Sodium in PDB 8bih: O-Methyltransferase PLU4890 in Complex with Sah and Aq-284B

The structure of O-Methyltransferase PLU4890 in Complex with Sah and Aq-284B, PDB code: 8bih 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 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	91, 91.13, 150.41, 89.96, 106.18, 119.97
R / Rfree (%)	26.7 / 29.6

The structure of O-Methyltransferase PLU4890 in Complex with Sah and Aq-284B also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-284B (pdb code 8bih). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-284B, PDB code: 8bih:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-284B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of O-Methyltransferase PLU4890 in Complex with Sah and Aq-284B within 5.0Å range: probe atom residue distance (Å) B Occ H:Na403 b:66.3 occ:1.00 O H:ASN203 2.9 75.8 1.0 ND1 H:HIS188 3.8 87.8 1.0 C H:ASN203 4.0 75.5 1.0 N H:TYR189 4.1 84.0 1.0 O H:TYR189 4.2 82.3 1.0 CA H:HIS188 4.3 86.1 1.0 O H:LYS187 4.3 85.8 1.0 CE1 H:HIS188 4.6 87.8 1.0 C H:HIS188 4.6 84.5 1.0 N H:ILE204 4.8 75.2 1.0 CG H:HIS188 4.8 87.7 1.0 CA H:ASN203 4.8 75.8 1.0 N H:ASP205 4.8 71.6 1.0 C H:ILE204 4.9 72.9 1.0 CB H:ASP205 5.0 71.7 1.0 CA H:TYR189 5.0 83.2 1.0 C H:TYR189 5.0 82.0 1.0 CB H:HIS188 5.0 87.2 1.0

Sodium binding site 2 out of 2 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-284B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of O-Methyltransferase PLU4890 in Complex with Sah and Aq-284B within 5.0Å range: probe atom residue distance (Å) B Occ K:Na402 b:59.1 occ:1.00 OH K:TYR104 2.6 55.2 1.0 O D:ARG48 2.6 59.6 1.0 OD2 K:ASP273 2.6 58.1 1.0 C D:ARG48 3.6 60.5 1.0 CG K:ASP273 3.6 57.8 1.0 CZ K:TYR104 3.6 55.1 1.0 CE1 K:TYR104 3.9 55.1 1.0 CB K:ASP273 4.0 57.0 1.0 CD1 K:ILE270 4.0 59.0 1.0 CA D:ARG48 4.1 61.5 1.0 N D:LEU52 4.1 55.9 1.0 CB D:ARG51 4.1 55.8 1.0 CB D:ARG48 4.2 61.3 1.0 CB D:LEU52 4.3 56.4 1.0 CD2 K:LEU108 4.4 59.6 1.0 NE D:ARG51 4.5 55.6 1.0 CA D:LEU52 4.5 56.3 1.0 CZ D:ARG51 4.6 55.3 1.0 C D:ARG51 4.7 55.6 1.0 OD1 K:ASP273 4.7 58.3 1.0 N D:PHE49 4.7 60.4 1.0 NH2 D:ARG51 4.7 54.8 1.0 CG2 K:ILE270 4.8 58.7 1.0 CE2 K:TYR104 4.9 55.0 1.0 CA D:ARG51 4.9 55.9 1.0 CA K:ILE270 4.9 58.3 1.0 CD D:ARG51 4.9 56.0 1.0

E.M.Huber, L.Kreling, A.K.Heinrich, M.Duennebacke, A.Poethig, H.B.Bode, M.Groll. A Set of Closely Related Methyltransferases For Site-Specific Tailoring of Anthraquinone Pigments Structure 2023.
ISSN: ISSN 0969-2126