Sodium in PDB 8bid: O-Methyltransferase PLU4890 (Mutant H229N) in Complex with Sah and Aq- 270A

The structure of O-Methyltransferase PLU4890 (Mutant H229N) in Complex with Sah and Aq- 270A, PDB code: 8bid 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 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.4, 77.67, 167.33, 90, 95.49, 90
R / Rfree (%)	18 / 21.7

The structure of O-Methyltransferase PLU4890 (Mutant H229N) in Complex with Sah and Aq- 270A also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Sodium atom in the O-Methyltransferase PLU4890 (Mutant H229N) in Complex with Sah and Aq- 270A (pdb code 8bid). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 19 binding sites of Sodium where determined in the O-Methyltransferase PLU4890 (Mutant H229N) in Complex with Sah and Aq- 270A, PDB code: 8bid:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 19 in the O-Methyltransferase PLU4890 (Mutant H229N) 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 (Mutant H229N) in Complex with Sah and Aq- 270A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:48.2 occ:1.00 O A:HOH548 2.6 37.5 1.0 OAP A:QPF402 3.1 55.8 1.0 OH A:TYR97 3.2 29.4 1.0 OAL A:QPF402 3.3 51.3 1.0 CAM A:QPF402 3.5 58.0 1.0 CE1 A:TYR97 3.6 23.8 1.0 CD2 A:LEU142 3.7 33.9 1.0 CZ A:TYR97 3.8 26.8 1.0 CD1 A:LEU91 4.0 32.5 1.0 CB A:LEU91 4.0 29.7 1.0 CAO A:QPF402 4.2 56.3 1.0 OAS A:QPF402 4.4 61.9 1.0 CAK A:QPF402 4.5 48.3 1.0 CG A:LEU91 4.6 31.8 1.0 CD2 A:LEU271 4.8 29.4 1.0 CD1 A:TYR97 4.8 24.7 1.0 CAN A:QPF402 4.8 50.3 1.0 CD1 A:PHE139 4.9 32.1 1.0 OE1 A:GLU92 4.9 38.5 1.0

Sodium binding site 2 out of 19 in the O-Methyltransferase PLU4890 (Mutant H229N) 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 (Mutant H229N) in Complex with Sah and Aq- 270A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:58.3 occ:1.00 NE2 A:HIS26 3.2 38.3 1.0 CD2 A:HIS26 4.1 36.0 1.0 CB A:SER42 4.2 47.9 1.0 O A:THR21 4.2 32.3 1.0 CE1 A:HIS26 4.3 40.2 1.0 O A:GLY22 4.3 37.3 1.0 CD2 A:LEU23 4.4 33.0 1.0 C A:GLY22 4.4 33.6 1.0 N A:LEU23 4.5 29.2 1.0 CA A:LEU23 4.6 30.0 1.0 CG A:LEU23 4.9 32.5 1.0

Sodium binding site 3 out of 19 in the O-Methyltransferase PLU4890 (Mutant H229N) 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 (Mutant H229N) in Complex with Sah and Aq- 270A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:57.5 occ:1.00 OD1 B:ASN138 2.4 30.6 1.0 O B:HOH630 3.1 48.8 1.0 CG B:ASN138 3.4 28.4 1.0 ND2 B:ASN138 3.6 32.4 1.0 CE1 B:PHE87 3.8 23.1 1.0 NZ B:LYS90 3.8 41.7 1.0 CD B:LYS90 3.8 30.7 1.0 CD1 B:PHE87 4.1 24.8 1.0 O B:HOH526 4.4 52.3 1.0 CE B:LYS90 4.4 34.2 1.0 O B:HOH653 4.4 53.6 1.0 O B:HOH501 4.5 45.9 1.0 CB B:ASN138 4.8 25.1 1.0 CZ B:PHE87 4.9 24.2 1.0

Sodium binding site 4 out of 19 in the O-Methyltransferase PLU4890 (Mutant H229N) 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 (Mutant H229N) in Complex with Sah and Aq- 270A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:54.7 occ:1.00 OG B:SER234 2.4 51.1 1.0 OD1 B:ASP235 2.7 33.7 1.0 CB B:SER234 3.4 40.8 1.0 C B:SER234 3.6 32.2 1.0 N B:ASP235 3.6 29.3 1.0 CG B:ASP235 3.7 32.0 1.0 O B:SER234 3.8 31.4 1.0 CA B:ASP235 3.9 29.0 1.0 CA B:SER234 4.1 33.6 1.0 O B:HOH523 4.3 42.0 1.0 O B:HOH607 4.3 53.2 1.0 CB B:ASP235 4.4 32.1 1.0 OD2 B:ASP235 4.5 35.0 1.0 CD2 B:LEU238 4.8 39.9 1.0 OG B:SER232 5.0 29.6 1.0 CB B:LEU238 5.0 34.0 1.0

Sodium binding site 5 out of 19 in the O-Methyltransferase PLU4890 (Mutant H229N) 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 (Mutant H229N) in Complex with Sah and Aq- 270A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:47.5 occ:1.00 OD2 B:ASP168 2.2 34.5 1.0 O B:HOH566 3.0 34.1 1.0 N B:LEU177 3.2 33.6 1.0 CG B:ASP168 3.3 30.8 1.0 N B:LEU176 3.4 30.8 1.0 CB B:LEU176 3.4 32.6 1.0 C B:GLY174 3.5 26.1 1.0 CA B:GLY174 3.5 27.8 1.0 O B:GLY174 3.6 29.0 1.0 CB B:ASP168 3.7 30.8 1.0 O B:GLY171 3.7 28.5 1.0 O B:HOH530 3.7 33.4 1.0 CA B:LEU176 3.8 31.1 1.0 CB B:LEU177 3.9 38.8 1.0 C B:LEU176 3.9 34.2 1.0 N B:GLU175 4.0 28.4 1.0 CG B:LEU177 4.1 40.3 1.0 CG2 B:VAL191 4.1 27.8 1.0 CA B:GLY171 4.2 25.5 1.0 CA B:LEU177 4.2 35.8 1.0 C B:GLU175 4.3 30.7 1.0 C B:GLY171 4.4 27.9 1.0 OD1 B:ASP168 4.4 36.3 1.0 N B:GLY174 4.5 26.6 1.0 CG1 B:VAL191 4.5 28.6 1.0 CG B:LEU176 4.6 35.2 1.0 CD2 B:LEU176 4.8 32.7 1.0 CD1 B:LEU177 4.8 44.1 1.0 CA B:GLU175 4.8 31.7 1.0 CB B:VAL191 5.0 28.2 1.0

Sodium binding site 6 out of 19 in the O-Methyltransferase PLU4890 (Mutant H229N) 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 6 of O-Methyltransferase PLU4890 (Mutant H229N) in Complex with Sah and Aq- 270A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:49.3 occ:1.00 OE2 B:GLU85 2.7 25.4 1.0 O B:HOH534 3.4 38.8 1.0 CD B:GLU85 3.7 22.5 1.0 CD2 D:LEU2 3.9 28.7 1.0 CG B:GLU85 4.0 24.4 1.0 OG D:SER0 4.1 46.4 1.0 CB D:LEU2 4.2 26.1 1.0 OG B:SER306 4.3 58.1 1.0 CG D:LEU2 4.4 24.2 1.0 CZ B:PHE84 4.6 22.7 1.0 CG2 D:THR3 4.6 29.4 1.0 CE2 B:PHE84 4.7 25.6 1.0 OE1 B:GLU85 4.8 22.7 1.0 O B:GLU74 4.9 25.7 1.0 CG2 B:VAL77 4.9 24.5 1.0

Sodium binding site 7 out of 19 in the O-Methyltransferase PLU4890 (Mutant H229N) 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 7 of O-Methyltransferase PLU4890 (Mutant H229N) in Complex with Sah and Aq- 270A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:31.6 occ:1.00 O B:ILE31 2.6 33.1 1.0 O B:PHE27 2.7 24.5 1.0 N B:LEU71 3.0 20.9 1.0 N B:ILE31 3.3 27.6 1.0 C B:GLY30 3.3 24.5 1.0 CA B:GLY30 3.4 27.3 1.0 CA B:ARG70 3.5 19.0 1.0 CB B:ARG70 3.5 20.1 1.0 C B:PHE27 3.6 24.6 1.0 CB B:PHE27 3.6 25.3 1.0 C B:ILE31 3.7 24.1 1.0 C B:ARG70 3.8 19.9 1.0 CA B:PHE27 3.8 24.8 1.0 N B:GLY30 3.8 28.1 1.0 CB B:LEU71 3.9 22.2 1.0 O B:HOH590 3.9 22.7 1.0 O B:GLY30 4.0 23.6 1.0 CA B:LEU71 4.0 21.7 1.0 CA B:ILE31 4.1 24.4 1.0 CD1 B:PHE27 4.2 29.4 1.0 CG B:LEU71 4.3 21.4 1.0 O B:LEU71 4.4 26.2 1.0 CG B:PHE27 4.4 28.9 1.0 CG2 B:ILE31 4.4 31.0 1.0 O B:HOH641 4.5 31.6 1.0 O B:LYS28 4.5 27.7 1.0 CD1 B:LEU71 4.6 22.4 1.0 N B:LYS28 4.7 26.4 1.0 C B:LEU71 4.7 22.5 1.0 CG B:ARG70 4.8 20.5 1.0 N B:TYR32 4.8 29.2 1.0 C B:LYS28 4.8 27.3 1.0 CB B:ILE31 4.9 28.9 1.0 N B:ARG70 4.9 19.2 1.0 O B:ARG70 5.0 23.4 1.0 O B:PHE69 5.0 24.0 1.0 C B:ASP29 5.0 25.9 1.0

Sodium binding site 8 out of 19 in the O-Methyltransferase PLU4890 (Mutant H229N) 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 8 of O-Methyltransferase PLU4890 (Mutant H229N) in Complex with Sah and Aq- 270A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na409 b:36.1 occ:1.00 OG B:SER98 2.4 20.7 0.5 NA D:NA406 2.5 38.4 1.0 OD1 B:ASN99 2.8 22.5 1.0 OG D:SER98 3.4 23.9 0.5 CB B:SER98 3.4 19.8 0.5 CG B:ASN99 3.4 19.6 1.0 CB B:SER98 3.6 22.7 0.5 CA D:SER95 3.6 18.9 1.0 CB D:SER98 3.8 22.1 0.5 CB D:SER95 3.8 20.2 1.0 CB D:SER98 3.9 20.3 0.5 ND2 B:ASN99 3.9 23.4 1.0 N B:ASN99 3.9 17.8 1.0 CD1 B:LEU102 3.9 23.2 1.0 O D:HOH501 3.9 36.2 1.0 C B:SER98 4.0 18.7 0.5 C B:SER98 4.1 18.6 0.5 O D:SER95 4.1 19.0 1.0 O D:HOH618 4.1 31.2 1.0 CA B:ASN99 4.2 17.9 1.0 O B:SER95 4.3 17.8 1.0 CA B:SER98 4.4 20.7 0.5 CA B:SER98 4.4 21.6 0.5 O B:SER98 4.4 21.5 0.5 CB B:ASN99 4.4 19.1 1.0 C D:SER95 4.4 17.8 1.0 OG D:SER98 4.5 21.4 0.5 O B:SER98 4.6 21.2 0.5 ND2 D:ASN99 4.6 22.2 1.0 N D:SER95 4.6 22.0 1.0 OD1 D:ASN99 4.6 22.6 1.0 OG B:SER98 4.8 29.0 0.5 CG D:ASN99 4.9 20.0 1.0 CG B:LEU102 5.0 24.4 1.0

Sodium binding site 9 out of 19 in the O-Methyltransferase PLU4890 (Mutant H229N) 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 9 of O-Methyltransferase PLU4890 (Mutant H229N) in Complex with Sah and Aq- 270A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na410 b:45.3 occ:1.00 OH B:TYR310 2.3 32.4 1.0 OAE B:QPF402 2.6 42.6 1.0 OH B:TYR307 2.7 40.5 1.0 CAB B:QPF402 3.2 41.1 1.0 CE1 B:TYR307 3.3 35.4 1.0 CZ B:TYR307 3.4 36.6 1.0 CZ B:TYR310 3.4 31.9 1.0 CAD B:QPF402 3.6 42.0 1.0 CE2 B:TYR310 3.7 30.8 1.0 SD B:MET258 3.7 48.5 1.0 CG B:MET258 3.8 41.6 1.0 CAC B:QPF402 3.9 39.8 1.0 CB B:VAL146 3.9 25.0 1.0 CG2 B:VAL146 3.9 27.6 1.0 ND2 B:ASN226 4.0 27.8 1.0 CG1 B:VAL146 4.2 28.0 1.0 CAA B:QPF402 4.2 39.4 1.0 O B:HOH545 4.3 33.3 1.0 CD1 B:TYR307 4.5 33.1 1.0 CE B:MET258 4.6 49.0 1.0 O B:HOH514 4.6 30.4 1.0 CE1 B:TYR310 4.6 30.1 1.0 CE2 B:TYR307 4.7 36.3 1.0 O B:HOH580 4.9 45.2 1.0 CAF B:QPF402 4.9 40.4 1.0 CG B:ASN226 4.9 27.4 1.0

Sodium binding site 10 out of 19 in the O-Methyltransferase PLU4890 (Mutant H229N) 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 10 of O-Methyltransferase PLU4890 (Mutant H229N) in Complex with Sah and Aq- 270A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:64.5 occ:1.00 OD2 C:ASP130 3.0 45.9 1.0 CB C:ASP130 3.7 36.5 1.0 CG C:ASP130 3.8 38.0 1.0 O C:GLU127 3.9 35.3 1.0 NH2 C:ARG194 4.7 36.7 1.0 CA C:GLU127 4.7 30.8 1.0 C C:GLU127 4.8 31.2 1.0 CB C:GLU127 4.9 34.5 1.0 OD1 C:ASP130 4.9 32.6 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