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

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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

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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

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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

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