Sodium in PDB 8bgx: O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A

The structure of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A, PDB code: 8bgx 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 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.14, 78.37, 167.73, 90, 96.31, 90
R / Rfree (%)	17.9 / 22

The structure of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A 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-270A (pdb code 8bgx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A, PDB code: 8bgx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A


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-270A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:68.4 occ:1.00 O A:HOH650 2.4 49.1 1.0 OD2 A:ASP20 2.6 46.2 1.0 O D:HOH534 3.0 37.3 1.0 CG A:ASP20 3.6 39.0 1.0 CE D:LYS106 3.9 46.7 1.0 CB A:ASP20 3.9 34.9 1.0 C A:ASP20 4.1 29.7 1.0 CG2 A:THR21 4.2 27.7 1.0 O A:ASP20 4.2 28.6 1.0 N A:THR21 4.2 28.0 1.0 CE1 A:HIS16 4.3 26.6 1.0 CG D:LYS106 4.4 38.9 1.0 CA A:THR21 4.6 28.0 1.0 CA A:ASP20 4.7 30.6 1.0 CD D:LYS106 4.7 44.8 1.0 OD1 A:ASP20 4.7 45.0 1.0 O D:LEU102 4.7 24.7 1.0 N D:LYS106 4.9 28.6 1.0

Sodium binding site 2 out of 5 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A


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-270A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:47.8 occ:1.00 O D:HOH573 2.2 38.9 1.0 O A:ILE93 2.5 25.9 1.0 OG A:SER98 2.5 26.7 0.5 OG D:SER98 2.6 24.5 0.5 CB D:SER98 3.6 26.3 0.5 C A:ILE93 3.6 25.2 1.0 CB D:SER98 3.6 25.2 0.5 CB A:SER98 3.6 25.8 0.5 CB A:SER98 3.7 24.2 0.5 O D:SER98 3.7 25.1 0.5 CB A:ILE93 3.8 28.6 1.0 OG D:SER98 3.8 26.1 0.5 O D:SER98 3.8 23.2 0.5 OG A:SER98 3.9 24.0 0.5 CG D:LEU102 4.0 24.1 1.0 CA A:ILE93 4.0 25.9 1.0 CA D:SER98 4.0 24.4 0.5 CA D:SER98 4.0 24.9 0.5 CD1 D:LEU102 4.1 25.2 1.0 NA D:NA403 4.1 38.0 1.0 C D:SER98 4.1 24.1 0.5 C D:SER98 4.2 23.6 0.5 CD2 D:LEU102 4.3 25.9 1.0 CD1 A:ILE93 4.4 30.8 1.0 CG1 A:ILE93 4.4 28.7 1.0 O A:CYS94 4.4 23.4 1.0 C A:CYS94 4.7 23.3 1.0 N A:CYS94 4.7 24.2 1.0 CG2 A:ILE93 4.9 30.4 1.0 CA A:SER98 4.9 23.8 0.5 CA A:SER98 4.9 24.6 0.5 O A:HOH590 5.0 50.0 1.0 O D:HOH501 5.0 38.0 1.0

Sodium binding site 3 out of 5 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:55.9 occ:1.00 OAP A:QPF402 2.5 56.8 1.0 O A:HOH534 2.9 36.2 1.0 OH A:TYR97 3.2 28.0 1.0 OAL A:QPF402 3.3 57.6 1.0 OAS A:QPF402 3.5 73.4 1.0 CAO A:QPF402 3.6 58.5 1.0 CE1 A:TYR97 3.7 25.5 1.0 CD2 A:LEU142 3.7 34.4 1.0 CAM A:QPF402 3.8 58.7 1.0 CZ A:TYR97 3.9 25.9 1.0 CAK A:QPF402 4.3 57.6 1.0 CD1 A:LEU91 4.4 31.1 1.0 CD2 A:LEU271 4.4 27.4 1.0 CB A:LEU91 4.4 27.9 1.0 CAR A:QPF402 4.5 65.7 1.0 CAN A:QPF402 4.5 56.3 1.0 CAQ A:QPF402 4.5 61.5 1.0 OE1 A:GLU92 4.9 34.1 1.0 CD1 A:TYR97 4.9 25.4 1.0

Sodium binding site 4 out of 5 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:60.6 occ:1.00 OE1 C:GLU4 2.6 41.8 1.0 O C:ALA7 3.2 33.1 1.0 O C:GLU4 3.3 41.0 1.0 CD C:GLU4 3.7 47.0 1.0 CG C:ARG11 3.7 45.5 1.0 C C:ALA7 3.9 35.1 1.0 CA C:GLU4 3.9 43.5 1.0 CB C:GLU4 4.0 45.5 1.0 C C:GLU4 4.0 38.9 1.0 CD C:ARG11 4.1 52.5 1.0 CB C:ALA7 4.2 33.7 1.0 CG C:GLU4 4.3 48.6 1.0 N C:SER8 4.4 36.7 1.0 CA C:SER8 4.5 36.4 1.0 CB C:ARG10 4.5 33.0 1.0 CZ C:PHE55 4.6 36.5 1.0 CA C:ALA7 4.7 34.7 1.0 OE2 C:GLU4 4.7 46.6 1.0 NH1 C:ARG11 4.8 68.9 1.0 CE1 C:PHE55 4.9 36.6 1.0 N C:ARG11 4.9 35.5 1.0 O C:SER8 4.9 37.8 1.0 CD C:ARG10 5.0 33.9 1.0

Sodium binding site 5 out of 5 in the O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of O-Methyltransferase PLU4890 in Complex with Sah and Aq-270A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na403 b:38.0 occ:1.00 OG D:SER98 2.4 24.5 0.5 OD1 D:ASN99 2.6 27.5 1.0 O A:HOH502 2.9 35.8 1.0 CG D:ASN99 3.3 26.2 1.0 CB D:SER98 3.4 25.2 0.5 CA A:SER95 3.6 23.7 1.0 CB D:SER98 3.6 26.3 0.5 OG A:SER98 3.6 24.0 0.5 CD1 D:LEU102 3.8 25.2 1.0 N D:ASN99 3.8 22.9 1.0 CB A:SER98 3.8 24.2 0.5 CB A:SER95 3.8 25.9 1.0 ND2 D:ASN99 3.8 27.0 1.0 CB A:SER98 3.8 25.8 0.5 C D:SER98 3.9 24.1 0.5 C D:SER98 4.0 23.6 0.5 O A:HOH615 4.0 25.8 1.0 NA A:NA404 4.1 47.8 1.0 CA D:ASN99 4.1 22.9 1.0 O A:SER95 4.2 21.9 1.0 O D:SER95 4.2 21.1 1.0 OG A:SER98 4.2 26.7 0.5 O D:SER98 4.3 25.1 0.5 CA D:SER98 4.3 24.4 0.5 CB D:ASN99 4.3 24.2 1.0 CA D:SER98 4.4 24.9 0.5 C A:SER95 4.4 22.7 1.0 O D:SER98 4.5 23.2 0.5 N A:SER95 4.5 23.2 1.0 ND2 A:ASN99 4.7 27.9 1.0 OG D:SER98 4.7 26.1 0.5 OD1 A:ASN99 4.8 29.1 1.0 CG D:LEU102 4.8 24.1 1.0 CG A:ASN99 5.0 26.8 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