Arsenic in PDB 5mdi: Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution

The structure of Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution, PDB code: 5mdi was solved by T.Afroz, E.-M.Hock, P.Ernst, C.Foglieni, M.Jambeau, L.Gilhespy, F.Laferriere, Z.Maniecka, A.Plueckthun, P.Mittl, P.Paganetti, F.H.T.Allain, M.Polymenidou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.76 / 2.10
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	89.518, 89.518, 49.153, 90.00, 90.00, 120.00
R / Rfree (%)	16.4 / 20.6

The binding sites of Arsenic atom in the Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution (pdb code 5mdi). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution, PDB code: 5mdi:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in the Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:As39 b:49.5 occ:1.00 AS A:CAF39 0.0 49.5 1.0 O1 A:CAF39 1.7 65.5 1.0 CE2 A:CAF39 1.9 50.6 1.0 CE1 A:CAF39 2.0 50.6 1.0 SG A:CAF39 2.3 48.9 1.0 HE21 A:CAF39 2.5 50.2 1.0 HE23 A:CAF39 2.5 53.2 1.0 HE22 A:CAF39 2.5 49.9 1.0 HE12 A:CAF39 2.5 52.0 1.0 HE11 A:CAF39 2.5 53.4 1.0 HE13 A:CAF39 2.5 50.6 1.0 HD22 A:ASN76 2.9 20.0 0.0 HB3 A:CAF39 3.0 47.8 1.0 CB A:CAF39 3.1 47.2 1.0 HB2 A:ASN76 3.2 40.0 1.0 O B:ALA33 3.3 47.6 1.0 HB3 A:ASN76 3.3 41.6 1.0 O A:CAF39 3.5 38.5 1.0 C A:CAF39 3.5 39.7 1.0 CB A:ASN76 3.7 40.4 1.0 HA3 A:GLY40 3.8 37.5 1.0 ND2 A:ASN76 3.8 35.6 1.0 CA A:CAF39 3.9 42.4 1.0 N A:GLY40 3.9 37.9 1.0 HD3 B:PRO36 3.9 49.8 1.0 HB2 A:CAF39 4.1 49.3 1.0 HG3 B:PRO36 4.1 56.2 1.0 O A:HOH112 4.1 38.3 1.0 HA B:GLN34 4.3 41.4 1.0 CG A:ASN76 4.3 39.4 1.0 H A:CAF39 4.3 40.7 1.0 CA A:GLY40 4.3 37.2 1.0 C B:ALA33 4.3 46.2 1.0 H A:GLY40 4.3 37.7 1.0 HD21 A:ASN76 4.5 20.0 0.0 N A:CAF39 4.6 40.9 1.0 CD B:PRO36 4.7 50.6 1.0 O A:ASN76 4.7 42.9 1.0 O A:HOH114 4.8 51.9 1.0 HA A:CAF39 4.8 43.6 1.0 CG B:PRO36 4.9 55.0 1.0 C A:ASN76 4.9 41.7 1.0 HA A:PRO78 4.9 60.4 1.0 HA B:ALA33 4.9 49.6 1.0 CA B:GLN34 5.0 39.4 1.0 CA A:ASN76 5.0 38.0 1.0

Arsenic binding site 2 out of 4 in the Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:As50 b:52.7 occ:1.00 AS A:CAF50 0.0 52.7 1.0 CE1 A:CAF50 1.8 47.3 1.0 O1 A:CAF50 1.8 58.8 1.0 CE2 A:CAF50 1.8 50.5 1.0 HE13 A:CAF50 2.3 48.3 1.0 SG A:CAF50 2.4 38.6 1.0 HE21 A:CAF50 2.4 51.4 1.0 HE11 A:CAF50 2.4 48.0 1.0 HE12 A:CAF50 2.4 50.8 1.0 HE22 A:CAF50 2.4 53.4 1.0 HE23 A:CAF50 2.4 52.6 1.0 HB2 A:CAF50 2.8 33.8 1.0 CB A:CAF50 3.2 32.6 1.0 HD2 B:PRO15 3.8 40.6 1.0 HB3 A:CAF50 3.9 32.7 1.0 HA A:CAF50 4.0 33.3 1.0 O B:PRO15 4.1 33.9 1.0 HG2 B:GLU14 4.2 50.1 1.0 HG3 B:GLU14 4.2 52.7 1.0 CA A:CAF50 4.2 32.1 1.0 O B:HOH202 4.3 28.6 1.0 O B:HOH227 4.3 41.5 1.0 HG2 B:PRO15 4.3 38.3 1.0 CG B:GLU14 4.6 51.9 1.0 HB2 B:PRO15 4.6 35.7 1.0 CD B:PRO15 4.7 39.2 1.0 HG2 B:ARG6 4.7 43.5 1.0 OE2 B:GLU14 4.7 52.9 1.0 CD B:GLU14 4.9 54.7 1.0 CG B:PRO15 4.9 39.0 1.0 C B:PRO15 4.9 36.8 1.0 HG3 B:GLU17 4.9 34.4 1.0 HD3 B:ARG6 5.0 50.2 1.0

Arsenic binding site 3 out of 4 in the Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:As39 b:58.2 occ:1.00 AS B:CAF39 0.0 58.2 1.0 O1 B:CAF39 1.7 60.9 1.0 CE1 B:CAF39 1.9 59.3 1.0 CE2 B:CAF39 2.0 62.9 1.0 SG B:CAF39 2.3 52.6 1.0 HE11 B:CAF39 2.5 62.0 1.0 HE12 B:CAF39 2.5 60.7 1.0 HE13 B:CAF39 2.5 59.4 1.0 HE22 B:CAF39 2.5 63.6 1.0 HE23 B:CAF39 2.5 63.0 1.0 HE21 B:CAF39 2.5 60.1 1.0 HB3 B:CAF39 2.9 49.5 1.0 CB B:CAF39 3.2 48.6 1.0 HB3 B:ASN76 3.5 49.9 1.0 HD22 B:ASN76 3.7 20.0 0.0 HB2 B:ASN76 3.7 47.4 1.0 C B:CAF39 3.8 41.5 1.0 O B:CAF39 3.8 40.7 1.0 HB2 B:CAF39 4.0 50.9 1.0 CA B:CAF39 4.0 44.0 1.0 CB B:ASN76 4.1 49.0 1.0 N B:GLY40 4.2 38.2 1.0 O B:HOH208 4.2 44.4 1.0 HA3 B:GLY40 4.3 37.7 1.0 ND2 B:ASN76 4.4 49.6 1.0 H B:CAF39 4.4 42.6 1.0 H B:GLY40 4.5 38.5 1.0 O B:HOH244 4.6 75.0 1.0 CG B:ASN76 4.7 51.8 1.0 N B:CAF39 4.8 41.4 1.0 CA B:GLY40 4.8 37.8 1.0 HA B:PRO78 4.8 65.4 1.0 HG3 B:PRO78 4.9 60.7 1.0 HA B:CAF39 4.9 44.3 1.0 C B:TYR77 5.0 55.7 1.0

Arsenic binding site 4 out of 4 in the Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of Tdp-43 N-Terminal Domain at 2.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:As50 b:80.9 occ:1.00 AS B:CAF50 0.0 80.9 1.0 O1 B:CAF50 1.7 79.3 1.0 CE2 B:CAF50 2.0 86.9 1.0 CE1 B:CAF50 2.0 89.5 1.0 SG B:CAF50 2.2 82.0 1.0 HE11 B:CAF50 2.5 85.8 1.0 HE21 B:CAF50 2.5 89.7 1.0 HE23 B:CAF50 2.5 85.3 1.0 HE22 B:CAF50 2.5 87.2 1.0 HE13 B:CAF50 2.5 90.3 1.0 HE12 B:CAF50 2.5 89.7 1.0 HB2 B:CAF50 2.8 64.3 1.0 CB B:CAF50 2.9 62.6 1.0 HA B:CAF50 3.1 58.8 1.0 CA B:CAF50 3.5 57.7 1.0 HB3 B:CAF50 3.9 62.6 1.0 N B:CAF50 4.3 59.1 1.0 O B:HOH232 4.3 67.3 1.0 H B:CAF50 4.5 59.8 1.0 HB2 B:SER48 4.7 71.9 1.0 C B:CAF50 4.8 47.1 1.0 HG B:SER48 5.0 20.0 0.0 H B:MET51 5.0 46.2 1.0

T.Afroz, E.M.Hock, P.Ernst, C.Foglieni, M.Jambeau, L.A.B.Gilhespy, F.Laferriere, Z.Maniecka, A.Pluckthun, P.Mittl, P.Paganetti, F.H.T.Allain, M.Polymenidou. Functional and Dynamic Polymerization of the Als-Linked Protein Tdp-43 Antagonizes Its Pathologic Aggregation. Nat Commun V. 8 45 2017.
ISSN: ESSN 2041-1723
PubMed: 28663553
DOI: 10.1038/S41467-017-00062-0