Sodium in PDB 7m6k: Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Vmn

All present enzymatic activity of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Vmn:
3.2.2.6;

The structure of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Vmn, PDB code: 7m6k was solved by W.Gu, Z.Luo, B.Kobe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.36 / 1.69
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.065, 51.01, 76.56, 103.49, 101.78, 96.07
R / Rfree (%)	19 / 22.6

The binding sites of Sodium atom in the Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Vmn (pdb code 7m6k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Vmn, PDB code: 7m6k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Vmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Vmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:56.2 occ:1.00 HE2 A:LYS549 1.9 63.1 1.0 OD1 A:ASP546 2.4 55.6 1.0 HE3 A:LYS549 2.5 63.1 1.0 CE A:LYS549 2.6 52.6 1.0 HA A:ASP546 2.7 46.1 1.0 HD2 A:LYS549 2.9 52.7 1.0 O A:ASN544 3.0 45.5 1.0 CD A:LYS549 3.3 43.9 1.0 HB3 A:LYS549 3.4 39.4 1.0 CA A:ASP546 3.5 38.4 1.0 CG A:ASP546 3.5 56.5 1.0 C A:ASN544 3.6 45.8 1.0 HB2 A:LYS549 3.6 39.4 1.0 N A:ASP546 3.6 37.8 1.0 HA A:ASN544 3.6 56.1 1.0 C A:ASP545 3.7 39.0 1.0 O A:HIS543 3.7 37.1 1.0 O A:ASP545 3.8 35.2 1.0 NZ A:LYS549 3.8 43.1 1.0 CB A:LYS549 3.9 32.9 1.0 HZ3 A:LYS549 3.9 51.8 1.0 HD3 A:LYS549 4.0 52.7 1.0 H A:ASP546 4.0 45.4 1.0 CB A:ASP546 4.1 48.3 1.0 HZ2 A:LYS549 4.2 51.8 1.0 CA A:ASN544 4.2 46.7 1.0 CG A:LYS549 4.2 39.8 1.0 N A:ASP545 4.3 41.7 1.0 HD2 A:PHE581 4.3 50.0 1.0 HE2 A:PHE581 4.4 52.5 1.0 HZ1 A:LYS549 4.5 51.8 1.0 CA A:ASP545 4.5 39.5 1.0 HB3 A:ASP546 4.6 58.0 1.0 OD2 A:ASP546 4.6 57.4 1.0 O A:HOH888 4.6 46.1 1.0 HA A:ASP545 4.7 47.5 1.0 C A:ASP546 4.7 35.0 1.0 C A:HIS543 4.7 40.2 1.0 HG2 A:LYS549 4.8 47.8 1.0 HG3 A:LYS549 4.8 47.8 1.0 HB2 A:ASP546 4.8 58.0 1.0 H A:LYS549 4.9 32.2 1.0 H A:ASP545 4.9 50.0 1.0 O A:ASP546 5.0 35.8 1.0 N A:ASN544 5.0 45.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Vmn


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Vmn within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:48.6 occ:1.00 O A:HOH828 2.8 37.6 1.0 HB1 A:ALA598 2.9 46.2 1.0 O A:HOH831 2.9 40.1 1.0 HB3 A:PRO388 3.1 42.7 1.0 HG2 A:ARG592 3.1 56.2 1.0 HA A:PRO388 3.6 40.2 1.0 CB A:ALA598 3.8 38.5 1.0 CB A:PRO388 4.0 35.6 1.0 H A:THR389 4.0 36.9 1.0 O A:ALA598 4.0 37.3 1.0 HA A:ARG592 4.0 52.5 1.0 CG A:ARG592 4.1 46.9 1.0 HB2 A:ALA598 4.2 46.2 1.0 HB3 A:ALA598 4.2 46.2 1.0 HG3 A:PRO388 4.2 46.4 1.0 CA A:PRO388 4.3 33.5 1.0 HG3 A:ARG592 4.4 56.2 1.0 HB2 A:PRO388 4.6 42.7 1.0 HA A:ALA598 4.6 43.6 1.0 CA A:ALA598 4.6 36.4 1.0 C A:ALA598 4.6 34.0 1.0 HD2 A:ARG592 4.7 63.9 1.0 CG A:PRO388 4.7 38.6 1.0 N A:THR389 4.7 30.7 1.0 HD3 A:ARG592 4.7 63.9 1.0 CD A:ARG592 4.8 53.2 1.0 HB3 A:ARG592 4.8 56.7 1.0 CB A:ARG592 4.8 47.3 1.0 CA A:ARG592 4.8 43.8 1.0

A.Loreto, C.Angeletti, W.Gu, A.Osborne, B.Nieuwenhuis, J.Gilley, E.Merlini, P.Arthur-Farraj, A.Amici, Z.Luo, L.Hartley-Tassell, T.Ve, L.M.Desrochers, Q.Wang, B.Kobe, G.Orsomando, M.P.Coleman. Neurotoxin-Mediated Potent Activation of the Axon Degeneration Regulator SARM1. Elife V. 10 2021.
ISSN: ESSN 2050-084X
PubMed: 34870595
DOI: 10.7554/ELIFE.72823