Sodium in PDB 8rvs: Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam

The structure of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam, PDB code: 8rvs was solved by S.Gerhardt, J.N.Andexer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.53 / 1.63
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	147.246, 65.68, 74.58, 90, 90, 90
R / Rfree (%)	18.3 / 21

The structure of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam (pdb code 8rvs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam, PDB code: 8rvs:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam


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 Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1003 b:32.2 occ:1.00 O A:GLN327 2.3 28.1 1.0 O A:THR325 2.4 23.2 1.0 O A:HIS322 2.4 26.1 1.0 O A:HOH1314 2.9 32.6 1.0 C A:GLN327 3.4 26.1 1.0 N A:GLN327 3.6 25.4 1.0 C A:HIS322 3.6 23.8 1.0 C A:THR325 3.6 22.5 1.0 CZ3 A:TRP148 3.9 28.8 1.0 CH2 A:TRP148 4.1 29.6 1.0 CA A:GLN327 4.2 26.3 1.0 C A:CYS323 4.2 21.6 1.0 CA A:CYS323 4.2 21.0 1.0 N A:THR325 4.3 21.2 1.0 N A:LEU328 4.4 24.0 1.0 N A:CYS323 4.4 21.3 1.0 O A:CYS323 4.5 22.8 1.0 O A:HOH1107 4.5 29.6 1.0 CA A:ASN326 4.5 24.8 1.0 N A:ASN326 4.5 22.7 1.0 C A:ASN326 4.5 25.6 1.0 CA A:LEU328 4.5 24.0 1.0 CA A:THR325 4.6 20.7 1.0 CE3 A:TRP148 4.6 27.7 1.0 CA A:HIS322 4.6 22.2 1.0 O A:HOH1277 4.6 23.3 1.0 N A:PHE324 4.7 20.4 1.0 OG1 A:THR325 4.9 21.2 1.0 CZ2 A:TRP148 4.9 29.7 1.0 CD1 A:LEU328 4.9 29.0 1.0 CB A:GLN327 5.0 28.2 1.0 CB A:LEU328 5.0 25.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam


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 Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1004 b:40.3 occ:1.00 O A:HOH1272 2.2 29.4 1.0 O A:HOH1184 2.2 24.8 1.0 O A:HOH1146 2.3 39.3 1.0 O A:HOH1145 2.5 25.2 1.0 OH A:TYR314 3.2 21.2 1.0 CZ A:PHE261 3.7 23.9 1.0 O A:HOH1224 3.8 21.3 1.0 CE2 A:PHE261 3.8 23.9 1.0 CG2 A:ILE163 3.9 21.4 1.0 CE1 A:PHE261 4.1 23.8 1.0 OD2 A:ASP167 4.1 23.4 1.0 CZ A:TYR314 4.3 20.0 1.0 O A:HOH1197 4.3 37.1 1.0 CD2 A:PHE261 4.4 22.8 1.0 OG A:SER160 4.5 30.9 1.0 CB A:ILE163 4.5 20.4 1.0 CD1 A:ILE163 4.6 21.2 1.0 CD1 A:PHE261 4.7 22.9 1.0 OD1 A:ASP167 4.7 22.1 1.0 CE2 A:TYR314 4.8 19.3 1.0 CG A:PHE261 4.8 23.2 1.0 CG A:ASP167 4.9 22.1 1.0 OE1 A:GLU362 4.9 25.6 1.0 OG A:SER164 4.9 27.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1003 b:30.0 occ:1.00 O B:GLN327 2.3 23.1 1.0 O B:HOH1408 2.3 50.4 1.0 O B:HIS322 2.4 25.8 1.0 O B:THR325 2.4 20.9 1.0 O B:HOH1379 2.8 39.5 1.0 C B:GLN327 3.4 22.2 1.0 N B:GLN327 3.6 23.3 1.0 C B:HIS322 3.6 22.4 1.0 C B:THR325 3.7 21.5 1.0 CZ3 B:TRP148 3.9 28.5 1.0 CH2 B:TRP148 4.1 29.4 1.0 CA B:GLN327 4.2 23.1 1.0 C B:CYS323 4.2 19.6 1.0 CA B:CYS323 4.2 19.4 1.0 N B:THR325 4.4 20.5 1.0 N B:CYS323 4.4 19.6 1.0 O B:HOH1140 4.4 30.1 1.0 N B:LEU328 4.4 20.9 1.0 C B:ASN326 4.4 24.6 1.0 CA B:ASN326 4.5 23.5 1.0 O B:CYS323 4.5 20.6 1.0 CA B:LEU328 4.5 20.6 1.0 N B:ASN326 4.5 21.3 1.0 CE3 B:TRP148 4.5 27.7 1.0 O B:HOH1329 4.6 21.1 1.0 CA B:HIS322 4.6 20.8 1.0 CA B:THR325 4.7 21.4 1.0 N B:PHE324 4.7 18.3 1.0 OG1 B:THR325 4.9 23.1 1.0 CD1 B:LEU328 4.9 25.6 1.0 CZ2 B:TRP148 4.9 29.5 1.0 CB B:LEU328 4.9 21.8 1.0 CB B:GLN327 5.0 25.7 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Alpha Keto Acid C-Methyl-Transferases Mrsa Bound to Sam within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1004 b:42.0 occ:1.00 O B:HOH1102 2.2 19.0 0.5 O B:HOH1174 2.3 27.4 1.0 O B:HOH1304 2.4 29.7 1.0 O B:HOH1284 2.5 50.6 1.0 OH B:TYR314 3.3 21.7 1.0 O B:HOH1298 3.4 21.9 1.0 CZ B:PHE261 3.4 23.6 1.0 CE2 B:PHE261 3.7 22.9 1.0 CE1 B:PHE261 3.9 23.0 1.0 OD2 B:ASP167 3.9 24.0 1.0 CG2 B:ILE163 4.0 17.6 1.0 CZ B:TYR314 4.3 20.1 1.0 CD2 B:PHE261 4.4 21.3 1.0 OE1 B:GLU362 4.4 25.4 1.0 CD1 B:PHE261 4.6 22.5 1.0 OD1 B:ASP167 4.6 20.4 1.0 CG B:ASP167 4.7 21.3 1.0 CE2 B:TYR314 4.7 19.5 1.0 CG B:PHE261 4.8 20.9 1.0 CB B:ILE163 4.8 17.3 1.0 OG B:SER160 4.9 30.2 1.0 CD1 B:ILE163 4.9 19.7 1.0 CD B:GLU362 4.9 23.1 1.0

C.Sommer-Kamann, J.Breiltgens, Z.Zou, S.Gerhardt, R.Saleem-Batcha, F.Kemper, O.Einsle, J.N.Andexer, M.Muller. Structures and Protein Engineering of the Alpha-Keto Acid C-Methyltransferases Sgvm and Mrsa For Rational Substrate Transfer. Chembiochem 00258 2024.
ISSN: ESSN 1439-7633
PubMed: 38887142
DOI: 10.1002/CBIC.202400258