i

Go back to Fluorine Binding Sites List in 8d0i
Fluorine binding site 1 out of 6 in the Human SARM1 Bound to An Nb-3 Eadpr Adduct


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human SARM1 Bound to An Nb-3 Eadpr Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:32.2
occ:1.00
 F09 A:PZ7801 0.0 32.2 1.0
C08 A:PZ7801 1.4 24.6 1.0
F11 A:PZ7801 2.3 33.3 1.0
F10 A:PZ7801 2.3 24.6 1.0
C07 A:PZ7801 2.4 33.5 1.0
O B:HOH979 3.4 42.4 1.0
CA A:VAL595 3.4 19.6 1.0
CG1 A:VAL595 3.7 22.5 1.0
N06 A:PZ7801 3.7 27.0 1.0
O A:HOH924 3.7 29.7 1.0
CB A:VAL595 3.9 20.4 1.0
O A:ASP594 4.0 17.2 1.0
N A:VAL595 4.1 23.0 1.0
O A:VAL595 4.2 29.6 1.0
C A:VAL595 4.2 23.8 1.0
O12 A:PZ7801 4.3 29.7 1.0
C A:ASP594 4.3 21.2 1.0
C05 A:PZ7801 4.5 28.9 1.0
NH2 A:ARG570 4.6 26.3 1.0
CG B:GLU686 4.8 26.7 1.0
O A:HOH908 5.0 41.7 1.0

Fluorine binding site 2 out of 6 in 8d0i

Go back to Fluorine Binding Sites List in 8d0i
Fluorine binding site 2 out of 6 in the Human SARM1 Bound to An Nb-3 Eadpr Adduct


Mono view


Stereo pair view

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

b:24.6
occ:1.00
 F10 A:PZ7801 0.0 24.6 1.0
C08 A:PZ7801 1.4 24.6 1.0
F11 A:PZ7801 2.2 33.3 1.0
F09 A:PZ7801 2.3 32.2 1.0
C07 A:PZ7801 2.4 33.5 1.0
N06 A:PZ7801 2.8 27.0 1.0
O12 A:PZ7801 2.8 29.7 1.0
NH2 A:ARG570 3.0 26.3 1.0
C05 A:PZ7801 3.0 28.9 1.0
OD2 A:ASP594 3.7 19.6 1.0
CB A:ASP594 3.8 19.9 1.0
CG A:ASP594 3.8 22.4 1.0
C A:ASP594 4.0 21.2 1.0
O A:ASP594 4.0 17.2 1.0
CZ A:ARG570 4.1 40.7 1.0
N A:VAL595 4.1 23.0 1.0
C55 A:PZ7801 4.1 19.7 1.0
CA A:VAL595 4.2 19.6 1.0
CG1 A:VAL595 4.2 22.5 1.0
N03 A:PZ7801 4.2 23.8 1.0
O B:HOH979 4.4 42.4 1.0
CA A:ASP594 4.5 21.9 1.0
O A:HOH908 4.5 41.7 1.0
CD2 A:LEU598 4.6 21.1 1.0
OD1 A:ASP594 4.6 18.3 1.0
NH1 A:ARG570 4.7 34.8 1.0
C54 A:PZ7801 4.7 16.6 1.0
CB A:VAL595 4.8 20.4 1.0
O A:HOH924 4.9 29.7 1.0
C13 A:PZ7801 4.9 23.4 1.0
NE A:ARG570 4.9 30.8 1.0

Fluorine binding site 3 out of 6 in 8d0i

Go back to Fluorine Binding Sites List in 8d0i
Fluorine binding site 3 out of 6 in the Human SARM1 Bound to An Nb-3 Eadpr Adduct


Mono view


Stereo pair view

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

b:33.3
occ:1.00
 F11 A:PZ7801 0.0 33.3 1.0
C08 A:PZ7801 1.4 24.6 1.0
F10 A:PZ7801 2.2 24.6 1.0
F09 A:PZ7801 2.3 32.2 1.0
C07 A:PZ7801 2.4 33.5 1.0
N06 A:PZ7801 3.0 27.0 1.0
O A:HOH924 3.2 29.7 1.0
O A:ASP594 3.5 17.2 1.0
CD2 A:LEU598 3.6 21.1 1.0
CB A:LEU598 3.8 21.4 1.0
O A:LEU598 4.0 20.8 1.0
C05 A:PZ7801 4.0 28.9 1.0
C A:ASP594 4.1 21.2 1.0
CG A:LEU598 4.1 22.7 1.0
CA A:VAL595 4.4 19.6 1.0
O12 A:PZ7801 4.4 29.7 1.0
N A:VAL595 4.6 23.0 1.0
C A:LEU598 4.7 27.9 1.0
CA A:LEU598 4.7 21.1 1.0
CB A:ASP594 4.8 19.9 1.0
CA A:ASP594 4.9 21.9 1.0

Fluorine binding site 4 out of 6 in 8d0i

Go back to Fluorine Binding Sites List in 8d0i
Fluorine binding site 4 out of 6 in the Human SARM1 Bound to An Nb-3 Eadpr Adduct


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human SARM1 Bound to An Nb-3 Eadpr Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:20.8
occ:1.00
 F09 B:PZ7801 0.0 20.8 1.0
C08 B:PZ7801 1.4 27.8 0.6
F11 B:PZ7801 2.3 27.2 0.9
F10 B:PZ7801 2.3 29.1 0.8
C07 B:PZ7801 2.4 23.3 1.0
N06 B:PZ7801 2.8 27.6 1.0
O12 B:PZ7801 2.9 24.8 1.0
NH2 B:ARG570 3.0 29.3 1.0
C05 B:PZ7801 3.0 30.2 1.0
OD2 B:ASP594 3.8 20.6 1.0
CG B:ASP594 4.0 21.4 1.0
CB B:ASP594 4.0 13.9 1.0
C B:ASP594 4.0 26.4 1.0
O B:ASP594 4.0 20.7 1.0
N B:VAL595 4.1 24.1 1.0
CA B:VAL595 4.1 22.4 1.0
CZ B:ARG570 4.1 29.5 1.0
CG1 B:VAL595 4.1 24.4 1.0
N03 B:PZ7801 4.2 22.7 1.0
C55 B:PZ7801 4.2 18.9 1.0
CD2 B:LEU598 4.5 18.4 1.0
O A:HOH950 4.6 47.8 1.0
CA B:ASP594 4.6 16.9 1.0
OD1 B:ASP594 4.7 19.2 1.0
O B:HOH910 4.7 28.6 1.0
CB B:VAL595 4.8 20.3 1.0
NH1 B:ARG570 4.8 29.5 1.0
C54 B:PZ7801 4.8 15.9 1.0
C13 B:PZ7801 5.0 18.7 1.0
NE B:ARG570 5.0 28.0 1.0

Fluorine binding site 5 out of 6 in 8d0i

Go back to Fluorine Binding Sites List in 8d0i
Fluorine binding site 5 out of 6 in the Human SARM1 Bound to An Nb-3 Eadpr Adduct


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human SARM1 Bound to An Nb-3 Eadpr Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:29.1
occ:0.80
 F10 B:PZ7801 0.0 29.1 0.8
C08 B:PZ7801 1.4 27.8 0.6
F11 B:PZ7801 2.2 27.2 0.9
F09 B:PZ7801 2.3 20.8 1.0
C07 B:PZ7801 2.4 23.3 1.0
CA B:VAL595 3.5 22.4 1.0
O B:HOH910 3.6 28.6 1.0
N06 B:PZ7801 3.7 27.6 1.0
CG1 B:VAL595 3.9 24.4 1.0
O A:HOH950 3.9 47.8 1.0
CB B:VAL595 4.1 20.3 1.0
O B:ASP594 4.2 20.7 1.0
O B:VAL595 4.3 33.4 1.0
N B:VAL595 4.3 24.1 1.0
C B:VAL595 4.3 25.0 1.0
O12 B:PZ7801 4.3 24.8 1.0
C05 B:PZ7801 4.5 30.2 1.0
C B:ASP594 4.5 26.4 1.0
NH2 B:ARG570 4.7 29.3 1.0
CG A:GLU686 4.8 26.7 1.0

Fluorine binding site 6 out of 6 in 8d0i

Go back to Fluorine Binding Sites List in 8d0i
Fluorine binding site 6 out of 6 in the Human SARM1 Bound to An Nb-3 Eadpr Adduct


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human SARM1 Bound to An Nb-3 Eadpr Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:27.2
occ:0.86
 F11 B:PZ7801 0.0 27.2 0.9
C08 B:PZ7801 1.4 27.8 0.6
F10 B:PZ7801 2.2 29.1 0.8
F09 B:PZ7801 2.3 20.8 1.0
C07 B:PZ7801 2.4 23.3 1.0
O B:HOH910 2.9 28.6 1.0
N06 B:PZ7801 3.0 27.6 1.0
O B:ASP594 3.5 20.7 1.0
CD2 B:LEU598 3.8 18.4 1.0
CB B:LEU598 3.9 17.2 1.0
O B:LEU598 4.0 25.8 1.0
C05 B:PZ7801 4.1 30.2 1.0
C B:ASP594 4.2 26.4 1.0
CG B:LEU598 4.2 23.8 1.0
CA B:VAL595 4.4 22.4 1.0
O12 B:PZ7801 4.4 24.8 1.0
N B:VAL595 4.7 24.1 1.0
C B:LEU598 4.8 18.4 1.0
CA B:LEU598 4.9 22.5 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 17:20:53 2024

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