Sodium in PDB 8rdn: Holomycin Methyltransferase Dtpm with Sah and Xrd-271

The structure of Holomycin Methyltransferase Dtpm with Sah and Xrd-271, PDB code: 8rdn was solved by E.M.Huber, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	112.4, 218.83, 55.35, 90, 90, 90
R / Rfree (%)	19.3 / 22.2

The structure of Holomycin Methyltransferase Dtpm with Sah and Xrd-271 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Holomycin Methyltransferase Dtpm with Sah and Xrd-271 (pdb code 8rdn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Holomycin Methyltransferase Dtpm with Sah and Xrd-271, PDB code: 8rdn:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Holomycin Methyltransferase Dtpm with Sah and Xrd-271


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Holomycin Methyltransferase Dtpm with Sah and Xrd-271 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:49.8 occ:1.00 OD1 B:ASP180 2.3 36.1 1.0 O B:VAL181 2.7 35.5 1.0 N B:LYS247 3.0 32.9 1.0 O B:GLY182 3.1 31.4 1.0 N B:SAH401 3.3 34.3 1.0 CG B:ASP180 3.4 36.9 1.0 C B:GLY182 3.5 32.3 1.0 O B:HOH527 3.6 35.2 1.0 C B:VAL181 3.6 34.3 1.0 O B:LYS247 3.6 31.7 1.0 CA B:VAL246 3.7 34.1 1.0 C B:VAL246 3.8 33.1 1.0 CA B:LYS247 3.8 32.7 1.0 CA B:GLY183 3.9 32.5 1.0 CB B:LYS247 3.9 34.2 1.0 N B:GLY183 3.9 32.1 1.0 OD2 B:ASP180 3.9 36.3 1.0 O B:LEU245 4.0 34.7 1.0 OG1 B:THR249 4.1 31.2 1.0 N B:VAL181 4.2 34.5 1.0 C B:LYS247 4.2 32.3 1.0 CA B:GLY182 4.3 33.3 1.0 N B:VAL246 4.3 35.0 1.0 N B:GLY182 4.3 34.2 1.0 C B:LEU245 4.3 35.2 1.0 C B:ASP180 4.5 35.8 1.0 CA B:VAL181 4.5 34.3 1.0 CB B:ASP180 4.7 35.8 1.0 CA B:SAH401 4.7 34.6 1.0 CA B:ASP180 4.8 35.9 1.0 CB B:VAL246 4.9 35.1 1.0 CG2 B:VAL246 4.9 35.0 1.0 C B:GLY183 5.0 32.0 1.0

Sodium binding site 2 out of 3 in the Holomycin Methyltransferase Dtpm with Sah and Xrd-271


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Holomycin Methyltransferase Dtpm with Sah and Xrd-271 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na404 b:46.9 occ:1.00 OG1 C:THR179 2.5 36.7 1.0 O C:PRO238 3.1 46.3 1.0 CB C:THR179 3.5 36.9 1.0 CG2 C:THR179 3.7 38.1 1.0 OH C:TYR244 3.8 38.2 1.0 C C:PRO238 3.9 45.9 1.0 CB C:ALA241 3.9 45.0 1.0 CB C:PRO238 3.9 45.1 1.0 CE1 C:TYR244 4.0 38.9 1.0 CZ C:TYR244 4.3 38.9 1.0 O C:GLY239 4.3 48.3 1.0 CA C:PRO238 4.5 44.6 1.0 N C:ALA241 4.6 46.5 1.0 N C:GLY239 4.7 46.8 1.0 CB C:THR202 4.7 39.1 1.0 C C:GLY239 4.7 48.2 1.0 CG C:PRO238 4.7 44.8 1.0 OG1 C:THR202 4.8 39.1 1.0 CA C:THR179 4.8 37.0 1.0 CG2 C:THR202 4.9 39.3 1.0 CA C:ALA241 4.9 45.0 1.0

Sodium binding site 3 out of 3 in the Holomycin Methyltransferase Dtpm with Sah and Xrd-271


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Holomycin Methyltransferase Dtpm with Sah and Xrd-271 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na404 b:61.5 occ:1.00 OD1 D:ASP6 2.5 62.9 1.0 CG D:ASP6 3.7 64.2 1.0 CB D:ALA9 4.1 38.2 1.0 OD2 D:ASP6 4.4 66.2 1.0 CB D:ASP6 4.7 61.9 1.0 O D:ASP6 4.7 56.1 1.0 CA D:ASP6 4.8 59.9 1.0 N D:GLY10 4.9 36.0 1.0

L.Su, E.M.Huber, M.Westphalen, J.Gellner, E.Bode, T.Kobel, P.Grun, M.M.Alanjary, T.Glatter, K.Cirnski, R.Muller, D.Schindler, M.Groll, H.B.Bode. Isofunctional But Structurally Different Methyltransferases For Dithiolopyrrolone Diversification. Angew.Chem.Int.Ed.Engl. 10799 2024.
ISSN: ESSN 1521-3773
PubMed: 39185606
DOI: 10.1002/ANIE.202410799